Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA.
BMC Genomics. 2024 May 10;25(1):459. doi: 10.1186/s12864-024-10380-5.
Genome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.
The genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an F analysis. However, the low F observed in these islands is not caused by low interspecies sequence divergence (d) but rather by exceptionally high estimated intraspecies nucleotide diversity (π). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.
This study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for F values between Atlantic and Pacific herring.
群体全基因组比较被广泛用于探索核苷酸多样性和序列分化模式，以提供有关自然选择和遗传漂变如何影响基因组的知识。在这项研究中，我们比较了大西洋和太平洋鲱这两个大约在 200 万年前分化的姐妹种的全基因组测序数据，以探索这两个物种之间遗传分化的模式。
这两个物种的基因组比较显示出高度的全基因组分化，但具有显著低遗传分化的岛屿，如 F 分析所示。然而，这些岛屿中观察到的低 F 值并不是由种间序列分化（d）低引起的，而是由异常高的种内核苷酸多样性（π）引起的。这些低分化和高核苷酸多样性的区域，在本研究中称为高多样性区域，不富含重复序列，但富含与免疫相关的基因。这种富集包括适应性免疫系统的基因，如免疫球蛋白、T 细胞受体和主要组织相容性复合体基因，以及在固有免疫系统中起重要作用的大量基因，如新型免疫型受体、三部分基序和肿瘤坏死因子受体基因。对来自两个大西洋鲱个体的基于长读长的组装的分析显示，这些基因组区域存在广泛的拷贝数变异，表明升高的种内核苷酸多样性部分是由于短读长的交叉映射。
本研究表明，拷贝数变异是鲱鱼免疫性状基因座的一个特征。另一个重要的启示是，这些基因座是使用短读长数据进行全基因组遗传分化经典基因组筛选的盲点，不仅在鲱鱼中，可能在其他在免疫性状基因座中具有类似定性变异的物种中也是如此。这些基因座在本研究中引人注目，是因为大西洋和太平洋鲱之间的 F 值具有相对较高的全基因组基线。
