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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| Veröffentlicht in: | PloS one 2021-06, Vol.16 (6), p.e0252207-e0252207 |
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| creator | Nagano, Yukio Kimura, Kei Kobayashi, Genta Kawamura, Yoshio |
| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0252207 |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0252207</identifier><identifier>PMID: 34106965</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>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</subject><ispartof>PloS one, 2021-06, Vol.16 (6), p.e0252207-e0252207</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Nagano et al. 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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. 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P.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic diversity of 39 samples of Pyropia species grown in Japan</atitle><jtitle>PloS one</jtitle><date>2021-06-09</date><risdate>2021</risdate><volume>16</volume><issue>6</issue><spage>e0252207</spage><epage>e0252207</epage><pages>e0252207-e0252207</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><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.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>34106965</pmid><doi>10.1371/journal.pone.0252207</doi><tpages>e0252207</tpages><orcidid>https://orcid.org/0000-0001-5030-676X</orcidid><oa>free_for_read</oa></addata></record> |
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| 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 |
| title | Genomic diversity of 39 samples of Pyropia species grown in Japan |
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