Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis

Vigil-Stenman, Theoden; Larsson, John; Nylander, Johan A A; Bergman, Birgitta

doi:10.1186/s12864-015-1386-7

Table 1 Organisms included in the study

From: Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis

Organism	Abbreviation	Genome size (Mbp) ^a	GC content	Habitat	Morphology	Symbiotic state	Total repeathits	Total IS hits	Annotated pseudo- genes	Repeats/ Mbp	Pseudo- genes/ Mbp
Cyanobacteria
Acaryochloris marina MBIC 11017	Acam	8.36	0.47	Marine	unicellular	Free-living	588	553	32	70	4
Anabaena variabilis ATCC 29413	Anav	7.11	0.41	Terrestrial	filamentous, heterocystous	Free-living	329	313	40	46	6
Arthrospira maxima CS-328	Artm	6.00	0.45	High-salt lakes	filamentous, non-heterocystous	Free-living	1208	906	0	201	0
Arthrospira platensis str. Paraca	Artp	5.00	0.44	High-salt lakes	filamentous, non-heterocystous	Free-living	206	141	0	41	0
Crocosphaera watsonii WH 8501	Crow	6.24	0.37	Marine	unicellular	Free-living	1611	1494	0	258	0
cyanobacterium UCYN-A	Ucyn	1.44	0.31	Marine, Host: prymnesiophytes	unicellular	obligate unclassified symbiont	1	1	0	1	0
Cyanothece sp. PCC 8802	Cya8802	4.80	0.40	Marine	unicellular	Free-living	203	176	204	42	43
Cyanothece	Cya	6.09⁵	0.41	Marine	unicellular	Free-living	246	205	167	40	27
Cylindrospermopsis raciborskii CS-505	Cylr	3.88	0.40	Freshwater lakes	filamentous, heterocystous	Free-living	517	303	1	133	0
Gloeobacter violaceus PCC 7421	Glov	4.66	0.62	Terrestrial	unicellular	Free-living	143	82	0	31	0
Lyngbya sp. PCC 8106	Lyns	7.04	0.41	Marine, Freshwater	filamentous, non-heteroc	Free-living	443	339	0	63	0
Microcystis aeruginosa NIES-843	Mica	5.84	0.42	Freshwater lake	unicellular	Free-living	1664	1563	0	285	0
Nodularia spumigena CCY9414	Nods	5.32	0.41	Brackish water	filamentous, heterocystous	Free-living	352	294	0	66	0
‘Nostoc azollae 0708’	NoAz	5.49	0.38	Host: Azolla ferns	filamentous, heterocystous	obligate extracellular symbiont	970	907	1670	177	304
Nostoc punctiforme PCC 73102	Nosp	9.06	0.41	Terrestrial	filamentous, heterocystous	facultative intracellular	399	366	371	44	41
Nostoc sp. PCC 7120	Noss	7.21	0.41	Terrestrial	filamentous, heterocystous	Free-living	311	278	0	43	0
Prochlorococcus marinus strains	Prom	1.86¹²	0.36	Marine	unicellular	Free-living	18	12	15	10	8
Raphidiopsis brookii D9	Rapb	3.19	0.40	Freshwater lake	filamentous,non-heterocystous	Free-living	109	80	0	34	0
Synechococcus elongatus species	Syne	2.7²	0.55	Freshwater lake	unicellular	Free-living	8.00	7.00	2	3	1
Synechococcus JA species	SynJA	2.99²	0.59	Hot spring	unicellular	Free-living	331	330	51	111	17
Synechococcus species	Syn	2.5⁷	0.56	Marine	unicellular	Free-living	6	5	10	2	4
Synechocystis sp. PCC 6803	Scys6803	3.95	0.47	Freshwater lake	unicellular	Free-living	161	151	0	41	0
Thermosynechococcus elongatusBP-1	Thee	2.59	0.54	Hot spring	unicellular	Free-living	128	99	0	49	0
Trichodesmium erythraeum IMS101	Trie	7.75	0.34	Marine	filamentous,non-heterocystous	Free-living	1311	1144	625	169	81
Non cyanobacterial symbionts
Bordetella pertussis Tohama I	Borp	4.09	0.68	Host: Human	unicellular	obligate intracellular	388	380	358	95	88
Candidatus amoebophilus asiaticus 5a2	Cana	1.88	0.35	Host: Acanthamoeba	unicellular	obligate intracellular	315	273	222	168	118
Frankia	Fra	7.00⁵	0.71	Host: Plants	filamentous	facultative intracellular	139	130	53	20	8
Onion yellows phytoplasma OY-M	PhyOY	0.85	0.28	Host: Plants	unicellular	obligate intracellular	113	29	0	133	0
Orientia tsutsugamushi str. Boryong	Orit	2.13	0.31	Host: Human	unicellular	obligate intracellular	1122	703	997	527	468
Shigella flexneri 2a str. 2457 T	Shif	4.60	0.51	Host: Human	unicellular	facultative intracellular	466	450	378	101	82
Mycoplasma mycoides subspecies	Myc	1.18²	0.24	Host: Animals	unicellular	obligate intracellular	77	75	1	65	1
Yersinia pestis strains	Yer	4.8²	0.48	Host: Animals	unicellular	facultative intracellular	306	294	155	63	32
Wolbachia subspecies	Wol	1.38⁶	0.35	Host: insects and nematodes	unicellular	obligate intracellular	361	161	67	260	48

^aSeveral similar bacteria are included in entries with superscripts. Genome sizes are averages, with the number of species indicated by the superscript.
Table of genomes included in the study. Very similar organisms, e.g. several genomes of Cyanothece, have been included as a single row, and the numbers therein represents averages of the data found. The numbers of organisms included in such groups are indicated with a superscript in the Size column of the table. Total repeat hits: The number of hits received to repeated sequences of any kind. Repeated genes with known functions that are not mobile DNA are not included in this count. Total IS hits: number of hits received to repeated sequences that are Insertion Sequences. Annotated pseudogenes: number of pseudogenes in the genome, according to the integrated microbial genomes and metagenomes database (IMG Data Management and Analysis Systems). The following two columns show number of repeated sequences and pseudogenes per Mbps of genome.

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ISSN: 1471-2164

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