Dataset Information

Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas.

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.

SUBMITTER: Song K

PROVIDER: S-EPMC7674689 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas.

Song Kai K

Genome biology and evolution 20201101 11

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 nee ...[more]

PMID: 32722758

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Project description:BackgroundLow salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas is considered to be tolerant to relative low salinity. The genes that regulate C. gigas responses to osmotic stress were monitored using the next-generation sequencing of whole transcriptome with samples taken from gills. By RNAseq technology, transcript catalogs of up- and down-regulated genes were generated from the oysters exposed to low and optimal salinity seawater.Methodology/principal findingsThrough Illumina sequencing, we reported 1665 up-regulated transcripts and 1815 down-regulated transcripts. A total of 45771 protein-coding contigs were identified from two groups based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes that changed expression significantly were highly represented in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlighted genes related to osmoregulation, signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytoskeleton and cell cycle.Conclusions/significanceThrough more than 1.5 million sequence reads and the expression data of the two libraries, the study provided some useful insights into signal transduction pathways in oysters and offered a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will not only provide a better understanding of the molecular mechanisms about the response to osmotic stress of the oysters, but also facilitate research into biological processes to find underlying physiological adaptations to hypoosmotic shock for marine invertebrates.

Dataset Information

Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas.

Publications

Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas.

Similar Datasets

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