Analysis of intra-genomic GC content homogeneity within prokaryotes
<p>Abstract</p> <p>Background</p> <p>Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions signif...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-08-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/464 |
| _version_ | 1811257922125037568 |
|---|---|
| author | Bohlin Jon Snipen Lars Hardy Simon P Kristoffersen Anja B Lagesen Karin Dønsvik Torunn Skjerve Eystein Ussery David W |
| author_facet | Bohlin Jon Snipen Lars Hardy Simon P Kristoffersen Anja B Lagesen Karin Dønsvik Torunn Skjerve Eystein Ussery David W |
| author_sort | Bohlin Jon |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity <it>GCVAR</it>, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low <it>GCVAR </it>indicates intra-genomic GC homogeneity and high <it>GCVAR </it>heterogeneity.</p> <p>Results</p> <p>The regression analyses indicated that <it>GCVAR </it>was significantly associated with domain (i.e. archaea or bacteria), phylum, and oxygen requirement. <it>GCVAR </it>was significantly higher among anaerobes than both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between <it>GCVAR </it>and mean GC content was also found but appears to be non-linear and varies greatly among phyla.</p> <p>Conclusions</p> <p>Our findings show that <it>GCVAR </it>is linked with oxygen requirement, while mean genomic GC content is not. We therefore suggest that <it>GCVAR </it>should be used as a complement to mean GC content.</p> |
| first_indexed | 2024-04-12T18:04:58Z |
| format | Article |
| id | doaj.art-3a9995e3ba6a48bf8c095581885cac89 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T18:04:58Z |
| publishDate | 2010-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-3a9995e3ba6a48bf8c095581885cac892022-12-22T03:22:01ZengBMCBMC Genomics1471-21642010-08-0111146410.1186/1471-2164-11-464Analysis of intra-genomic GC content homogeneity within prokaryotesBohlin JonSnipen LarsHardy Simon PKristoffersen Anja BLagesen KarinDønsvik TorunnSkjerve EysteinUssery David W<p>Abstract</p> <p>Background</p> <p>Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity <it>GCVAR</it>, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low <it>GCVAR </it>indicates intra-genomic GC homogeneity and high <it>GCVAR </it>heterogeneity.</p> <p>Results</p> <p>The regression analyses indicated that <it>GCVAR </it>was significantly associated with domain (i.e. archaea or bacteria), phylum, and oxygen requirement. <it>GCVAR </it>was significantly higher among anaerobes than both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between <it>GCVAR </it>and mean GC content was also found but appears to be non-linear and varies greatly among phyla.</p> <p>Conclusions</p> <p>Our findings show that <it>GCVAR </it>is linked with oxygen requirement, while mean genomic GC content is not. We therefore suggest that <it>GCVAR </it>should be used as a complement to mean GC content.</p>http://www.biomedcentral.com/1471-2164/11/464 |
| spellingShingle | Bohlin Jon Snipen Lars Hardy Simon P Kristoffersen Anja B Lagesen Karin Dønsvik Torunn Skjerve Eystein Ussery David W Analysis of intra-genomic GC content homogeneity within prokaryotes BMC Genomics |
| title | Analysis of intra-genomic GC content homogeneity within prokaryotes |
| title_full | Analysis of intra-genomic GC content homogeneity within prokaryotes |
| title_fullStr | Analysis of intra-genomic GC content homogeneity within prokaryotes |
| title_full_unstemmed | Analysis of intra-genomic GC content homogeneity within prokaryotes |
| title_short | Analysis of intra-genomic GC content homogeneity within prokaryotes |
| title_sort | analysis of intra genomic gc content homogeneity within prokaryotes |
| url | http://www.biomedcentral.com/1471-2164/11/464 |
| work_keys_str_mv | AT bohlinjon analysisofintragenomicgccontenthomogeneitywithinprokaryotes AT snipenlars analysisofintragenomicgccontenthomogeneitywithinprokaryotes AT hardysimonp analysisofintragenomicgccontenthomogeneitywithinprokaryotes AT kristoffersenanjab analysisofintragenomicgccontenthomogeneitywithinprokaryotes AT lagesenkarin analysisofintragenomicgccontenthomogeneitywithinprokaryotes AT dønsviktorunn analysisofintragenomicgccontenthomogeneitywithinprokaryotes AT skjerveeystein analysisofintragenomicgccontenthomogeneitywithinprokaryotes AT usserydavidw analysisofintragenomicgccontenthomogeneitywithinprokaryotes |