Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

Frontiers in Marine Science

Kuipeng Xu¹  Fanna Kong²  Xianghai Tang²  Xinzi Yu²  Yunxiang Mao⁴ 

[1] College of Horticulture, Qingdao Agricultural University, Qingdao, China;College of Marine Life Sciences, Ocean University of China, Qingdao, China;Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China;Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Ministry of Education, Sanya, China;Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China;

关键词: organellar genome;    intraspecific variation;    organelle heteroplasmy;    single-nucleotide polymorphisms;    genetic diversity;    Pyropia yezoensis;   

DOI  :  10.3389/fmars.2019.00756

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown