Table_2_Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis.DOCX

Pyropia yezoensis is an economically important marine algae crop that, due to its large economic value, has generated considerable interest in the development of breeding programs to improve its production rates. Here, we sequenced the complete mitochondrial and plastid genomes of the P. yezoensis strain RZ-58 using the PacBio RS II sequencing technology. The mitochondrial genome (mtDNA) is 41,692 bp in size with an overall guanine–cytosine (GC) content of 32.72%, and the plastid genome (ptDNA) is 191,977 bp with a GC content of 33.09%. The complete mitochondrial and plastid genomes of 53 individuals from three geographical populations were then resequenced using the next-generation sequencing (NGS) technology to characterize their molecular features. When compared, the plastid genomes displayed similar genomic lengths and conserved gene synteny. However, mitochondrial genomes were quite different in length, which was mainly due to the different patterns of intron distributions. Single-nucleotide polymorphisms (SNPs) were examined to evaluate the genetic diversity of different geographical populations. High diversity was observed across the whole collection with moderate genetic variation between populations. In total, there were 463 and 366 high-quality SNPs detected in the mtDNA and ptDNA, respectively. The Qingdao wild group has the highest diversity with a mean pi of 0.00348 for mtDNA and 0.000388 for ptDNA, while the Yantai group had the lowest diversity. Cluster-based grouping and principal component analysis revealed three subpopulations in the whole collections. However, a genetic break of organellar DNA was observed in populations at sympatric localities, which was inferred as the result of historic biogeographic events. Our findings provide important information to guide marker-assisted selective breeding of Chinese P. yezoensis in the future.

条斑紫菜（Pyropia yezoensis）是一种具有重要经济价值的海洋藻类栽培作物，因其可观的经济价值，围绕提升其产量的育种项目开发受到了广泛关注。本研究采用PacBio RS II测序技术，对条斑紫菜RZ-58菌株的完整线粒体基因组（mitochondrial genome, mtDNA）与质体基因组（plastid genome, ptDNA）进行了测序。该线粒体基因组全长41692 bp，总鸟嘌呤-胞嘧啶（GC）含量为32.72%；质体基因组全长191977 bp，GC含量为33.09%。随后，本研究采用下一代测序（next-generation sequencing, NGS）技术，对来自3个地理种群的53个个体的完整线粒体与质体基因组进行了重测序，以解析其分子特征。比对分析显示，质体基因组的长度较为一致，基因共线性（gene synteny）也较为保守；但线粒体基因组的长度差异显著，这一差异主要源于内含子分布模式的不同。为评估不同地理种群的遗传多样性，本研究对单核苷酸多态性（Single-nucleotide polymorphisms, SNPs）进行了检测。整个样本集展现出较高的遗传多样性，种群间则存在中等程度的遗传分化。最终，在线粒体基因组中共检测到463个高质量SNPs，质体基因组中共检测到366个高质量SNPs。青岛野生种群的遗传多样性最高，其线粒体基因组的平均核苷酸多样度（π）为0.00348，质体基因组为0.000388；而烟台种群的遗传多样性最低。基于聚类的分组分析与主成分分析结果显示，整个样本集可划分为3个亚种群。但在同域分布的种群中，细胞器DNA（organellar DNA）呈现出遗传分化断裂的现象，这被推断为历史生物地理事件作用的结果。本研究结果可为未来中国条斑紫菜的标记辅助选择育种提供重要的理论指导。