Supplement material

Genomewide comparison and novel ncRNAs in Aquificales

Marcus Lechner , Astrid Nickel , Stefanie Wehner , Konstantin Riege, Nicolas Wieseke, Benedikt M. Beckmann, Roland K. Hartmann, Manja Marz

Overview

used genomes
Annotated proteins
Codon usage
non-coding RNAs
Riboswitches
CRISPR results
Novel non-coding RNAs in A. aeolicus
Phylogeny
In vitro transcripts, probes and primers

Genomes

Organism	Genome	external Link	download Date
Aminobacterium colombiense DSM	download	download Link	12.01.2013
Aquifex aeolicus VF5	download	download Link	12.01.2013
Archaeoglobus fulgidus DSM	download	download Link	12.01.2013
Bacillus subtilis 168	download	download Link	12.01.2013
Chloroflexus aurantiacus J-10-fl	download	download Link	12.01.2013
Chlorobium limicola DSM	download	download Link	12.01.2013
Chlamydia trachomatis A/HAR-13	download	download Link	12.01.2013
Deferribacter desulfuricans SSM1	download	download Link	12.01.2013
Desulfobacterium autotrophicum HRM2	download	download Link	12.01.2013
Desulfurispirillum indicum S5	download	download Link	12.01.2013
Desulfurobacterium thermolithotrophum DSM 11699	download	download Link	12.01.2013
Dictyoglomus thermophilum H-6-12	download	download Link	12.01.2013
Escherichia coli str. K-12 substr. MG1655	download	download Link	12.01.2013
Fibrobacter succinogenes S85	download	download Link	12.01.2013
Flavobacterium johnsoniae UW101	download	download Link	12.01.2013
Fusobacterium nucleatum subsp. nucleatum	download	download Link	12.01.2013
Geobacter metallireducens GS-15	download	download Link	12.01.2013
Hydrogenivirga sp 128-5-R1-1	download	download Link	12.01.2013
Hydrogenobaculum sp. Y04AAS1	download	download Link	12.01.2013
Hydrogenobacter thermophilus TK-6	download	download Link	12.01.2013
Hydrogenobacter thermophilus TK-6	download	download Link	12.01.2013
Magnetococcus sp. MC-1	download	download Link	12.01.2013
Methanobacterium sp. AL-21	download	download Link	12.01.2013
Neisseria gonorrhoeae FA 1090	download	download Link	12.01.2013
Persephonella marina EX-H1	download	download Link	12.01.2013
Pirellula staleyi DSM 6068	download	download Link	12.01.2013
Rhodobacter sphaeroides 2.4.1	download	download Link	12.01.2013
Rickettsia felis URRWXCal2	download	download Link	12.01.2013
Spirochaeta thermophila DSM 6578	download	download Link	12.01.2013
Streptomyces coelicolor A3 2	download	download Link	12.01.2013
Sulfurihydrogenibium azorense Az-Fu1	download	download Link	12.01.2013
Sulfurihydrogenibium sp. YO3AOP1	download	download Link	12.01.2013
Synechocystis sp. PCC 6803	download	download Link	12.01.2013
Thermocrinis albus	download	download Link	12.01.2013
Thermovibrio ammonificans HB-1	download	download Link	12.01.2013
Thermobifida fusca YX	download	download Link	12.01.2013
Thermodesulfatator indicus DSM 15286	download	download Link	12.01.2013
Thermotoga maritima MSB8	download	download Link	12.01.2013
Thermocrinis ruber	download	download Link	09.04.2013
Thermoanaerobacter tengcongensis MB4	download	download Link	12.01.2013
Thermobaculum terrenum ATCC BAA-798	download	download Link	12.01.2013
Thermus thermophilus HB27	download	download Link	12.01.2013
Wolinella succinogenes DSM 1740	download	download Link	12.01.2013

Annotated proteins

Species	BacProt GFF	CDS comparison to NCBI
A. aeolicus	GFF	Equal: 954 Start shifted: 116 End shifted: 124 NCBI only: 366 BacProt only: 61
D. thermolithotrophum	GFF	Equal: 1092 Start shifted: 86 End shifted: 105 NCBI only: 230 BacProt only: 100
Hydrogenobaculum	GFF	Equal: 1040 Start shifted: 119 End shifted: 126 NCBI only: 344 BacProt only: 55
H. thermophilus	GFF	Equal: 1069 Start shifted: 111 End shifted: 129 NCBI only: 584 BacProt only: 52
Hydrogenivirga sp.	GFF	Equal: 1537 Start shifted: 302 End shifted: 306 NCBI only: 1663 BacProt only: 182
P. marina	GFF	Equal: 1286 Start shifted: 129 End shifted: 122 NCBI only: 514 BacProt only: 56
S. azorense	GFF	Equal: 1190 Start shifted: 90 End shifted: 99 NCBI only: 344 BacProt only: 48
Sulfurihydrogenibium	GFF	Equal: 1225 Start shifted: 76 End shifted: 108 NCBI only: 313 BacProt only: 123
T. albus	GFF	Equal: 903 Start shifted: 93 End shifted: 127 NCBI only: 470 BacProt only: 22
T. ammonificans	GFF	Equal: 1014 Start shifted: 90 End shifted: 99 NCBI only: 611 BacProt only: 40
T. ruber	GFF	-

Codon usage

Organism	Codon usage
A. aeolicus	pdf
Hydrogenivirga	pdf
H. thermophilus	pdf
T. albus	pdf
T. ruber	pdf
Hydrogenobaculum	pdf
P. marina	pdf
S. azorense	pdf
Sulfurihydrogenibium	pdf
D. thermolithotrophum	pdf
T. ammonificans	pdf

Non-coding RNAs

Organism	FASTA	GFF	Infernal_RNaseP_bact_a		6S		tmRNA		TPP		Bacteria_small_SRP		Cobalamin		crcB		MOCO_RNA_motif		RtT		23s_rRNA	5s_rRNA	16s_rRNA	tRNA	RNase_P_bacA	RNase_P_bacB
			FASTA	STK	FASTA	STK	FASTA	STK	FASTA	STK	FASTA	STK	FASTA	STK	FASTA	STK	FASTA	STK	FASTA	STK	FASTA	FASTA	FASTA	FASTA	FASTA	FASTA
			COPY		COPY		COPY		COPY		COPY		COPY		COPY		COPY		COPY		COPY	COPY	COPY	COPY	COPY	COPY
A. colombiense	FASTA	GFF	1		1		1		2		1		2		1		0		0		3	3	3	46	1	0
A. aeolicus	FASTA	GFF	0		1		1		0		1		0		0		0		0		2	2	2	44	1	0
A. fulgidus	FASTA	GFF	1		0		0		0		0		0		1		0		0		1	1	1	44	1	0
B. subtilis	FASTA	GFF	0		2		1		5		1		1		0		0		0		10	10	10	86	0	1
C. aurantiacus	FASTA	GFF	1		0		1		4		1		0		1		0		0		3	3	3	49	1	0
C. limicola	FASTA	GFF	1		1		1		1		1		4		0		0		0		2	2	2	48	1	0
C. trachomatis	FASTA	GFF	1		0		1		0		1		0		0		0		0		2	2	2	37	1	0
T. ruber	FASTA	GFF	0		1		1		0		1		0		0		0		0		1	1	1	44	1	0
D. desulfuricans	FASTA	GFF	1		1		1		1		1		3		0		1		0		2	2	2	44	1	0
D. autotrophicum	FASTA	GFF	1		1		1		3		1		9		0		0		0		6	8	6	50	1	0
D. indicum	FASTA	GFF	1		1		1		1		1		5		0		0		0		3	3	3	37	1	0
D. thermolithotrophum	FASTA	GFF	1		0		1		1		1		2		0		0		0		2	2	2	43	1	0
D. thermophilum	FASTA	GFF	1		1		1		2		1		0		1		0		0		2	2	2	46	1	0
E. coli	FASTA	GFF	1		1		1		3		1		1		0		1		7		7	8	7	88	1	0
F. succinogenes	FASTA	GFF	1		0		1		2		1		1		0		0		0		3	3	3	58	1	0
F. johnsoniae	FASTA	GFF	1		0		1		2		1		3		0		0		0		6	6	6	62	1	0
F. nucleatum	FASTA	GFF	1		0		1		2		1		3		0		0		0		5	5	5	47	1	0
G. metallireducens	FASTA	GFF	1		1		1		2		1		1		0		4		0		2	2	2	49	1	0
Hydrogenobaculum	FASTA	GFF	0		1		1		0		1		0		2		0		0		2	2	2	45	1	0
H. thermophilus	FASTA	GFF	0		1		1		0		1		0		0		0		0		1	1	1	44	1	0
H. thermophilus	FASTA	GFF	0		1		1		0		1		0		0		0		0		1	1	1	44	1	0
Magnetococcus	FASTA	GFF	1		4		1		0		1		1		0		0		0		3	3	3	45	1	0
Methanobacterium	FASTA	GFF	1		0		0		0		0		0		1		0		0		2	3	2	42	1	0
N. gonorrhoeae	FASTA	GFF	1		1		1		2		1		0		0		0		0		4	4	4	55	1	0
Hydrogenivirga	FASTA	GFF	0		2		2		1		2		0		0		0		0		2	2	2	57	1	0
P. marina	FASTA	GFF	1		1		1		0		1		0		0		0		0		2	3	2	40	1	0
P. staleyi	FASTA	GFF	1		0		1		0		1		2		0		0		0		1	1	1	46	1	0
R. sphaeroides	FASTA	GFF	1		1		0		2		1		6		0		0		0		3	3	3	53	1	0
R. felis	FASTA	GFF	1		1		0		0		1		0		0		0		0		1	1	1	33	1	0
S. thermophila	FASTA	GFF	1		0		1		1		1		0		0		0		0		2	2	2	46	1	0
S. coelicolor	FASTA	GFF	1		0		1		3		1		5		0		0		0		6	6	6	66	1	0
S. azorense	FASTA	GFF	1		1		1		1		1		0		0		0		0		2	2	2	39	1	0
Sulfurihydrogenibium	FASTA	GFF	1		1		1		1		1		0		0		0		0		3	3	3	40	1	0
Synechocystis	FASTA	GFF	1		1		1		1		1		0		0		0		0		2	2	2	41	1	0
T. albus	FASTA	GFF	0		1		1		0		1		0		0		0		0		1	1	1	44	1	0
T. ammonificans	FASTA	GFF	1		0		1		1		1		2		0		1		0		3	3	3	46	1	0
T. fusca	FASTA	GFF	1		0		1		3		1		2		0		0		0		4	4	4	52	1	0
T. indicus	FASTA	GFF	1		1		1		0		1		3		0		0		0		2	2	2	49	1	0
T. maritima	FASTA	GFF	1		0		1		1		1		1		0		0		0		1	1	1	46	1	0
T. tengcongensis	FASTA	GFF	1		2		1		4		1		2		3		0		0		4	4	4	55	1	0
T. terrenum	FASTA	GFF	1		1		1		2		1		1		2		0		0		2	2	2	51	1	0
T. thermophilus	FASTA	GFF	1		0		1		2		1		0		0		1		0		2	2	2	47	1	0
W. succinogenes	FASTA	GFF	1		0		1		0		1		0		0		0		0		3	3	3	40	1	0

Riboswitches

Riboswitch	Alignments (coloured by)				Secondary structure
	stk	base identity	structure consensus	conservation
Cobalamin	stk	ps	ps	ps
TPP	stk	ps	ps	ps
CrcB	stk	ps	ps	ps	hba1.eps	hba2.eps
MOCO	stk	ps	ps	ps	tam.eps

Organism	tmRNA
A. aeolicus	eps
Hydrogenivirga - 1	eps
Hydrogenivirga - 2	eps
H. thermophilus	eps
T. albus	eps
T. ruber	eps
Hydrogenobaculum	eps
P. marina	eps
S. azorense	eps
Sulfurihydrogenibium	eps
D. thermolithotrophum	eps
T. ammonificans	eps

CRISPR results

The following PDF shows the found CRISPR locations per Genome. The first column indicates the number of repeats of a CRISPR-locus
File: PDF-Table

A. aeolicus

Hydrogenivirga sp.

H. thermophilus, chromosomes

H. thermophilus

Desulfobacterium autotrophicum

Hydrogenobaculum Y04AA1

T. albus

T. ruber

P. marina

S. azorense

Sulfurihydrogenibium YO3AOP1

D. thermolithotrophum

T. ammonificans

crispfinder

GFF

crt

GFF

cas proteins

merge-GFF

Novel non-coding RNAs in A. aeolicus

Download PDF
Download GFF
Download FASTA

Phylogeny

Organism	NEWICK	PDF
11	Aquificales only: 16S rRNA Mafft LINSI alignment 1000 iterations, MrBayes 4by4 1mio generations tree	PDF
11	Aquificales only: 16S rRNA Mafft LINSI alignment 1000 iterations, Neighbour Joining tree with Kimura correction model and 1000 bootstraps	PDF
11	Aquificales only: 16S rRNA Mafft LINSI alignment 1000 iterations, RAxML tree with GTRGAMMA substitution model during maximum likelyhood search and GTRCATduring the 200 bootstrap replicates	PDF
11	Aquificales only: 16S rRNA Mafft LINSI alignment 1000 iterations, RAxML tree with GTRGAMMA substitution model during maximum likelyhood search and during the 200 bootstrap replicates	PDF
11	Whole genome alignment by Pomago, RAxML tree with GTRGAMMA substitution model during maximum likelyhood search and during the 100 bootstrap replicates	PDF
ALL	50% equal proteome detected by Proteinortho whole aligned by DIALIGN, RAxML PROTGAMMALG tree of concatenated alignments with 10 bootstrap replicates	PDF
ALL	NCBI provided taxonomy, phylogenetic subtree of used organisms	PDF
ALL	16S rRNA Mafft LINSI alignment 1000 iterations, MrBayes	PDF
ALL	16S rRNA Mafft LINSI alignment 1000 iterations, Neighbour Joining tree with Kimura correction model and 1000 bootstraps	PDF
ALL	16S rRNA Infernals cmalign alignment, RAxML tree with secondary structure constrain and GTRGAMMA substitution model during maximum likelyhood search and GTRCAT during the 200 bootstrap replicates	PDF
ALL	16S rRNA Mafft LINSI alignment 1000 iterations, RAxML tree with GTRGAMMA substitution model during maximum likelyhood search and GTRCAT during the 200 bootstrap replicates	PDF
ALL	16S rRNA Infernals cmalign alignment, RAxML tree with secondary structure constrain and GTRGAMMA substitution model during maximum likelyhood search and during the 200 bootstrap replicates	PDF
ALL	16S rRNA Mafft LINSI alignment 1000 iterations, RAxML tree with GTRGAMMA substitution model during maximum likelyhood search and during the 200 bootstrap replicates	PDF
ALL	Maximum likelyhood tree reconstruction by Sate, 200 iterative refining runs of tree decomposed Mafft subalignments and combined Muscle alignments	PDF

In vitro transcripts, probes and primers

Download PDF

Supplement material

Genomewide comparison and novel ncRNAs in Aquificales

Marcus Lechner , Astrid Nickel , Stefanie Wehner , Konstantin Riege, Nicolas Wieseke, Benedikt M. Beckmann, Roland K. Hartmann, Manja Marz

Overview

Secondary structures of RNase P RNAs in Aquificales