Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

Abstract

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 highquality 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.

Genomic diversity of 39 samples ofPyropiaspecies grown in Japan

“…Mitochondrial sequences separated Chinese P. yezoensis into three clusters as reported previously. 26 Thus, mitochondrial sequences are determinant for clustering in the previous report. 26 The analysis did not separate Japanese from Chinese P. yezoensis .…”

“…The chloroplast genomes of Pyropia species contain two direct repeats carrying ribosomal RNA (rRNA) operon copies. 26 The circular chloroplast genome has a large single-copy section and a short single-copy section between two rRNA repeats. Mapping of the short reads to the assembled chloroplast genome detected two types of reads in the rRNA operons (Supplementary Figure 1) in all 39 cases, reflecting the presence of two non-identical direct repeats carrying two different rRNA operons.…”

“…Mapping of the short reads to the assembled chloroplast genome detected two types of reads in the rRNA operons (Supplementary Figure 1) in all 39 cases, reflecting the presence of two non-identical direct repeats carrying two different rRNA operons. 26 The presence of two types of reads in the rRNA operons might cause the unsuccessful assembly of the whole chloroplast genome of the 9 samples. Indeed, we succeeded in assembling the long single section sequences of all 39 samples.…”

“…Previous research reported that wild varieties of P. yezoensis from Shandong Province, China, can be classified into three clusters. 26 We also assembled the chloroplast genome of one accession of each cluster. By using the assembled sequences of large single copy sections and publicly available chloroplast sequences, we created a phylogenetic tree based on the maximum likelihood method (Figure 2).…”

“…For example, to study the genetic diversity of P. yezoensis in China, high-throughput DNA sequencing analysed variations in the organellar genome. 26 This study divided wild P. yezoensis from Shandong Province, China, into three clusters. Several methods, such as restriction-site associated DNA sequencing, 27 genotyping by sequencing, 28 and whole-genome resequencing 29,30 use high-throughput DNA sequencing and can be applied to the analysis of the nuclear genome.…”