Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas

• Published in: Genome Biology and Evolution
• Main Author: Song, Kai
• Other Authors: Piganeau, Gwenael
• Format: Article in Journal/Newspaper
• Language: English
• Published: Oxford University Press (OUP) 2020
• Subjects: Genetics; Ecology, Evolution, Behavior and Systematics; Pacific; Crassostrea gigas; Pacific oyster
• Online Access: http://dx.doi.org/10.1093/gbe/evaa160; http://academic.oup.com/gbe/advance-article-pdf/doi/10.1093/gbe/evaa160/33539769/evaa160.pdf; http://academic.oup.com/gbe/article-pdf/12/11/1943/34389359/evaa160.pdf

Abstract Mutation is a driving force of evolution that has been shaped by natural selection and is universally biased. Previous studies determined genome-wide mutational patterns for several species and investigated the heterogeneity of mutational patterns at fine-scale levels. However, little evidence of the heterogeneity of mutation rates over large genomic regions was shown. Hence, the mutational patterns of different large-scale genomic regions and their association with selective pressures still need to be explored. As the second most species-rich animal phylum, little is known about the mutational patterns in Mollusca, especially oysters. In this study, the mutational bias patterns are characterized by using whole-genome resequencing data in the Crassostrea gigas genome. I studied the genome-wide relative rates of the pair mutations and found that the predominant mutation is GC -> AT, irrespective of the genomic regions. This analysis reveals that mutational biases were associated with gene expression levels across the C. gigas genome. Genes with higher expression levels and breadth expression patterns, longer coding length, and more exon numbers had relatively higher GC -> AT rates. I also found that genes with larger dN/dS values had relatively higher GC -> AT rates. This work represents the first comprehensive research on the mutational biases in Mollusca species. Here, I comprehensively investigated the relationships between mutational biases with some intrinsic genetic factors and evolutionary indicators and proposed that selective pressures are important forces shaping the mutational biases across the C. gigas genome.