Supplement material

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial Mucorales (Mucoromycotina)

(Volker U. Schwartze, Sascha Winter, Ekaterina Shelest, Marina Marcet-Houben, Stefanie Wehner, Kerstin Hoffmann, Konstantin Riege, Michael Sammeth, Minou Nowrousian, Vito Valiante, Ilse D. Jacobsen, Manja Marz, Axel A. Brakhage, Toni Gabaldón, Sebastian Böcker, Kerstin Voigt)

Overview

Databases used for this work
Overview on all annotated ncRNAs
GFF, FASTA, files of all annotated ncRNAs
STK Alignment files of all ncRNAs except tRNAs and 18s, 28s rRNA
Results of RNAfold for U1, U2, U5, U11, U12 snRNA
Phylogeny based on all ncRNAs shown in figure below
NcRNAs used for Phylogeny

Databases used for this work

s-scaffold/superscaffold; c-contig/supercontig
OrganismAssemblyReal genomesize (bp)Expected genomesize (Mbp) www.zbi.eeDownload dateDownloadExternal link
Lichtheimia corymbiferas3361890108.06.12Download
Rhizopus oryzaec4608711740.36702.01.12DownloadBROAD Institute
Schizosaccharomyces pombes1257182013.36719.06.12DownloadNCBI Assembly

Overview on all annotated ncRNAs


GFF, FASTA files of all annotated ncRNAs

OrganismGFFFASTA
Lichtheimia corymbiferalco.nc.gfflco.nc.fa
Rhizopus oryzaeror.nc.gffror.nc.fa

STK Alignment files of all ncRNAs except tRNAs and 18s, 28s rRNA

RNASTK
5.8s5.8S_rRNA.stk
5s5S_rRNA.stk
RNase PRNaseP.stk
RNase MRPRNaseMRP.stk
SRPSRP.stk
TPPTPP.stk
TelomeraseTelomerase.stk
U1U1.stk
U2U2.stk
U4U4.stk
U5U5.stk
U6U6.stk
U11U11.stk
U12U12.stk
U4atacU4atac.stk
U6atacU6atac.stk
U7U7.stk
U3U3.stk
U14U14.stk
U27/snR74U27.stk
U79U79.stk
R38R38.stk
snR60snR60.stk
snR61/Z1/Z11snR61.stk
snR79snR79.stk
snR75snR75.stk
snR56snR56.stk
snoR53YsnoR53Y.stk
U19/SNORA74U19.stk
snR35snR35.stk
snR191snR191.stk

Results of RNAfold for U1, U2, U5, U11, U12 snRNA


Phylogeny based on all ncRNAs shown in figure below

Outgroup MrBayes Neighborjoining
Schizosaccharomyces pombe
Batrachochytrium dendrobatidis

NcRNAs used for phylogeny