EurekaMag.com logo
+ Site Statistics
References:
53,623,987
Abstracts:
29,492,080
+ Search Articles
+ Subscribe to Site Feeds
EurekaMag Most Shared ContentMost Shared
EurekaMag PDF Full Text ContentPDF Full Text
+ PDF Full Text
Request PDF Full TextRequest PDF Full Text
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter
Follow on LinkedInFollow on LinkedIn

+ Translate

Trends between gene content and genome size in prokaryotic species



Trends between gene content and genome size in prokaryotic species



Abstracts of the General Meeting of the American Society for Microbiology 103: R-046



To determine whether there are universal trends between the relative number of genes attributable to specific cellular functions and genome size, we functionally characterized the fully sequenced prokaryotic genomes (81 genomes as of July 2002) using the COGs database. COGs provides convenient means of annotation by grouping all proteins in eighteen functional categories. All possible ORFs from the 81 genomes were assigned to a functional category according to the category where their best COG homolog has been classified. Our results showed that the portion of the genome devoted to translation and biogenesis, DNA replication and repair, nucleotide transport and metabolism, was negatively correlated with genome size, whereas the portion devoted to transcription, signal transduction, inorganic ion transport, amino acid and carbohydrate transport and metabolism, secondary metabolite biosynthesis and unknown function (or conserved hypothetical) was positively correlated. The remaining categories showed no correlation with genome size. These results are supported by our independent analysis of the publicly available data from TIGR's CMR and KEGG's Orthology databases. It is thus conclusive that large genomes preferentially accumulate metabolic, transport and regulatory genes as opposed to informational ones. These results correlate with the metabolic versatility and boarder ecological success shown by species with larger genomes and predict that such species are more successful in diverse resource habitats. However genomic data is currently heavily biased towards small genome clinical strains make it difficult to evaluate the origins of the larger genomes. Archaea, compared to Bacteria of the same genome size, had proportionally more genes in energy production and poorly characterized categories and fewer in cell envelope biogenesis and cell motility and secretion systems. Lastly, our analysis of the 23 environmental strains partially sequenced by JGI showed that JGI's genomes poorly matched COG database compared to the fully sequenced ones, indicating that they posses more of the uncharacterized genes in nature.

(PDF 0-2 workdays service: $29.90)

Accession: 035985122

Download citation: RISBibTeXText



Related references

Trends between gene content and genome size in prokaryotic species with larger genomes. Proceedings of the National Academy of Sciences of the United States of America 101(9): 3160-3165, 2004

The impact of long-distance horizontal gene transfer on prokaryotic genome size. Proceedings of the National Academy of Sciences of the United States of America 106(51): 21748-21753, 2010

Evolution of prokaryotic gene order: Genome rearrangements in closely related species. Trends in Genetics 17(1): 10-13, January, 2001

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 21(3): 293-306, 2004

Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics 177(3): 1277-1290, 2007

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Research 11(3): 356-372, 2001

Genome size and AT-DNA content in thirteen species of Decapoda. Unknown, 1999

Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks. Mbio 5(6): E01867-E01867, 2015

Gene-centric association analysis for the correlation between the guanine-cytosine content levels and temperature range conditions of prokaryotic species. Bmc Bioinformatics 11 Suppl 11(): S7-S7, 2011

Size and structure of the bird genome--I. DNA content of 48 species of Neognathae. Comparative Biochemistry and Physiology. B, Comparative Biochemistry 85(1): 61-65, 1986

Assessment of phylogenetic structure in genome size--gene content correlations. Genome 55(5): 391-395, 2012

Genome size and A-T base content in five Palinuridae species Crustacea Decapoda. Biologia Marina Mediterranea 6. 1, 1999

Genome size and AT-DNA nuclear content in three species of the genus Syngnathus Teleostei, Syngnathidae. Biologia Marina Mediterranea, Suppl. (Parte Seconda) 9. 1, 2002

Did prokaryotic DNA content evolve by a series of genome doublings?. Origins of Life and Evolution of the Biosphere 30(2-4): 316, 2000

Genome Update: AT content in sequenced prokaryotic genomes. Microbiology 150 pt4: 9-52, 2004