State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
BMC Biol. 2023 Aug 8;21(1):168. doi: 10.1186/s12915-023-01668-1.
Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid-autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual.
Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture.
Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.
自体多倍体是一种研究全基因组加倍（WGD）而无需杂交的有价值的模型，但人们对 WGD 后自体多倍体基因组中发生的结构和功能变化知之甚少。青钱柳（胡桃科）是一种天然的二倍体-自体四倍体物种。我们生成了一个等位基因感知的自体四倍体基因组、一个嵌合染色体水平的二倍体基因组，以及 106 个自体四倍体个体的全基因组重测序数据，每个个体的平均深度为 60×，以及 12 个二倍体个体的平均深度为 90×。
自体四倍体青钱柳有 64 条染色体聚集到 16 个同源组中，大多数同源染色体表现出相似的染色体长度、基因数量和表达。同线性、结构变异和与二倍体基因组不匹配的区域分别占自体四倍体基因组的 81.3%、8.8%和 9.9%。我们的分析确定了 20626 个基因（69.18%）有四个等位基因，9191 个基因（30.82%）有一个、两个或三个等位基因，表明多倍体后等位基因丢失。发生等位基因丢失的基因更常发生在结构变异附近或内部，并且与转座元件有明显的重叠。此外，这些基因与其他基因相互作用的趋势降低。我们还在自体四倍体基因组中发现了 102 个具有超过四个拷贝的基因，它们的表达水平明显高于二倍体。这些基因在参与应激反应和植物防御的酶中富集，可能有助于自体四倍体的进化成功。我们的群体基因组分析表明，自体四倍体只有一个起源，并且与二倍体最近才发生分化（约 0.57 Mya），其间很少有杂交种的混合。
我们的研究结果表明，基因组和功能的重新组织是可能的，这可能有助于青钱柳自体四倍体的进化成功。
