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The Curated Archaeal Genomes Data Mart of the Integrated Microbial Genomes (IMG) contains 22 archaeal genomes curated at JGI together with the 22 original genomes collected from the public domain.

Microbial genomes have been sequenced by many different sequencing centers, and these centers used different programs and parameters for identifying protein-coding genes (CDSs). In order to standardize gene model across publicly available genomes, the Genome Biology Program (GBP) at JGI has started to curate these genomes. The curation process is carried out using a pipeline developed at JGI followed by manual revisions. The pipeline identifies three types of problems:

1. Missing genes. Intergenic regions and regions containing unique genes (no hits in databases) are searched against the GenBank nonredundant protein database using blastx to identify potential new coding regions.
2. Overlapping genes. Genes in prokaryotic genomes do not often overlap by more than a few base pairs. If predicted genes overlap, the start sites may not be correct, or one of the genes may not be real.
3. 5' end problems. The pipeline identifies genes with 5' ends that are either shorter or longer than homologous genes. A curator determines whether the gene should be extended or truncated.

In many genomes, no pseudogenes were identified, and truncated genes were treated as real genes. During the manual curation process, pseudogenes are identified and labeled. If a gene corresponds to less than 30% of a COG hit its IMG ORF type is set as img_pseudo. Also if a gene has more than one internal stop codon or frameshift, its ORF type is set to img_pseudo. Pseudogenes identified in the original annotation are labeled pseudo. If a gene has one frameshift, it is assumed that this might be the result of a sequencing artifact, and therefore the frameshift fragments are merged to produce a full-length translation. Such genes have IMG ORF type set to frameshift. If two or more genes are combined to make a gene with a frameshift or pseudogene, the original genes are labeled obsolete and the new gene is given a unique locus tag (for example APE0258n). The Gene Details pages for the obsolete genes have links to the new gene and vice versa.

Not all CDSs identified by gene finding programs are real. A CDS that is considered not real is labeled as dubious. If a gene without hits to any other proteins overlaps with a real gene and can not be truncated to remove the overlap, it is labeled dubious. A gene is also labeled as dubious if it is less than 70 amino acids and has no hits to other proteins.

Genome	Accession Number	Authors’ CDSs	Authors’ pseudo	IMG CDSs	IMG pseudo	IMG frameshift	IMG dubious	CDSs added	CDSs modified	Modified % of authors'
Aeropyrum pernix K1	BA000002	2694	0	1652	24	10	1087	77	1586	58.9
Sulfolobus acidocaldarius DSM639	CP000077	2223	36	2211	59	0	15	34	160	7.1
Sulfolobus solfataricus P2	AE006641	2995	0	2887	154	25	7	121	410	13.4
Sulfolobus tokodaii 7	BA000023	2826	0	2692	98	15	125	114	461	16.3
Pyrobaculum aerophilum IM2	AE009441	2605	0	2473	91	11	11	10	188	7.2
Archaeoglobus fulgidus DSM 4304	AE000782	2407	30	2348	64	45	41	32	285	11.7
Haloarcula marismortui ATCC 43049 chromosome I	AY596297	3131	0	3163	24	3	26	90	362	11.5
Haloarcula marismortui ATCC 43049 chromosome II	AY596298	281	0	273	10	0	1	7	34	11.9
Halobacterium salinarum NRC-1 chromosome	AE004437	2058	0	2075	30	0	22	70	326	15.3
Methanothermobacter thermoautotrophicus Delta H	AE000666	1869	0	1787	25	42	34	4	183	9.8
Methanocaldococcus jannaschii DSM 2661	NC000909	1729	1	1702	29	14	1	17	118	6.8
Methanococcus maripaludis S2	BX950229	1722	0	1705	8	5	14	11	49	3.4
Methanosarcina acetivorans C2A	AE010299	4540	112	4380	278	44	63	174	744	16
Methanosarcina mazei Go1	AE008384	3371	0	3269	94	12	35	72	330	9.8
Methanopyrus kandleri AV19	AE009439	1687	4	1710	13	16	0	53	102	6
Pyrococcus abyssi GE5	NC000868	1896	0	1855	35	10	12	23	137	7.2
Pyrococcus furiosus DSM 3638	AE009950	2065	0	1971	86	32	12	44	263	12.7
Pyrococcus horikoshii OT3	BA000001	2061	0	1803	38	9	355	140	609	29.5
Thermococcus kodakaraensis KOD1	NC006624	2306	0	2270	26	8	1	2	58	2.5
Picrophilus torridus DMS9790	NC005877	1535	0	1530	21	8	0	24	80	5.2
Thermoplasma acidophilum DSM 1728	AL139299	1478	0	1482	24	16	21	63	214	14.5
Thermoplasma volcanium GSS1	BA000011	1526	0	1483	64	13	14	53	185	12.1
Nanoarchaeum equitans Kin4-M	AE017199	534	2	540	16	0	0	20	54	10.7

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Version 1.5, June 1, 2006

This is the sixth release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 1.5. IMG 1.5 contains a total of 741 genomes consisting of 435 bacterial, 32 archaeal, 15 eukaryotic genomes and 259 bacterial phages. Among these genomes, 602 are finished and 139 are draft genomes.

IMG 1.5 contains 162 microbial genomes sequenced at JGI. The JGI and its collaborators have recently released the sequences of 38 (17 Finished (replaced old drafts), 21 new Drafts) genomes, bringing the total to 62 finished and 100 draft genomes sequenced by JGI. The previously released 17 draft genomes have been replaced with the finished versions. See IMG Data Evolution History for details. JGI genomes are also available through individual microbial portals at Microbial Genomics.

The finished genomes in IMG include 234 (5 new) bacterial and 1 (1 new) archaeal genomes from EBI Genome Reviews (version 48.0, April 17, 2006), 9 eukaryotic genomes from EMBL (as of January 17, 2005), 2 eukaryotic genomes from RefSeq (as of March 21, 2005), and 4 eukaryotic genomes from GenBank (as of July 27, 2005). Compared to IMG 1.4, IMG 1.5 contains 21 (15 RefSeq, 6 EBIGR) new public microbial genomes.

IMG 1.5 has been extended with a number of data analysis features, especially in the area of functional and comparative genome analysis.

IMG continues to be updated on a quarterly basis with new public and JGI genomes. The next update is scheduled for September 1st, 2006.

Quick Genome Search :

News

The Curated Archaeal Genomes Data Mart of the Integrated Microbial Genomes (IMG) contains 22 archaeal genomes curated at JGI together with the 22 original genomes collected from the public domain.

Microbial genomes have been sequenced by many different sequencing centers, and these centers used different programs and parameters for identifying protein-coding genes (CDSs). In order to standardize gene model across publicly available genomes, the Genome Biology Program (GBP) at JGI has started to curate these genomes. The curation process is carried out using a pipeline developed at JGI followed by manual revisions. The pipeline identifies three types of problems:

1. Missing genes. Intergenic regions and regions containing unique genes (no hits in databases) are searched against the GenBank nonredundant protein database using blastx to identify potential new coding regions.
2. Overlapping genes. Genes in prokaryotic genomes do not often overlap by more than a few base pairs. If predicted genes overlap, the start sites may not be correct, or one of the genes may not be real.
3. 5' end problems. The pipeline identifies genes with 5' ends that are either shorter or longer than homologous genes. A curator determines whether the gene should be extended or truncated.

In many genomes, no pseudogenes were identified, and truncated genes were treated as real genes. During the manual curation process, pseudogenes are identified and labeled. If a gene corresponds to less than 30% of a COG hit its IMG ORF type is set as img_pseudo. Also if a gene has more than one internal stop codon or frameshift, its ORF type is set to img_pseudo. Pseudogenes identified in the original annotation are labeled pseudo. If a gene has one frameshift, it is assumed that this might be the result of a sequencing artifact, and therefore the frameshift fragments are merged to produce a full-length translation. Such genes have IMG ORF type set to frameshift. If two or more genes are combined to make a gene with a frameshift or pseudogene, the original genes are labeled obsolete and the new gene is given a unique locus tag (for example APE0258n). The Gene Details pages for the obsolete genes have links to the new gene and vice versa.

Not all CDSs identified by gene finding programs are real. A CDS that is considered not real is labeled as dubious. If a gene without hits to any other proteins overlaps with a real gene and can not be truncated to remove the overlap, it is labeled dubious. A gene is also labeled as dubious if it is less than 70 amino acids and has no hits to other proteins.

Genome	Accession Number	Authors’ CDSs	Authors’ pseudo	IMG CDSs	IMG pseudo	IMG frameshift	IMG dubious	CDSs added	CDSs modified	Modified % of authors'
Aeropyrum pernix K1	BA000002	2694	0	1652	24	10	1087	77	1586	58.9
Sulfolobus acidocaldarius DSM639	CP000077	2223	36	2211	59	0	15	34	160	7.1
Sulfolobus solfataricus P2	AE006641	2995	0	2887	154	25	7	121	410	13.4
Sulfolobus tokodaii 7	BA000023	2826	0	2692	98	15	125	114	461	16.3
Pyrobaculum aerophilum IM2	AE009441	2605	0	2473	91	11	11	10	188	7.2
Archaeoglobus fulgidus DSM 4304	AE000782	2407	30	2348	64	45	41	32	285	11.7
Haloarcula marismortui ATCC 43049 chromosome I	AY596297	3131	0	3163	24	3	26	90	362	11.5
Haloarcula marismortui ATCC 43049 chromosome II	AY596298	281	0	273	10	0	1	7	34	11.9
Halobacterium salinarum NRC-1 chromosome	AE004437	2058	0	2075	30	0	22	70	326	15.3
Methanothermobacter thermoautotrophicus Delta H	AE000666	1869	0	1787	25	42	34	4	183	9.8
Methanocaldococcus jannaschii DSM 2661	NC000909	1729	1	1702	29	14	1	17	118	6.8
Methanococcus maripaludis S2	BX950229	1722	0	1705	8	5	14	11	49	3.4
Methanosarcina acetivorans C2A	AE010299	4540	112	4380	278	44	63	174	744	16
Methanosarcina mazei Go1	AE008384	3371	0	3269	94	12	35	72	330	9.8
Methanopyrus kandleri AV19	AE009439	1687	4	1710	13	16	0	53	102	6
Pyrococcus abyssi GE5	NC000868	1896	0	1855	35	10	12	23	137	7.2
Pyrococcus furiosus DSM 3638	AE009950	2065	0	1971	86	32	12	44	263	12.7
Pyrococcus horikoshii OT3	BA000001	2061	0	1803	38	9	355	140	609	29.5
Thermococcus kodakaraensis KOD1	NC006624	2306	0	2270	26	8	1	2	58	2.5
Picrophilus torridus DMS9790	NC005877	1535	0	1530	21	8	0	24	80	5.2
Thermoplasma acidophilum DSM 1728	AL139299	1478	0	1482	24	16	21	63	214	14.5
Thermoplasma volcanium GSS1	BA000011	1526	0	1483	64	13	14	53	185	12.1
Nanoarchaeum equitans Kin4-M	AE017199	534	2	540	16	0	0	20	54	10.7