Publications

@article{nokey_67,

title = {AnchoRNA: Full virus genome alignments through conserved anchor regions},

author = {Tom Eulenfeld and Sandra Triebel and Manja Marz},

doi = {10.1101/2025.01.30.635689},

year  = {2025},

date = {2025-12-15},

urldate = {2025-02-01},

journal = {bioRxiv},

abstract = {Multiple sequence alignment of full viral genomes can be challenging due to factors such as long sequences, large insertions/deletions (spanning several 100 nucleotides), large number of sequences, sequence divergence, and high computational complexity in particular when computing alignments based on RNA secondary structures. Standard alignment methods often face these issues, in particular when processing highly variable sequences or when specific phylogenetic analysis is required on selected subsequences.

We present an algorithm to determine high quality anchors that define partitions of sequences and guide the alignment of viral genomes to respect well conserved, and therefore functionally significant, regions. This new approach is implemented in the Python-based command line tool AnchoRNA, which is designed to identify conserved regions, or anchors, within coding sequences. By default, anchors are searched in translated coding sequences accounting for high mutation rates in viral genomes. AnchoRNA enhances the accuracy and efficiency of full-genome alignment by focusing on these crucial conserved regions. AnchoRNA guided alignments are systematically compared to the results of 3 alignment programs. Utilizing a dataset of 55 representative Pestivirus genomes, AnchoRNA identified 55 anchors that are used for guiding the alignment process. The incorporation of these anchors led to improvements across tested alignment tools, highlighting the effectiveness of AnchoRNA in enhancing alignment quality, especially in viral genomes.},

keywords = {alignment, phylogenetics, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_78,

title = {Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella},

author = {Juliana Botero and Nikolas Basler and Margo Cnockaert and Charlotte Peeters and Maria Schreiber and Manja Marz and Dirk C. {de Graaf} and Jelle Matthijnssens and Peter Vandamme},

doi = {10.1016/j.syapm.2025.126625},

isbn = {0723-2020},

year  = {2025},

date = {2025-06-06},

journal = {Systematic and Applied Microbiology},

volume = {48},

abstract = {We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 Bartonella isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as Bartonella apihabitans and three as Bartonella choladocola was straightforward, the identification of 25 Bartonella apis-like isolates was challenging. A taxonomic and functional analysis of four B. apis-like genomes and of publicly available B. apis genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of B. apis and B. apis-like genomes. Different phylogenomic analyses showed that B. apis and B. apis-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as B. apis. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of Bartonella species which differed not only in phylogenomic position and ecology, but also in genome size and genomic percentage G + C content, and in many metabolic capabilities. We propose to reclassify the single species of the Bartonella tamiae clade into the novel genus Attibartonella gen. nov., with Attibartonella tamiae comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated Bartonella clade into the novel genus Ditibartonella gen. nov., with Ditibartonella apis comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional Ditibartonella species in honey bee samples, highlighted an evolutionary adaptation of Ditibartonella bacteria to bee hosts and suggested shared transmission routes.},

keywords = {bacteria, classification, DNA / genomics, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_77,

title = {First full-genome alignment representative for the genus \textit{Pestivirus}},

author = {Sandra Triebel and Tom Eulenfeld and Nancy Ontiveros-Palacios and Blake Sweeney and Norbert Tautz and Manja Marz},

url = {https://doi.org/10.5281/zenodo.15490752},

doi = {10.1101/2025.05.22.655560},

year  = {2025},

date = {2025-05-27},

journal = {bioRxiv},

abstract = {The members of the genus Pestivirus in the family Flaviviridae comprise economically important pathogens of life stock like classical swine fever (CSFV) and bovine viral diarrhea virus (BVDV). Intense research over the last years revealed that at least 11 recognized and eight proposed pestivirus species exist. The single-stranded, positive-sense RNA genome encodes for one large polyprotein which is processed by viral and cell-derived proteases into 12 mature proteins. Besides its protein-coding function, the RNA genome also contains RNA secondary structures with critical importance for various stages of the viral life cycle. Some of those RNA secondary structures, like the internal ribosome entry site (IRES) and a 3’ stem-loop essential for genome replication, had already been studied for a few individual pestiviruses.

In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5’ stem-loop structure, the IRES element, and the 3’ stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3’ untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3’ end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.},

keywords = {alignment, evolution, phylogenetics, RNA structure, RNA-RNA interactions, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_66,

title = {Endogenous viral elements: insights into data availability and accessibility},

author = {Muriel Ritsch and Nadja Brait and Erin Harvey and Manja Marz and Sebastian Lequime},

doi = {10.1093/ve/veae099},

issn = {2057-1577},

year  = {2024},

date = {2024-11-23},

journal = {Virus Evolution},

volume = {10},

number = {1},

pages = {veae099},

abstract = {Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR (‘findable, accessible, interoperable, and reusable’) principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host–virus interactions and their evolutionary history.},

keywords = {evolution, phylogenetics, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_66,

title = {Endogenous Bornavirus-like Elements in Bats: Evolutionary Insights from the Conserved Riboviral L-Gene in Microbats and Its Antisense Transcription in \textit{Myotis daubentonii}},

author = {Muriel Ritsch and Tom Eulenfeld and Kevin Lamkiewicz and Andreas Schoen and Friedemann Weber and Martin Hölzer and Manja Marz},

doi = {10.3390/v16081210},

issn = {1999-4915},

year  = {2024},

date = {2024-07-27},

urldate = {2024-07-27},

journal = {Viruses},

volume = {16},

issue = {8},

abstract = {Bats are ecologically diverse vertebrates characterized by their ability to host a wide range of viruses without apparent illness and the presence of numerous endogenous viral elements (EVEs). EVEs are well preserved, expressed, and may affect host biology and immunity, but their role in bat immune system evolution remains unclear. Among EVEs, endogenous bornavirus-like elements (EBLs) are bornavirus sequences integrated into animal genomes. Here, we identified a novel EBL in the microbat \textit{Myotis daubentonii}, EBLL-Cultervirus.10-MyoDau (short name is CV.10-MyoDau) that shows protein-level conservation with the L-protein of a \textit{Cultervirus} (Wuhan sharpbelly bornavirus). Surprisingly, we discovered a transcript on the antisense strand comprising three exons, which we named AMCR-MyoDau. The active transcription in \textit{Myotis daubentonii} tissues of AMCR-MyoDau, confirmed by RNA-Seq analysis and RT-PCR, highlights its potential role during viral infections. Using comparative genomics comprising 63 bat genomes, we demonstrate nucleotide-level conservation of CV.10-MyoDau and AMCR-MyoDau across various bat species and its detection in 22 \textit{Yangochiropera<i/> and 12 \textit{Yinpterochiroptera} species. To the best of our knowledge, this marks the first occurrence of a conserved EVE shared among diverse bat species, which is accompanied by a conserved antisense transcript. This highlights the need for future research to explore the role of EVEs in shaping the evolution of bat immunity.},

keywords = {evolution, phylogenetics, RNA / transcriptomics, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_62,

title = {Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus},

author = {Sandra Triebel and Kevin Lamkiewicz and Nancy Ontiveros and Blake Sweeney and Peter F. Stadler and Anton I. Petrov and Michael Niepmann and Manja Marz},

doi = {10.1038/s41598-024-62897-0},

year  = {2024},

date = {2024-07-02},

urldate = {2024-07-02},

journal = {Scientific Reports},

volume = {14},

issue = {1},

abstract = {Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large ‘cloud’ of RNA genomes (quasispecies) which—by trial and error—comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.},

keywords = {evolution, ncRNAs, phylogenetics, RNA structure, RNA-RNA interactions, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_44,

title = {\textit{De novo} genome assembly resolving repetitive structures enables genomic analysis of 35 European \textit{Mycoplasmopsis bovis} strains},

author = {Sandra Triebel and Konrad Sachse and Michael Weber and Martin Heller and Celia Diezel and Martin Hölzer and Christiane Schnee and Manja Marz },

doi = {10.1186/s12864-023-09618-5},

isbn = {1471-2164},

year  = {2023},

date = {2023-09-16},

urldate = {2023-09-16},

journal = {BMC Genomics},

volume = {24},

number = {548},

issue = {1},

abstract = {Mycoplasmopsis (M.) bovis, the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome of approximately 1 Mbp. Combining data from Illumina and Nanopore technologies, we sequenced and assembled the genomes of 35 European strains and isolate DL422_88 from Cuba. While the high proportion of repetitive structures in M. bovis genomes represent a particular challenge, implementation of our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista ) in a hybrid approach enabled contiguous assembly of the genomes and, consequently, improved annotation rates considerably. To put our European strain panel in a global context, we analyzed the new genome sequences together with 175 genome assemblies from public databases. Construction of a phylogenetic tree based on core genes of these 219 strains revealed a clustering pattern according to geographical origin, with European isolates positioned on clades 4 and 5. Genomic data allowing assignment of strains to tissue specificity or certain disease manifestations could not be identified. Seven strains isolated from cattle with systemic circular condition (SCC), still a largely unknown manifestation of M. bovis disease, were located on both clades 4 and 5. Pairwise association analysis revealed 108 genomic elements associated with a particular clade of the phylogenetic tree. Further analyzing these hits, 25 genes are functionally annotated and could be linked to a M. bovis protein, e.g. various proteases and nucleases, as well as ten variable surface lipoproteins (Vsps) and other surface proteins. These clade-specific genes could serve as useful markers in epidemiological and clinical surveys.},

keywords = {assembly, bacteria, DNA / genomics, nanopore, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models},

author = {Guillermo Rangel-Pineros and Alexandre Almeida and Martin Beracochea and Ekaterina Sakharova and Manja Marz and Alejandro Reyes Muñoz and Martin Hölzer and Robert D. Finn },

doi = {10.1371/journal.pcbi.1011422},

year  = {2023},

date = {2023-08-28},

journal = {PLOS Comput Biol},

volume = {19},

issue = {8},

pages = {e1011422},

abstract = {The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.},

keywords = {annotation, classification, metagenomics, phylogenetics, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_41,

title = {\textit{Streptomyces marispadix} sp. nov., isolated from marine beach sediment},

author = {José Diogo Neves Dos Santos and Inês Rosado Vitorino and Nicolai Kallscheuer and Akash Srivastava and Sebastian Krautwurst and Manja Marz and Christian Jogler and Alexandre Lobo-da-Cunha and José Catita and Hugo Gonçalves and Ignacio González and Fernando Reyes and Olga Maria Lage},

doi = {10.1099/ijsem.0.005956},

isbn = {1466-5034},

year  = {2023},

date = {2023-07-25},

urldate = {2023-07-25},

journal = {International Journal of Systematic and Evolutionary Microbiology},

volume = {73},

number = {7},

abstract = {A novel actinomycetal strain, designated M600PL45_2T, was isolated from marine sediments obtained from Ingleses beach, Porto, on the Northern Coast of Portugal and was subjected to a polyphasic taxonomic characterisation study. The here described Gram-reaction-positive strain is characterised by the production of a brown pigment in both solid and liquid medium and forms typical helical hyphae that differentiate into smooth spores. The results of a phylogenetic analysis based on the 16S rRNA gene sequence indicated that M600PL45_2T has a high similarity to two members of the genus Streptomyces , Streptomyces bathyalis ASO4wetT (98.51 %) and Streptomyces daqingensis NEAU ZJC8T (98.44 %). The genome of M600PL45_2T has a size of 6 695 159 bp, a DNA G+C content of 70.71 mol% and 5538 coding sequences. M600PL45_2T grows at 15–37 °C and with a maximal growth rate between 25 °C and 30 °C. Growth at pH 6.0 to 9.0 with the optimal range between 6.0 and 7.5 was observed. M600PL45_2T showed a high salinity tolerance, growing with 0–10 % (w/v) NaCl, with best growth with 1–3% (w/v) NaCl. Major cellular fatty acids are iso-C15:0 (25.03 %), anteiso-C15:0 (17.70) and iso-C16:0 (26.90 %). The novel isolate was able to grow in media containing a variety of nitrogen and carbon sources. An antimicrobial activity screening indicated that an extract of M600PL45_2T has inhibitory activity against Staphylococcus aureus . On the basis of the polyphasic data, M600PL45_2T (= CECT 30365T = DSM 114036T) is introduced as the type strain of a novel species, that we named Streptomyces marispadix sp. nov.},

keywords = {bacteria, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_35,

title = {Genomic analysis of 61 \textit{Chlamydia psittaci} strains reveals extensive divergence associated with host preference},

author = {Konrad Sachse and Martin Hölzer and Fabien Vorimore and Lisa-Marie Barf and Carsten Sachse and Karine Laroucau and Manja Marz and Kevin Lamkiewicz },

doi = {10.1186/s12864-023-09370-w},

isbn = {1471-2164},

year  = {2023},

date = {2023-05-29},

urldate = {2023-05-29},

journal = {BMC Genomics},

volume = {24},

issue = {1},

pages = {288},

abstract = {Background

Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid.



Results

Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2– 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps).



Conclusions

Our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors.},

keywords = {alignment, assembly, bacteria, DNA / genomics, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2},

author = {Kevin Lamkiewicz and Luis Roger Esquivel Gomez and Denise Kühnert and Manja Marz

},

doi = {10.1007/978-3-031-15640-3_9},

year  = {2023},

date = {2023-01-03},

journal = {Curr Top Microbiol Immunol},

volume = {439},

pages = {305-339},

abstract = {Coronaviruses have a broad host range and exhibit high zoonotic potential. In this chapter, we describe their genomic organization in terms of encoded proteins and provide an introduction to the peculiar discontinuous transcription mechanism. Further, we present evolutionary conserved genomic RNA secondary structure features, which are involved in the complex replication mechanism. With a focus on computational methods, we review the emergence of SARS-CoV-2 starting with the 2019 strains. In that context, we also discuss the debated hypothesis of whether SARS-CoV-2 was created in a laboratory. We focus on the molecular evolution and the epidemiological dynamics of this recently emerged pathogen and we explain how variants of concern are detected and characterised. COVID-19, the disease caused by SARS-CoV-2, can spread through different transmission routes and also depends on a number of risk factors. We describe how current computational models of viral epidemiology, or more specifically, phylodynamics, have facilitated and will continue to enable a better understanding of the epidemic dynamics of SARS-CoV-2.},

keywords = {coronavirus, DNA / genomics, evolution, phylogenetics, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_90,

title = {Description of Staphylococcal Strains from Straw-Coloured Fruit Bat (Eidolon helvum) and Diamond Firetail (Stagonopleura guttata) and a Review of their Phylogenetic Relationships to Other Staphylococci},

author = {Stefan Monecke and Frieder Schaumburg and Adebayo O. Shittu and Stefan Schwarz and Kristin Mühldorfer and Christian Brandt and Sascha D. Braun and Maximilian Collatz and Celia Diezel and Darius Gawlik and Dennis Hanke and Helmut Hotzel and Elke Müller and Martin Reinicke and Andrea T. Feßler and Ralf Ehricht},

doi = {10.3389/fcimb.2022.878137},

year  = {2022},

date = {2022-05-11},

urldate = {2022-05-11},

journal = {Frontiers in Cellular and Infection Microbiology},

volume = {12},

abstract = {The phylogenetic tree of the Staphylococcus aureus complex consists of several distinct clades and the majority of human and veterinary S. aureus isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named Staphylococcus argenteus, due to the lack of the “golden” pigment staphyloxanthin. The second one is S. schweitzeri, found in humans and animals from Central and West Africa. In late 2021, two additional species, S. roterodami and S. singaporensis, have been described from clinical samples from Southeast Asia.

In the present study, isolates and their genome sequences from wild Straw-coloured fruit bats (Eidolon helvum) and a Diamond firetail (Stagonopleura guttata, an estrildid finch) kept in a German aviary are described. The isolates possessed staphyloxanthin genes and were closer related to S. argenteus and S. schweitzeri than to S. aureus. Phylogenetic analysis revealed that they were nearly identical to both, S. roterodami and S. singaporensis.

We propose considering the study isolates, the recently described S. roterodami and S. singaporensis as well as some Chinese strains with MLST profiles stored in the PubMLST database as different clonal complexes within one new species. According to the principle of priority we propose it should be named S. roterodami. 

This species is more widespread than previously believed, being observed in Western Africa, Southeast Asia and Southern China. It has a zoonotic connection to bats and has been shown to be capable of causing skin and soft tissue infections in humans. It is positive for staphyloxanthin, and it could be mis-identified as S. aureus (or S. argenteus) using routine procedures. However, it can be identified based on distinct MLST alleles, and “S. aureus” sequence types ST2470, ST3135, ST3952, ST3960, ST3961, ST3963, ST3965, ST3980, ST4014, ST4075, ST4076, ST4185, ST4326, ST4569, ST6105, ST6106, ST6107, ST6108, ST6109, ST6999 and ST7342 belong to this species.},

keywords = {bacteria, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Comparative study of ten thogotovirus isolates and their distinct in vivo characteristics},

author = {Jonas Fuchs and Kevin Lamkiewicz and Larissa Kolesnikova and Martin Hölzer and Manja Marz and Georg Kochs},

doi = {10.1128/JVI.01556-21},

year  = {2022},

date = {2022-01-12},

journal = {J Virol},

abstract = {Thogotoviruses are tick-borne arboviruses that comprise a unique genus within the Orthomyxoviridae family. Infections with thogotoviruses primarily cause disease in livestock with occasional reports of human infections suggesting a zoonotic potential. In the past, multiple genetically distinct thogotoviruses were isolated mostly from collected ticks. However, many aspects regarding their phylogenetic relationships, morphological characteristics and virulence in mammals remain unclear. For the present comparative study, we used a collection of ten different thogotovirus isolates from different geographic areas. Next generation sequencing and subsequent phylogenetic analyses revealed a distinct separation of these viruses into two major clades - the Thogoto-like and Dhori-like viruses. Electron microscopy demonstrated a heterogeneous morphology with spherical and filamentous particles being present in virus preparations. To study their pathogenicity, we analyzed the viruses in a small animal model system. In intraperitoneally infected C57BL/6 mice, all isolates showed a tropism for liver, lung and spleen. Importantly, we did not observe horizontal transmission to uninfected, highly susceptible contact mice. The isolates enormously differed in their capacity to induce disease, ranging from subclinical to fatal outcomes. In vivo multi-step passaging experiments of two low-pathogenic isolates showed no increased virulence and sequence analyses of the passaged viruses indicated a high stability of the viral genomes after ten mouse passages. In summary, our analysis demonstrates the broad genetic and phenotypic variability within the thogotovirus genus. Moreover, thogotoviruses are well adapted to mammals but their horizontal transmission seems to depend on ticks as their vectors. Importance Since their discovery over sixty years ago, fifteen genetically distinct members of the thogotovirus genus have been isolated. These arboviruses belong to the Orthomyxovirus family and share many features with influenza viruses. However, numerous of these isolates have not been characterized in depth. In the present study, we comparatively analyzed a collection of ten different thogotovirus isolates to answer basic questions about their phylogenetic relationships, morphology and pathogenicity in mice. Our results highlight shared and unique characteristics of this diverse genus. Taken together, these observations provide a framework for the phylogenic classification and phenotypic characterization of newly identified thogotovirus isolates that could potentially cause severe human infections as exemplified by the recently reported, fatal Bourbon virus cases in the United States.},

keywords = {phylogenetics, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Yates:21,

title = {The evolution and changing ecology of the African hominid oral microbiome},

author = {James A. Fellows Yates and Irina M. Velsko and Franziska Aron and Cosimo Posth and Courtney A. Hofman and Rita M. Austin and Cody E. Parker and Allison E. Mann and Kathrin Nägele and Kathryn Weedman Arthur and John W. Arthur and Catherine C. Bauer and Isabelle Crevecoeur and Christophe Cupillard and Matthew C. Curtis and Love Dalén and Marta Díaz-Zorita Bonilla and J. Carlos Díez Fernández-Lomana and Dorothée G. Drucker and Elena Escribano Escrivá and Michael Francken and Victoria E. Gibbon and Manuel R. González Morales and Ana Grande Mateu and Katerina Harvati and Amanda G. Henry and Louise Humphrey and Mario Menéndez and Dušan Mihailović and Marco Peresani and Sofía Rodríguez Moroder and Mirjana Roksandic and Hélène Rougier and Sandra Sázelová and Jay T. Stock and Lawrence Guy Straus and Jiří Svoboda and Barbara Teßmann and Michael J. Walker and Robert C. Power and Cecil M. Lewis and Krithivasan Sankaranarayanan and Katerina Guschanski and Richard W. Wrangham and Floyd E. Dewhirst and Domingo C. Salazar-García and Johannes Krause and Alexander Herbig and Christina Warinner},

doi = {10.1073/pnas.2021655118},

year  = {2021},

date = {2021-05-18},

urldate = {2021-05-18},

journal = {Proc Natl Acad Sci},

volume = {118},

number = {20},

pages = {e2021655118},

publisher = {Proceedings of the National Academy of Sciences},

abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.},

keywords = {ancient DNA, bacteria, evolution, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Flores:20,

title = {A marine Chlamydomonas sp. emerging as an algal model},

author = {David Carrasco Flores and Markus Fricke and Valentin Wesp and Daniel Desirò and Anja Kniewasser and Martin Hölzer and Manja Marz and Maria Mittag},

doi = {10.1111/jpy.13083},

year  = {2020},

date = {2020-10-11},

urldate = {2020-10-11},

journal = {J Phycol},

volume = {57},

number = {1},

pages = {54--69},

publisher = {Wiley},

abstract = {The freshwater microalga Chlamydomonas reinhardtii, which lives in wet soil, has served for decades as a model for numerous biological processes, and many tools have been introduced for this organism. Here, we have established a stable nuclear transformation for its marine counterpart, Chlamydomonas sp. SAG25.89, by fusing specific cis-acting elements from its Actin gene with the gene providing hygromycin resistance and using an elaborated electroporation protocol. Like C. reinhardtii, Chlamydomonas sp. has a high GC content, allowing reporter genes and selection markers to be applicable in both organisms. Chlamydomonas sp. grows purely photoautotrophically and requires ammonia as a nitrogen source because its nuclear genome lacks some of the genes required for nitrogen metabolism. Interestingly, it can grow well under both low and very high salinities (up to 50 g · L-1) rendering it as a model for osmotolerance. We further show that Chlamydomonas sp. grows well from 15 to 28°C, but halts its growth at 32°C. The genome of Chlamydomonas sp. contains some gene homologs the expression of which is regulated according to the ambient temperatures and/or confer thermal acclimation in C. reinhardtii. Thus, knowledge of temperature acclimation can now be compared to the marine species. Furthermore, Chlamydomonas sp. can serve as a model for studying marine microbial interactions and for comparing mechanisms in freshwater and marine environments. Chlamydomonas sp. was previously shown to be immobilized rapidly by a cyclic lipopeptide secreted from the antagonistic bacterium Pseudomonas protegens PF-5, which deflagellates C. reinhardtii.},

keywords = {algae, bacteria, DNA / genomics, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Hoelzer:20a,

title = {PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection},

author = {Martin Hölzer and Manja Marz},

editor = {Alfonso Valencia},

url = {https://github.com/rnajena/poseidon},

doi = {10.1093/bioinformatics/btaa695},

year  = {2020},

date = {2020-07-31},

urldate = {2020-07-31},

journal = {Bioinformatics},

volume = {37},

number = {7},

pages = {1018-1020},

publisher = {Oxford University Press (OUP)},

abstract = {PoSeiDon is an easy-to-use pipeline that helps researchers to find recombination events and sites under positive selection in protein-coding sequences. By entering homologous sequences, PoSeiDon builds an alignment, estimates a best-fitting substitution model and performs a recombination analysis followed by the construction of all corresponding phylogenies. Finally, significantly positive selected sites are detected according to different models for the full alignment and possible recombination fragments. The results of PoSeiDon are summarized in a user-friendly HTML page providing all intermediate results and the graphical representation of recombination events and positively selected sites.



},

keywords = {alignment, evolution, phylogenetics, software},

pubstate = {published},

tppubtype = {article}

}

@article{Madhugiri:18,

title = {Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions},

author = {Ramakanth Madhugiri and Nadja Karl and Daniel Petersen and Kevin Lamkiewicz and Markus Fricke and Ulrike Wend and Robina Scheuer and Manja Marz and John Ziebuhr},

doi = {10.1016/j.virol.2017.11.025},

year  = {2017},

date = {2017-12-06},

urldate = {2017-12-06},

journal = {Virology},

volume = {517},

pages = {44--55},

abstract = {Structure predictions suggest a partial conservation of RNA structure elements in coronavirus terminal genome regions. Here, we determined the structures of stem-loops (SL) 1 and 2 of two alphacoronaviruses, human coronavirus (HCoV) 229E and NL63, by RNA structure probing and studied the functional relevance of these putative cis-acting elements. HCoV-229E SL1 and SL2 mutants generated by reverse genetics were used to study the effects on viral replication of single-nucleotide substitutions predicted to destabilize the SL1 and SL2 structures. The data provide conclusive evidence for the critical role of SL1 and SL2 in HCoV-229E replication and, in some cases, revealed parallels with previously characterized betacoronavirus SL1 and SL2 elements. Also, we were able to rescue viable HCoV-229E mutants carrying replacements of SL2 with equivalent betacoronavirus structural elements. The data obtained in this study reveal a remarkable degree of structural and functional conservation of 5'-terminal RNA structural elements across coronavirus genus boundaries.},

keywords = {coronavirus, phylogenetics, RNA / transcriptomics, RNA structure, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Hoelzer:17,

title = {Software Dedicated to Virus Sequence Analysis },

author = {Martin Hölzer and Manja Marz},

doi = {10.1016/bs.aivir.2017.08.004},

year  = {2017},

date = {2017-09-28},

urldate = {2017-09-28},

journal = {Adv Virus Res},

volume = {99},

pages = {233--257},

abstract = {Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.},

keywords = {DNA / genomics, evolution, phylogenetics, review, RNA / transcriptomics, RNA structure, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Fuchs:17,

title = {Evolution and Antiviral Specificities of Interferon-Induced Mx Proteins of Bats against Ebola, Influenza, and Other RNA Viruses},

author = {Jonas Fuchs and Martin Hölzer and Mirjam Schilling and Corinna Patzina and Andreas Schoen and Thomas Hoenen and Gert Zimmer and Manja Marz and Friedemann Weber and Marcel A Müller and Georg Kochs},

doi = {10.1128/JVI.00361-17},

year  = {2017},

date = {2017-07-12},

urldate = {2017-07-12},

journal = {J Virol},

volume = {91},

abstract = {Bats serve as a reservoir for various, often zoonotic viruses, including significant human pathogens such as Ebola and influenza viruses. However, for unknown reasons, viral infections rarely cause clinical symptoms in bats. A tight control of viral replication by the host innate immune defense might contribute to this phenomenon. Transcriptomic studies revealed the presence of the interferon-induced antiviral myxovirus resistance (Mx) proteins in bats, but detailed functional aspects have not been assessed. To provide evidence that bat Mx proteins might act as key factors to control viral replication we cloned cDNAs from three bat families, Pteropodidae, Phyllostomidae, and Vespertilionidae. Phylogenetically these bat genes cluster closely with their human ortholog MxA. Using transfected cell cultures, minireplicon systems, virus-like particles, and virus infections, we determined the antiviral potential of the bat Mx1 proteins. Bat Mx1 significantly reduced the polymerase activity of viruses circulating in bats, including Ebola and influenza A-like viruses. The related Thogoto virus, however, which is not known to infect bats, was not inhibited by bat Mx1. Further, we provide evidence for positive selection in bat genes that might explain species-specific antiviral activities of these proteins. Together, our data suggest a role for Mx1 in controlling these viruses in their bat hosts. Bats are a natural reservoir for various viruses that rarely cause clinical symptoms in bats but are dangerous zoonotic pathogens, like Ebola or rabies virus. It has been hypothesized that the interferon system might play a key role in controlling viral replication in bats. We speculate that the interferon-induced Mx proteins might be key antiviral factors of bats and have coevolved with bat-borne viruses. This study evaluated for the first time a large set of bat Mx1 proteins spanning three major bat families for their antiviral potential, including activity against Ebola virus and bat influenza A-like virus, and we describe here their phylogenetic relationship, revealing patterns of positive selection that suggest a coevolution with viral pathogens. By understanding the molecular mechanisms of the innate resistance of bats against viral diseases, we might gain important insights into how to prevent and fight human zoonotic infections caused by bat-borne viruses.},

keywords = {evolution, phylogenetics, RNA / transcriptomics, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Starke:17,

title = {Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer},

author = {Robert Starke and Martina Müller and Michael Gaspar and Manja Marz and Kirsten Küsel and Kai Uwe Totsche and Martin Bergen and Nico Jehmlich},

doi = {10.1016/j.jprot.2016.11.003},

year  = {2016},

date = {2016-11-10},

urldate = {2016-11-10},

journal = {J Proteomics},

volume = {152},

pages = {153--160},

abstract = {Groundwater-associated microorganisms are known to play an important role in the biogeochemical C, N and S cycling. Metaproteomics was applied to characterize the diversity and the activity of microbes to identify key species in major biogeochemical processes in the anoxic groundwater of a pristine karstic aquifer located in Hainich, central Germany. Sampling was achieved by pumping 1000L water from two sites of the upper aquifer assemblage and filtration on 0.3μm glass filters. In total, 3808 protein groups were identified. Interestingly, the two wells (H4/2 and H5/2) differed not only in microbial density but also in the prevalence of different C, N and S cycling pathways. The well H5/2 was dominated by the anaerobic ammonia-oxidizing (anammox) candidate Brocadiales (31%) while other orders such as Burkholderiales (2%) or Nitrospirales (3%) were less abundant. Otherwise, the well H4/2 featured only low biomass and remarkably fewer proteins (391 to 3631 at H5/2). Candidate Brocadiales was affiliated to all major carbon fixation strategies, and to the cycling of N and S implying a major role in biogeochemical processes of groundwater aquifers. The findings of our study support functions which can be linked to the ecosystem services provided by the microbial communities present in aquifers. Subsurface environments especially the groundwater ecosystems represent a large habitat for microbial activity. Microbes are responsible for energy and nutrient cycling and are massively involved in the planet's sustainability. Microbial diversity is tremendous and the central question in current microbial ecology is "Who eats what, where and when?". In this study, we characterize a natural aquifer inhabiting microbial community to obtain evidence for the phylogenetic diversity and the metabolic activity by protein abundance and we highlight important biogeochemical cycling processes. The aquifer was dominated by Candidatus Brocadiales while other phylotypes such as Burkholderiales, Caulobacterales and Nitrospirales were less abundant. The candidate comprised all major carbon fixation strategies, ammonification, anammox and denitrification as well as assimilatory sulfate reduction. Our findings have broad implications for the understanding of microbial activities in this aquifer and consequently specific functions can be linked to the ecosystem services provided by the microbial communities present in aquifers.},

keywords = {bacteria, groundwater, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Lechner:14,

title = {Genomewide comparison and novel ncRNAs of Aquificales},

author = {Marcus Lechner and Astrid I. Nickel and Stefanie Wehner and Konstantin Riege and Nicolas Wieseke and Benedikt M. Beckmann and Roland K. Hartmann and Manja Marz},

doi = {10.1186/1471-2164-15-522},

year  = {2014},

date = {2014-06-25},

urldate = {2014-06-25},

journal = {BMC Genomics},

volume = {15},

pages = {522},

abstract = {The Aquificales are a diverse group of thermophilic bacteria that thrive in terrestrial and marine hydrothermal environments. They can be divided into the families Aquificaceae, Desulfurobacteriaceae and Hydrogenothermaceae. Although eleven fully sequenced and assembled genomes are available, only little is known about this taxonomic order in terms of RNA metabolism. In this work, we compare the available genomes, extend their protein annotation, identify regulatory sequences, annotate non-coding RNAs (ncRNAs) of known function, predict novel ncRNA candidates, show idiosyncrasies of the genetic decoding machinery, present two different types of transfer-messenger RNAs and variations of the CRISPR systems. Furthermore, we performed a phylogenetic analysis of the Aquificales based on entire genome sequences, and extended this by a classification among all bacteria using 16S rRNA sequences and a set of orthologous proteins.Combining several in silico features (e.g. conserved and stable secondary structures, GC-content, comparison based on multiple genome alignments) with an in vivo dRNA-seq transcriptome analysis of Aquifex aeolicus, we predict roughly 100 novel ncRNA candidates in this bacterium. We have here re-analyzed the Aquificales, a group of bacteria thriving in extreme environments, sharing the feature of a small, compact genome with a reduced number of protein and ncRNA genes. We present several classical ncRNAs and riboswitch candidates. By combining in silico analysis with dRNA-seq data of A. aeolicus we predict nearly 100 novel ncRNA candidates.},

keywords = {alignment, annotation, assembly, bacteria, classification, ncRNAs, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Sachse:14,

title = {Evidence for the existence of two new members of the family Chlamydiaceae and proposal of \textit{Chlamydia avium} sp. nov. and \textit{Chlamydia gallinacea} sp. nov.},

author = {Konrad Sachse and Karine Laroucau and Konstantin Riege and Stefanie Wehner and Meik Dilcher and Heather Huot Creasy and Manfred Weidmann and Garry Myers and Fabien Vorimore and Nadia Vicari and Simone Magnino and Elisabeth Liebler-Tenorio and Anke Ruettger and Patrik M. Bavoil and Frank T. Hufert and Ramon Rosselló-Móra and Manja Marz},

doi = {10.1016/j.syapm.2013.12.004},

year  = {2014},

date = {2014-01-22},

urldate = {2014-01-22},

journal = {Syst Appl Microbiol},

volume = {37},

pages = {79--88},

abstract = {The family Chlamydiaceae with the recombined single genus Chlamydia currently comprises nine species, all of which are obligate intracellular organisms distinguished by a unique biphasic developmental cycle. Anecdotal evidence from epidemiological surveys in flocks of poultry, pigeons and psittacine birds have indicated the presence of non-classified chlamydial strains, some of which may act as pathogens. In the present study, phylogenetic analysis of ribosomal RNA and ompA genes, as well as multi-locus sequence analysis of 11 field isolates were conducted. All independent analyses assigned the strains into two different clades of monophyletic origin corresponding to pigeon and psittacine strains or poultry isolates, respectively. Comparative genome analysis involving the type strains of currently accepted Chlamydiaceae species and the designated type strains representing the two new clades confirmed that the latter could be classified into two different species as their average nucleotide identity (ANI) values were always below 94%, both with the closest relative species and between themselves. In view of the evidence obtained from the analyses, we propose the addition of two new species to the current classification: Chlamydia avium sp. nov. comprising strains from pigeons and psittacine birds (type strain 10DC88(T); DSMZ: DSM27005(T), CSUR: P3508(T)) and Chlamydia gallinacea sp. nov. comprising strains from poultry (type strain 08-1274/3(T); DSMZ: DSM27451(T), CSUR: P3509(T)).},

keywords = {bacteria, classification, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Li:13,

title = {Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach},

author = {Yang Li and Joshua D Podlevsky and Manja Marz and Xiaodong Qi and Steve Hoffmann and Peter F Stadler and Julian J-L Chen},

doi = {10.1261/rna.039131.113},

year  = {2013},

date = {2013-04-12},

urldate = {2013-04-12},

journal = {RNA},

volume = {19},

pages = {852--860},

abstract = {Telomerase is a ribonucleoprotein (RNP) enzyme essential for telomere maintenance and chromosome stability. While the catalytic telomerase reverse transcriptase (TERT) protein is well conserved across eukaryotes, telomerase RNA (TR) is extensively divergent in size, sequence, and structure. This diversity prohibits TR identification from many important organisms. Here we report a novel approach for TR discovery that combines in vitro TR enrichment from total RNA, next-generation sequencing, and a computational screening pipeline. With this approach, we have successfully identified TR from Strongylocentrotus purpuratus (purple sea urchin) from the phylum Echinodermata. Reconstitution of activity in vitro confirmed that this RNA is an integral component of sea urchin telomerase. Comparative phylogenetic analysis against vertebrate TR sequences revealed that the purple sea urchin TR contains vertebrate-like template-pseudoknot and H/ACA domains. While lacking a vertebrate-like CR4/5 domain, sea urchin TR has a unique central domain critical for telomerase activity. This is the first TR identified from the previously unexplored invertebrate clade and provides the first glimpse of TR evolution in the deuterostome lineage. Moreover, our TR discovery approach is a significant step toward the comprehensive understanding of telomerase RNP evolution.},

keywords = {evolution, phylogenetics, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Lechner:13,

title = {The correlation of genome size and DNA methylation rate in metazoans},

author = {Marcus Lechner and Manja Marz and Christian Ihling and Andrea Sinz and Peter F Stadler and Veiko Krauss},

doi = {10.1007/s12064-012-0167-y},

year  = {2012},

date = {2012-11-07},

urldate = {2012-11-07},

journal = {Theory Biosci},

volume = {132},

pages = {47--60},

abstract = {Total DNA methylation rates are well known to vary widely between different metazoans. The phylogenetic distribution of this variation, however, has not been investigated systematically. We combine here publicly available data on methylcytosine content with the analysis of nucleotide compositions of genomes and transcriptomes of 78 metazoan species to trace the evolution of abundance and distribution of DNA methylation. The depletion of CpG and the associated enrichment of TpG and CpA dinucleotides are used to infer the intensity and localization of germline CpG methylation and to estimate its evolutionary dynamics. We observe a positive correlation of the relative methylation of CpG motifs with genome size. We tested this trend successfully by measuring total DNA methylation with LC/MS in orthopteran insects with very different genome sizes: house crickets, migratory locusts and meadow grasshoppers. We hypothesize that the observed correlation between methylation rate and genome size is due to a dependence of both variables from long-term effective population size and is driven by the accumulation of repetitive sequences that are typically methylated during periods of small population sizes. This process may result in generally methylated, large genomes such as those of jawed vertebrates. In this case, the emergence of a novel demethylation pathway and of novel reader proteins for methylcytosine may have enabled the usage of cytosine methylation for promoter-based gene regulation. On the other hand, persistently large populations may lead to a compression of the genome and to the loss of the DNA methylation machinery, as observed, e.g., in nematodes.},

keywords = {DNA / genomics, evolution, insects, nucleic acid modifications, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Qi:13,

title = {The common ancestral core of vertebrate and fungal telomerase RNAs},

author = {Xiaodong Qi and Yang Li and Shinji Honda and Steve Hoffmann and Manja Marz and Axel Mosig and Joshua D Podlevsky and Peter F Stadler and Eric U Selker and Julian J-L Chen},

doi = {10.1093/nar/gks980},

year  = {2012},

date = {2012-10-23},

urldate = {2012-10-23},

journal = {Nucleic Acids Res},

volume = {41},

pages = {450--462},

abstract = {Telomerase is a ribonucleoprotein with an intrinsic telomerase RNA (TER) component. Within yeasts, TER is remarkably large and presents little similarity in secondary structure to vertebrate or ciliate TERs. To better understand the evolution of fungal telomerase, we identified 74 TERs from Pezizomycotina and Taphrinomycotina subphyla, sister clades to budding yeasts. We initially identified TER from Neurospora crassa using a novel deep-sequencing-based approach, and homologous TER sequences from available fungal genome databases by computational searches. Remarkably, TERs from these non-yeast fungi have many attributes in common with vertebrate TERs. Comparative phylogenetic analysis of highly conserved regions within Pezizomycotina TERs revealed two core domains nearly identical in secondary structure to the pseudoknot and CR4/5 within vertebrate TERs. We then analyzed N. crassa and Schizosaccharomyces pombe telomerase reconstituted in vitro, and showed that the two RNA core domains in both systems can reconstitute activity in trans as two separate RNA fragments. Furthermore, the primer-extension pulse-chase analysis affirmed that the reconstituted N. crassa telomerase synthesizes TTAGGG repeats with high processivity, a common attribute of vertebrate telomerase. Overall, this study reveals the common ancestral cores of vertebrate and fungal TERs, and provides insights into the molecular evolution of fungal TER structure and function.},

keywords = {evolution, fungi, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Dilcher:12,

title = {Genetic characterization of Tribeč virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses},

author = {Meik Dilcher and Lekbira Hasib and Marcus Lechner and Nicolas Wieseke and Martin Middendorf and Manja Marz and Andrea Koch and Martin Spiegel and Gerhard Dobler and Frank T Hufert and Manfred Weidmann},

doi = {10.1016/j.virol.2011.11.020},

year  = {2011},

date = {2011-12-20},

urldate = {2011-12-20},

journal = {Virology},

volume = {423},

pages = {68--76},

abstract = {We determined the complete genome sequences of Tribeč virus (TRBV) and Kemerovo virus (KEMV), two tick-transmitted Orbiviruses that can cause diseases of the central nervous system and that are currently classified into the Great Island virus serogroup. VP2 proteins of TRBV and KEMV show very low sequence similarity to the homologous VP4 protein of tick-transmitted Great Island virus (GIV). The new sequence data support previous serological classification of these Orbiviruses into the Kemerovo serogroup, which is different from the Great Island virus serogroup. Genome segment 9 of TRBV and KEMV encodes several overlapping ORF's in the +1 reading frame relative to VP6(Hel). A co-phylogenetic analysis indicates a host switch from insect-borne Orbiviruses toward Ixodes species, which is in disagreement with previously published data.},

keywords = {classification, evolution, insects, phylogenetics, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Lechner:11,

title = {Proteinortho: detection of (co-)orthologs in large-scale analysis},

author = {Marcus Lechner and Sven Findeiss and Lydia Steiner and Manja Marz and Peter F Stadler and Sonja J Prohaska},

url = {http://bioinf.pharmazie.uni-marburg.de/supplements/proteinortho/},

doi = {10.1186/1471-2105-12-124},

year  = {2011},

date = {2011-04-28},

urldate = {2011-04-28},

journal = {BMC Bioinf},

volume = {12},

pages = {124},

abstract = {Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.},

keywords = {alignment, bacteria, phylogenetics, proteins, software},

pubstate = {published},

tppubtype = {article}

}

@article{Hertel:06,

title = {The expansion of the metazoan microRNA repertoire},

author = {Jana Hertel and Manja Lindemeyer and Kristin Missal and Claudia Fried and Andrea Tanzer and Christoph Flamm and Ivo L. Hofacker and Peter F. Stadler and Students Bioinformatics Computer Labs 2004 & 2005},

doi = {10.1186/1471-2164-7-25},

year  = {2006},

date = {2006-02-15},

urldate = {2006-02-15},

journal = {BMC Genomics},

volume = {7},

pages = {25},

abstract = {MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species. This allows us to reliably identify microRNA clusters that are derived from a common transcript. We identify three episodes of microRNA innovation that correspond to major developmental innovations: A class of about 20 miRNAs is common to protostomes and deuterostomes and might be related to the advent of bilaterians. A second large wave of innovations maps to the branch leading to the vertebrates. The third significant outburst of miRNA innovation coincides with placental (eutherian) mammals. In addition, we observe the expected expansion of the microRNA inventory due to genome duplications in early vertebrates and in an ancestral teleost. The non-local duplications in the vertebrate ancestor are predated by local (tandem) duplications leading to the formation of about a dozen ancient microRNA clusters. Our results suggest that microRNA innovation is an ongoing process. Major expansions of the metazoan miRNA repertoire coincide with the advent of bilaterians, vertebrates, and (placental) mammals.},

keywords = {ncRNAs, phylogenetics},

pubstate = {published},

tppubtype = {article}

}