Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.
Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China.
Mar Biotechnol (NY). 2018 Oct;20(5):676-684. doi: 10.1007/s10126-018-9838-0. Epub 2018 Jul 3.
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.
太平洋牡蛎是一种模式软体动物，但它的遗传特征尚未得到全面研究。在这项研究中，我们使用全基因组重测序数据来鉴定和描述 21 个太平洋牡蛎样本的多样性和群体重组率。我们的分析表明，与其他分类群相比，太平洋牡蛎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（UTR）的多样性低于同义位点。较大的内含子往往具有较低的多样性。此外，我们发现非同义多样性与基因表达呈负相关，这表明纯化选择在塑造遗传多样性方面发挥了重要作用。100kb 和 50kb 水平的核苷酸多样性与群体重组率呈正相关，如果多样性是由纯化选择或有利突变的搭便车塑造的，则可以预期这种相关性。我们的工作提供了牡蛎多态性模式及其与重组率关联的总体情况。
