Genomic diversity of 39 samples of Pyropia species grown in Japan.

Yukio Nagano,Genta Kobayashi,Kei Kimura,Yoshio Kawamura,Randall P Niedz

doi:10.1371/journal.pone.0252207

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.

Highlights

The genus Pyropia is a marine red alga belonging to the family Bangiaceae
Within the genus Pyropia, P. yezoensis Ueda (Susabi-nori in Japanese) and P. haitanensis Chang et Zheng are economically important marine crops that are consumed in many countries [1]
A comparison of Japanese and Chinese samples of P. yezoensis revealed that the diversity of chloroplast and mitochondrial sequences in Japan is lower than that in China (Figs 2 and 3 and S6 Fig)

Summary

Introduction

The genus Pyropia is a marine red alga belonging to the family Bangiaceae. Within the genus Pyropia, P. yezoensis Ueda (Susabi-nori in Japanese) and P. haitanensis Chang et Zheng (tanzicai in Chinese) are economically important marine crops that are consumed in many countries [1]. These are farmed in Japan, China and Korea. In recent years, they have been eaten as ingredients of sushi and snacks around the world, and their consumption is increasing. P. tenera Kjellman (Asakusa-nori in Japanese) was once cultivated in Japan but has been replaced by P. yezoensis in many places.

Methods

Results

Conclusion