Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas
Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas
复制标题
太平洋牡蛎内含子长度、基因表达和核苷酸多样性的关系
DOI：
10.1007/s10126-018-9838-0
复制
发表时间：
2018-10-01
影响因子：
3
通讯作者：
Zhang, Guofan
中科院分区：
文献类型：
--
作者：
Song, Kai;Li, Li;Zhang, Guofan
长牡蛎是一种典型的软体动物，但其遗传特征尚未得到全面的研究。在这项研究中，我们使用全基因组重测序数据来鉴定和表征21种C. gigas样品的核苷酸多样性和群体重组率。我们的分析表明，与其他分类群相比，C. gigas在整个基因组中具有极高的遗传多样性和重组率。非编码区、内含子、基因间间隔区和非翻译区（UTRs）的多样性水平低于同义位点。内含子越大，多样性越低。此外，我们发现非同义多样性与基因表达呈负相关，这表明纯化选择在遗传多样性的形成中发挥了重要作用。100 kb和50 kb水平的核苷酸多样性与群体重组率正相关，如果多样性是通过纯化选择或搭便车的优势突变体形成的，这是可以预料的。我们的工作给出了牡蛎的多态性模式及其与重组率的关系的总体图景。
Crassostrea gigas is a model mollusk, but its genetic features have not been studied comprehensively. In this study, we used whole-genome resequencing data to identify and characterize nucleotide diversity and population recombination rate in a diverse collection of 21 C. gigas samples. Our analyses revealed that C. gigas harbors both extremely high genetic diversity and recombination rates across the whole genome as compared with those of the other taxa. The noncoding regions, introns, intergenic spacers, and untranslated regions (UTRs) showed a lower level diversity than the synonymous sites. The larger introns tended to have lower diversity. Moreover, we found a negative association of the non-synonymous diversity with gene expression, which suggested that purifying selection played an important role in shaping genetic diversity. The nucleotide diversity at the 100- and 50-kb levels was positively correlated with population recombination rates, which was expected if the diversity was shaped by purifying selection or hitchhiking of advantageous mutants. Our work gives a general picture of the oyster's polymorphism pattern and its association with recombination rates.