Genomic diversity of 39 samples of Pyropia species grown in Japan

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...

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Bibliographic Details
Published in:PloS one 2021-06, Vol.16 (6), p.e0252207-e0252207
Main Authors: Nagano, Yukio, Kimura, Kei, Kobayashi, Genta, Kawamura, Yoshio
Format: Article
Language:English
Subjects:
Algae
Analysis
Biological diversity
Biology and Life Sciences
Cell culture
Chloroplasts
Computer and Information Sciences
Diploids
Engineering and Technology
Genetic aspects
Genetic diversity
Genomes
Maximum likelihood method
Mitochondrial DNA
Nutrients
Phylogenetics
Phylogeny
Polymorphism
Red algae
Seaweeds
Sound
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0252207