Genomic diversity of 39 samples of Pyropia species grown in Japan

Abstract

Some Pyropia species, such as nori (P. yezoensis), are important marine crops. We conducted a phylogenetic analysis of 39 samples of Pyropia species grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and Chinese P. yezoensis. Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and Chinese P. yezoensis. Analysis of organellar genomes showed that the genetic diversity of Japanese P. yezoensis used in this study is lower than that of Chinese wild P. yezoensis. To analyze the genetic relationships between samples of Japanese Pyropia, we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding between P. yezoensis and P. tenera, nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of Japanese P. yezoensis is low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain of P. yezoensis showed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation of Pyropia species.

Characterization and organelle genome sequencing of Pyropia species from Myanmar

“…Similar characteristics were observed in P. dentata from Korea 33 . Interestingly, P. dentata collected from Japan 34 does not show the characteristics of lacking one repeat. (Given that the two sequences of the conserved unit of the rRNA genes of P. dentata (Neoporphyra dentata) in Japan have not yet been determined, this Japanese seaweed was not included in the phylogenetic analysis of the current study).…”

“…It is important to note the fact that the collection site was a nori farm in China, as outlined in the study 30 . However, another study 34 , which delved into the diversity of Pyropia species, inferred that the cultivated Chinese Pyropia are genetically similar to Japanese ones but not to Chinese wild ones from Shandong Province, China. Further research is necessary to fully understand the origin of the species.)…”