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Version History

Version 2.4, December 1, 2007

IMG 2.4 is the 12th release of the Integrated Microbial Genomes (IMG) genomic data management and analysis system. IMG 2.4 was released on Dec 1^st, 2007.

IMG 2.4 Content

Genomes

IMG 2.4 content has been updated with new microbial genomes available in RefSeq version 25 (September 14, 2007).

IMG 2.4 contains a total of 3,637 genomes consisting of 818 bacterial, 50 archaeal, 40 eukaryotic genomes, 2,042 viruses (including bacterial phages), and 687 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes:

• 3,334 are finished genomes, and 303 are draft genomes.
• 256 are JGI sequenced genomes: 185 finished and 71 draft genomes sequenced by JGI. JGI genomes are also available through individual microbial portals at http://genome.jgi-psf.org/microbial.

Plasmid names were curated by adding strain names to organism name when available from publications or other sources. For example, see plasmid (NC_001520) available at NCBI . The original name from NCBI/RefSeq is "Acidithiobacillus ferrooxidans plasmid pTF4.1". The name was changed in IMG to "Acidithiobacillus ferrooxidans MAL4-1 plasmid pTF4.1". In total 423 plasmid names were modified by adding the strain information that was not available in the Host name. More information is available on the Plasmids Page

Note that 32 microbial genomes from IMG 2.3 were replaced in IMG 2.4 because (1) a "Draft" genome has been replaced by its "Finished" version or (2) the composition of the genome has changed through the addition of new replicons, that is, plasmids or chromosomes. For replaced genomes, whenever possible, the gene object identifiers (gene OIDs) for the protein-coding genes (CDS) were mapped to their new version in IMG. 2.4. See IMG Data Evolution History for details.

Annotations

IMG Terms and Pathways

IMG’s native controlled vocabularies for gene function (IMG Terms) and organism-independent functional hierarchies (IMG Pathways and PartsLists) have been extended. IMG 2.4 has 4,148 IMG Terms (1,526 new terms compared to IMG 2.3), and 524 IMG Pathways and Parts Lists (29 new pathways compared to IMG 2.3). In addition, 546,169 IMG genes are associated with IMG Terms (105,063 new gene-term associations compared to IMG 2.3).

Small RNAs

Small RNA genes that are missing from the original RefSeq genome files are added based on the Rfam database (http://www.sanger.ac.uk/Software/Rfam/). In IMG 2.4 2,962 small RNA genes were detected in 162 genomes.

rRNAs and tRNAs

tRNA and rRNA genes (23S, 16S and 5S) that are missing from the original RefSeq genome files are added using tRNAscan-SE v1.23 for tRNA genes and similarity comparisons to existing RNA genes fro rRNA genes. In IMG 2.4 3,687 tRNA and 1,555 tRNA genes were added in 149 genomes.

Pfam and TIGRfam

Starting with IMG 2.4, genes are associated with Pfam and TIGRfam annotations using hmmsearch, a tool in the HMMER package (http://hmmer.janelia.org).

In order to speed up data processing at a slight cost to sensitivity, instead of a full scan of all available HMM models using HMM (which can run very slowly), BLAST was used as a pre-filter to narrow down the candidate HMM models. A non stringent e-value cutoff was used for BLAST in order to pick up any sub-sequence from the seed sequences of an HMM model that could be a candidate for full HMM scoring. Thus, the BLAST e-value cutoff was set to 10 for Pfam and 1 for TIGRfam seed sequences databases, respectively. hmmsearch was then applied on the candidate models with a per family noise cutoff (--cut_nc). The scoring for domain level hits were recorded for Pfam, while scoring for the full model is recorded for TIGRfam.

Fusions

A gene is defined as a fusion if it is formed from the composition (fusion) of two or more previously separate genes (component genes). The identification of such genes is based on the computation described in AboutIMG IMG Content/Fusions section.

Only genes from finished genomes were considered as putative components in order to avoid false predictions from fragmented genes in draft genomes. Furthermore, genes that frequently appear as fragmented in finished genomes, such as transposases and integrases, and pseudogenes were excluded from fusion calculations.

IMG 2.4 User Interface

The User Interface has been reorganized and extended in order to improve its overall usability.

Main Menu

The UI main menu was changed as follows (see UI Map):

• Find Genomes is ahead of Find Genes on the top level menu.
• UsingIMG is on the second level menu of AboutIMG. The UsingIMG sections in html format are replaced with a pdf document.
• News is included into What's New/Content of About IMG.

Genomes

Genes

Functions

Find Functions

• Pfam Browser: Pfam domains are organized, when possible, into Pfam Categories that are based on COG categories.
• External links to individual COGs, Pfams and TIGRfams have been provided in the COG Browser, Pfam Browser, and TIGRfam Browser, respectively.
• IMG Terms, IMG Pathways, IMG Parts List, and IMG Networks are consolidated under IMG Terms & Pathways.

Function Details

External links to COG, Pfam, and TIGRfam have been provided in the COG Category Details and Pfam Category Details, and TIGRfam Role Details, respectively.

Analysis Carts

Gene Cart

At the top of the Gene Cart page there are links to the main parts within the page: Gene List, Upload & Export, Comparison Tools, and Profile Tools.

Function Cart

At the top of the Function Cart page there are links to the main parts within the page: Function List, Upload & Export, and Profile Tools.

Version 2.3, September 1, 2007

IMG 2.3 is the 11th release of the Integrated Microbial Genomes (IMG) genomic data analysis system. IMG 2.3 content has been updated with new microbial genomes available in RefSeq version 23 (May 2007). Note that 29 microbial genomes in IMG 2.2 were replaced in IMG 2.3 because (1) a "Draft" genome has been replaced by its "Finished" version or (2) the composition of the genome has changed through the addition of new replicons, that is, plasmids or chromosomes. For replaced genomes, whenever possible, the gene object identifiers (gene OIDs) for the protein-coding genes (CDS) were mapped to their new version in IMG. See IMG Data Evolution History for details.

IMG 2.3 contains a total of 2,878 genomes consisting of 729 bacterial, 46 archaeal, 40 eukaryotic genomes, 1,661 bacterial phages, and 402 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes, 2,609 are finished and 269 are draft genomes.

IMG 2.3 contains 236 microbial genomes sequenced at JGI, consisting of 157 finished and 79 draft genomes sequenced by JGI. JGI genomes are also available through individual microbial portals at http://genome.jgi-psf.org/microbial.

The following new eukaryotic genomes have been included into IMG in order to increase its genomic context for comparative analysis:

1. Aspergillus nidulans FGSC A4
2. Aspergillus niger CBS 513.88
3. Aspergillus terreus NIH2624
4. Candida albicans SC5314
5. Cryptococcus neoformans var. neoformans B-3501A
6. Gibberella zeae PH-1
7. Magnaporthe grisea 70-15
8. Neurospora crassa OR74A
9. Pichia stipitis CBS 6054
10. Ustilago maydis 521
11. Cryptosporidium hominis TU502
12. Entamoeba histolytica HM-1:IMSS
13. Giardia lamblia ATCC 50803
14. Leishmania major Friedlin
15. Theileria parva Muguga
16. Plasmodium yoelii yoelii 17XNL
17. Ostreococcus lucimarinus CCE9901

For information regarding data sources used and integration details, please refer to: Eukaryotic Genomes in IMG.

Version 2.2, June 1, 2007

This is the 10th release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 2.2. IMG 2.2 content has been updated with new microbial genomes available in RefSeq version 22 (March 2007). Note that 14 microbial genomes in IMG 2.1 were replaced in IMG 2.2 because (1) a "Draft" genome has been replaced by its "Finished" version or (2) the composition of the genome has changed through the addition of new replicons, that is, plasmids or chromosomes. For replaced genomes, whenever possible, the gene object identifiers (gene OIDs) for the protein-coding genes (CDS) were mapped to their new version in IMG. See IMG Data Evolution History for details.

IMG 2.2 contains a total of 2,815 genomes consisting of 687 bacterial, 41 archaeal, 24 eukaryotic genomes, 1,661 bacterial phages, and 402 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes, 2,558 are finished and 257 are draft genomes.

IMG 2.2 contains 227 microbial genomes sequenced at JGI, consisting of 131 finished and 96 draft genomes sequenced by JGI. JGI genomes are also available through individual microbial portals at http://genome.jgi-psf.org/microbial.

Version 2.1, March 15, 2007

This is the 9th release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 2.1. IMG 2.1 content has been updated with new microbial genomes available in RefSeq version 21 (January 15, 2007). As a result several genomes from IMG 2.0 were replaced in IMG 2.1. However, for these replaced genomes, where possible, the gene object identifiers (gene OIDs) for the protein-coding genes (CDS) were mapped to their current version in IMG. 2.1.

IMG 2.1 contains a total of 2,782 genomes consisting of 661 bacterial, 34 archaeal, 24 eukaryotic genomes, 1,661 bacterial phages, and 402 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes, 2,524 are finished and 258 are draft genomes. Compared to IMG 2.0, IMG 2.1 contains 481 new public microbial, eukaryal and plasmid genomes.

IMG 2.1 contains 202 microbial genomes sequenced at JGI, consisting of 108 finished and 94 draft genomes sequenced by JGI. Compared to IMG 2.0, IMG 2.1 contains 29 finished and 28 draft genomes sequenced by JGI. JGI genomes are also available through individual microbial portals at http://genome.jgi-psf.org/microbial.

The following model organism eukaryotic genomes have been included into IMG in order to increase its genomic context for comparative analysis:

1. Anopheles gambiae PEST
2. Arabidopsis thaliana
3. Caenorhabditis elegans
4. Cryptosporidium parvum Iowa type II
5. Danio rerio
6. Dictyostelium discoideum AX4
7. Drosophila melanogaster
8. Homo sapiens
9. Mus musculus
10. Rattus norvegicus
11. Trypanosoma brucei TREU927

For information regarding data sources used and integration details, please refer to: Model Organism Eukaryotes.

Version 2.0, December 1, 2006

This is the eighth release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 2.0.| IMG 2.0 content has been entirely refreshed with the latest versions of genomes available in RefSeq version 19 (September 15, 2006). As a result several genomes from IMG 1.6 were replaced in IMG 2.0. However, for these replaced genomes, where possible, the gene object identifiers (gene OIDs) for the protein-coding genes (CDS) were mapped to their current version in IMG. 2.0. See IMG Data Evolution History for details.

IMG 2.0 contains a total of 2301 genomes consisting of 595 bacterial, 32 archaeal, 13 eukaryotic genomes, 1661 viruses. Among these genomes, 2058 are finished and 243 are draft genomes. Compared to IMG 1.6, IMG 2.0 contains 1541 new public microbial,viral and eukaryal genomes.

IMG 2.0 contains 177 microbial genomes sequenced at JGI, consisting of 79 finished and 98 draft genomes sequenced by JGI. JGI genomes are also available through individual microbial portals at Microbial Genomics.

IMG 2.0 contains 177 microbial genomes sequenced at JGI, consisting of 79 finished and 98 draft genomes sequenced by JGI. JGI genomes are also available through individual microbial portals at Microbial Genomics.

IMG 2.0 content extensions include gene based links via RefSeq GI (gene information) numbers to Entrez Gene, and other microbial genome systems, such as PUMA and MicrobesOnline.

Version 1.6, September 1, 2006

This is the seventh release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 1.6. IMG 1.6 contains a total of 760 genomes consisting of 454 bacterial, 32 archaeal, 15 eukaryotic genomes and 259 bacterial phages. Among these genomes, 624 are finished and 136 are draft genomes.

IMG 1.6 contains 170 microbial genomes sequenced at JGI. The JGI and its collaborators have recently released the sequences of 18 (11 Finished (replaced old drafts), 7 new Drafts) genomes, bringing the total to 73 finished and 97 draft genomes sequenced by JGI. The previously released 11 draft genomes have been replaced with the finished versions. JGI genomes are also available through individual microbial portals at Microbial Genomics.

The finished genomes in IMG include 245 (11 new) bacterial and (0 new) archaeal genomes from EBI Genome Reviews (version 55.0, July 11, 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 1.5, IMG 1.6 contains 11 (EBIGR) new public microbial genomes.

Version 1.5, June 1, 2006

This is the sixth release of the Integrated Microbial Genomes (IMG) genomic dat a 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 f inished and 139 are draft genomes.

IMG 1.5 contains 162 microbial genomes sequenced at JGI. The JGI and its collabo rators have recently released the sequences of 38 (17 Finished (replaced old dra fts), 21 new Drafts) genomes, bringing the total to 62 finished and 100 draft ge nomes sequenced by JGI. The previously released 17 draft genomes have been replaced with the finished ve rsions. 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 EMB L (as of January 17, 2005), 2 eukaryotic genomes from RefSeq (as of March 21, 20 05), and 4 eukaryotic genomes from GenBank (as of July 27, 2005). Compared to IM G 1.4, IMG 1.5 contains 21 (15 RefSeq, 6 EBIGR) new public microbial genomes.

Version 1.4, March 1, 2006

This is the fifth release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 1.4. IMG 1.4 contains a total of 699 genomes consisting of 395 bacterial, 30 archaeal, 15 eukaryotic genomes and 259 bacterial phages. Among these genomes, 566 are finished and 133 are draft genomes.

IMG 1.4 contains 141 microbial genomes sequenced at JGI. The JGI and its collaborators have recently released the sequences of 9 (3 finished, 6 drafts) genomes, bringing the total to 47 finished and 94 draft genomes sequenced by JGI. The previously released 3 draft genomes have been replaced with the finished versions. JGI genomes are also available through individual microbial portals at Microbial Genomics .

The finished genomes include 229 (12 new) bacterial and 23 (1 new) archaeal genomes from EBI Genome Reviews (version 43.0, January 17, 2006), 9 eukaryotic genomes from EMBL (as of January 17, 2005), and 2 eukaryotic genomes from RefSeq (as of March 21, 2005) and 4 eukaryotic genomes from GenBank (as of July 27, 2005). Compared to IMG 1.3, IMG 1.4 contains 18 (5 RefSeq, 13 EBIGR) new public microbial genomes.

Version 1.3, December 1, 2005

This is the fourth release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 1.3. IMG 1.3 contains a total of 674 genomes consisting of 373 bacterial, 26 archaeal, 15 eukaryotic genomes and 260 bacterial phages. Among these genomes, 551 are finished and 123 are draft genomes.

IMG 1.3 contains 134 microbial genomes sequenced at JGI. The JGI and its collaborators have recently released the sequences of 20 (4 finished, 16 drafts) genomes, bringing the total to 44 finished and 90 draft genomes sequenced by JGI. The previously released 4 draft genomes have been replaced with the finished versions. JGI genomes are also available through individual microbial portals at Microbial Genomics .

The finished genomes include 217 (12 new) bacterial and 22 (1 new) archaeal genomes from EBI Genome Reviews (version 38.0, October 25, 2005), 9 eukaryotic genomes from EMBL (as of January 17, 2005), and 2 eukaryotic genomes from RefSeq (as of March 21, 2005) and 4 eukaryotic genomes from GenBank (as of July 27, 2005). Compared to IMG 1.2, IMG 1.3 contains 42 (29 RefSeq, 13 EBIGR) new public genomes.

IMG 1.3 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 March 1^st, 2006.

Version 1.2, September 1, 2005

This is the third release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 1.2. IMG 1.2 contains a total of 618 genomes consisting of 318 bacterial, 25 archaeal, 15 eukaryotic genomes and 260 bacterial phages. Among these genomes, 534 are finished and 95 are draft genomes. The finished genomes include 204 bacterial and 21 archaeal genomes from EBI Genome Reviews (version 31, July 18, 2005), 9 eukaryotic genomes from EMBL (as of January 17, 2005), and 2 eukaryotic genomes from RefSeq (as of March 21, 2005) and 4 eukaryotic genomes from GenBank (as of July 27, 2005). Compared to IMG 1.1, IMG 1.2 contains 271 new public genomes: (breakdown: 6 from EBI GR, 5 GenBank, 260 from RefSeq ).

In addition, IMG 1.2 contains 120 microbial genomes sequenced at JGI. The JGI and its collaborators have recently released the sequences of 13 (4 finished, 9 drafts) genomes, bringing the total to 40 finished and 80 draft genomes sequenced by JGI. 4 finished genomes have been replaced with their newer versions. 4 draft genomes have been replaced with the finished versions. JGI genomes are also available through individual microbial portals at JGI Microbial Genomics.

IMG continues to be updated on a quarterly basis with new public and JGI genomes. The next update is scheduled for December 1st, 2005.

Version 1.1, June 1, 2005

This is the second release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 1.1. IMG 1.1 contains a total of 337 genomes consisting of 301 bacterial, 25 archaeal, and 11 eukaryotic genomes. Among these genomes, 262 are finished and 75 are draft genomes. The finished genomes include 198 bacterial and 21 archaeal genomes from EBI Genome Reviews (version 25, April 25, 2005), 7 bacterial genomes from Refseq (as of March 21, 2005), 7 eukaryotic genomes from EMBL (as of January 17, 2005), and 2 eukaryotic genomes from RefSeq (as of March 21, 2005). Compared to IMG 1.0, IMG 1.1 contains 32 new public genomes: (breakdown: 23 from EBI GR, 9 RefSeq).

In addition, IMG 1.1 contains 111 microbial genomes sequenced at JGI. The JGI and its collaborators have recently completed the sequences of 14 (6 finished, 8 drafts) genomes, bringing the total to 36 finished and 75 draft genomes sequenced by JGI. Of the 6 newly finished, 5 were previously released as drafts. As a result, the old draft genomes were replaced with the new finished versions, and mapping of CDS between the old and new is provided.

IMG 1.1 has been extended with a number of data analysis features. In addition to enhancing existing genome and gene analysis tools, several new features have been added, including comparison of gene occurrence profiles across genomes, improved suport for comparative genome statistics, and ability to save and load genome and gene analysis settings from local user files.

The documentation for IMG 1.1 has been also expanded with the goal of improving the overall comprehensibility of IMG analysis.

Version 1.01, March 22, 2005

This version of IMG, version 1.01, is a content update of the March 1 release. The tools and number of genomes have remained unchanged. The gene models of the 20 newly completed and 72 draft JGI genomes have, however, been updated to reflect the current status of the JGI annotation pipeline. Specifically, the gene models for the draft genomes have been updated through the automated pipeline at Oak Ridge National Laboratory, while the gene models for the finished genomes have undergone an additional QA step that involves expert curation, as described on the Data Processing page under Data Cleaning.

Version 1.0, March 1, 2005

This is the first release of the Integrated Microbial Genomes (IMG) genomic data analysis system, IMG 1.0.  IMG 1.0 contains a total of 296 genomes consisting of 263 bacterial, 24 archaeal, and 9 eukaryotic genomes. Among these genomes, 224 are finished and 72 are draft genomes. The finished genomes include 175 bacterial and 20 archaeal genomes from EBI Genome Reviews (version 18.0, Jan 10, 2005), 7 eukaryotic genomes from EMBL (as of January 17, 2005), and 2 eukaryotic genomes from RefSeq (as of January 17, 2005).

In addition, IMG v.1.0 contains 102 microbial genomes sequenced at JGI. The JGI and its collaborators have recently finished the sequences of 20 genomes, bringing the total to 30 finished and 72 draft genomes sequenced by JGI. Preliminary annotation of these newly released genomes is included in this IMG 1.0 release. The gene calls and functional assignments are under review and will be periodically updated in IMG. JGI genomes are also available through individual microbial portals at JGI Microbial Genomics.

JGI genome sequence and annotation data will continue to improve over the next several months, due to newer assemblies and the introduction of stricter quality controls for annotations. IMG and Genbank submissions will be updated in order to reflect this data quality improvement.

IMG will be updated on a quarterly basis with new public and JGI genomes, and as needed (out of cycle) in order to reflect data quality improvements in the genome sequences and annotations. The next such update is scheduled for late March and will include the revised genes and annotations for the 20 new JGI finished genomes.