Limits...
Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes).

Heras J, McClintock K, Sunagawa S, Aguilar A - BMC Genomics (2015)

Bottom Line: The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans.One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection.In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3' and 5' UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA. herasj@uci.edu.

ABSTRACT

Background: The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine rockfishes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates.

Results: We identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3' and 5' UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions.

Conclusions: We were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus.

No MeSH data available.


Related in: MedlinePlus

Plot of (Ka) nonsynonymous vs. (Ks) synonymous substitutions. Blue diamonds indicate values with a Ks < 0.1, whereas red triangles indicate Ks values greater than 0.1 but less than 0.5. The black line suggests neutrality, values above the line are subject to positive selection and values below are subject to purifying selection
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4557894&req=5

Fig1: Plot of (Ka) nonsynonymous vs. (Ks) synonymous substitutions. Blue diamonds indicate values with a Ks < 0.1, whereas red triangles indicate Ks values greater than 0.1 but less than 0.5. The black line suggests neutrality, values above the line are subject to positive selection and values below are subject to purifying selection

Mentions: Two hundred and nine ortholog pairs contained a Ka/Ks less than 0.1, 726 pairs were between 0.1–1.0 (Ka/Ks) and 144 pairs that were found greater than one (positive selection; Fig. 1), which amounts to 1079 orthologs in total. Seventy-one of these pairs were annotated with a majority of the sequences that were associated with macromolecule metabolic processes and regulation of biological processes based on the sequence distribution of Gene Ontologies (Table 1). Only a small fraction of the distribution of GOs were associated with reproductive process (11 orthologous pairs) and sexual reproduction (8 orthologous pairs). The average Ka/Ks value was 0.53 (s.d. = 0.62), and the average ortholog alignment length of 361.37 (s.d. = 132.45). There was no enrichment found between these two categories with a False Discovery Rate of (0.05).Fig. 1


Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes).

Heras J, McClintock K, Sunagawa S, Aguilar A - BMC Genomics (2015)

Plot of (Ka) nonsynonymous vs. (Ks) synonymous substitutions. Blue diamonds indicate values with a Ks < 0.1, whereas red triangles indicate Ks values greater than 0.1 but less than 0.5. The black line suggests neutrality, values above the line are subject to positive selection and values below are subject to purifying selection
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4557894&req=5

Fig1: Plot of (Ka) nonsynonymous vs. (Ks) synonymous substitutions. Blue diamonds indicate values with a Ks < 0.1, whereas red triangles indicate Ks values greater than 0.1 but less than 0.5. The black line suggests neutrality, values above the line are subject to positive selection and values below are subject to purifying selection
Mentions: Two hundred and nine ortholog pairs contained a Ka/Ks less than 0.1, 726 pairs were between 0.1–1.0 (Ka/Ks) and 144 pairs that were found greater than one (positive selection; Fig. 1), which amounts to 1079 orthologs in total. Seventy-one of these pairs were annotated with a majority of the sequences that were associated with macromolecule metabolic processes and regulation of biological processes based on the sequence distribution of Gene Ontologies (Table 1). Only a small fraction of the distribution of GOs were associated with reproductive process (11 orthologous pairs) and sexual reproduction (8 orthologous pairs). The average Ka/Ks value was 0.53 (s.d. = 0.62), and the average ortholog alignment length of 361.37 (s.d. = 132.45). There was no enrichment found between these two categories with a False Discovery Rate of (0.05).Fig. 1

Bottom Line: The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans.One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection.In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3' and 5' UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA. herasj@uci.edu.

ABSTRACT

Background: The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine rockfishes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates.

Results: We identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3' and 5' UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions.

Conclusions: We were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus.

No MeSH data available.


Related in: MedlinePlus