Yong Jin Lee, Yo Ram Uh, Yeon Mi Kim, Cheol Min Kim, Cheol Seong Jang
{"title":"三种红色大藻(Neoporphyra dentata、Neoporphyra seriata和Neopyropia yezoensis)细胞器全基因组的特征、比较分析及分子标记的开发。","authors":"Yong Jin Lee, Yo Ram Uh, Yeon Mi Kim, Cheol Min Kim, Cheol Seong Jang","doi":"10.1007/s13258-023-01472-9","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Many species of red algae belonging to the phylum Rhodophyta are consumed by humans as raw materials for nutrition and medicine. As the seaweed market grows, the importance of the laver species has increased. The classification of red algal species has changed significantly, and the accuracy of this classification has improved significantly in recent years. Here, we report the complete circular genomes of the chloroplasts (cp) and mitochondria (mt) of three laver species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis).</p><p><strong>Objective: </strong>This study aims to assemble, annotate, and characterize the organization of the organelle genomes of three laver species, conduct comparative genomic studies, and develop molecular markers based on SNPs.</p><p><strong>Methods: </strong>We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.</p><p><strong>Results: </strong>The chloroplast genomes of the three species contained an average of 212 protein-coding genes (PCGs), while the mitochondrial genomes contained an average of 25 PCGs. We reconstructed the phylogenetic trees based on both chloroplast and mitochondrial genomes using 201 and 23 PCGs (in cp and mt genomes, respectively) shared in the class Bangiophyceae (and five species of Florideophyceae class used as an outgroup). In addition, 12 species-specific molecular markers were developed for qRT-PCR analysis.</p><p><strong>Conclusions: </strong>This is the first report of Neoporphyra seriata complete organellar genomes. With the results, this study provides useful genetic information regarding taxonomic discrepancies, the reconstruction of phylogenetic trees, and the evolution of red algae. Moreover, the species-specific markers can be used as fast and easy methods to identify a target species.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"355-365"},"PeriodicalIF":1.6000,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Characterization and comparative analysis of the complete organelle genomes of three red macroalgae species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis) and development of molecular makers for their identification.\",\"authors\":\"Yong Jin Lee, Yo Ram Uh, Yeon Mi Kim, Cheol Min Kim, Cheol Seong Jang\",\"doi\":\"10.1007/s13258-023-01472-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Many species of red algae belonging to the phylum Rhodophyta are consumed by humans as raw materials for nutrition and medicine. As the seaweed market grows, the importance of the laver species has increased. The classification of red algal species has changed significantly, and the accuracy of this classification has improved significantly in recent years. Here, we report the complete circular genomes of the chloroplasts (cp) and mitochondria (mt) of three laver species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis).</p><p><strong>Objective: </strong>This study aims to assemble, annotate, and characterize the organization of the organelle genomes of three laver species, conduct comparative genomic studies, and develop molecular markers based on SNPs.</p><p><strong>Methods: </strong>We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.</p><p><strong>Results: </strong>The chloroplast genomes of the three species contained an average of 212 protein-coding genes (PCGs), while the mitochondrial genomes contained an average of 25 PCGs. We reconstructed the phylogenetic trees based on both chloroplast and mitochondrial genomes using 201 and 23 PCGs (in cp and mt genomes, respectively) shared in the class Bangiophyceae (and five species of Florideophyceae class used as an outgroup). In addition, 12 species-specific molecular markers were developed for qRT-PCR analysis.</p><p><strong>Conclusions: </strong>This is the first report of Neoporphyra seriata complete organellar genomes. With the results, this study provides useful genetic information regarding taxonomic discrepancies, the reconstruction of phylogenetic trees, and the evolution of red algae. Moreover, the species-specific markers can be used as fast and easy methods to identify a target species.</p>\",\"PeriodicalId\":12675,\"journal\":{\"name\":\"Genes & genomics\",\"volume\":\" \",\"pages\":\"355-365\"},\"PeriodicalIF\":1.6000,\"publicationDate\":\"2024-03-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genes & genomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1007/s13258-023-01472-9\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2023/11/23 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genes & genomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s13258-023-01472-9","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/11/23 0:00:00","PubModel":"Epub","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Characterization and comparative analysis of the complete organelle genomes of three red macroalgae species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis) and development of molecular makers for their identification.
Background: Many species of red algae belonging to the phylum Rhodophyta are consumed by humans as raw materials for nutrition and medicine. As the seaweed market grows, the importance of the laver species has increased. The classification of red algal species has changed significantly, and the accuracy of this classification has improved significantly in recent years. Here, we report the complete circular genomes of the chloroplasts (cp) and mitochondria (mt) of three laver species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis).
Objective: This study aims to assemble, annotate, and characterize the organization of the organelle genomes of three laver species, conduct comparative genomic studies, and develop molecular markers based on SNPs.
Methods: We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.
Results: The chloroplast genomes of the three species contained an average of 212 protein-coding genes (PCGs), while the mitochondrial genomes contained an average of 25 PCGs. We reconstructed the phylogenetic trees based on both chloroplast and mitochondrial genomes using 201 and 23 PCGs (in cp and mt genomes, respectively) shared in the class Bangiophyceae (and five species of Florideophyceae class used as an outgroup). In addition, 12 species-specific molecular markers were developed for qRT-PCR analysis.
Conclusions: This is the first report of Neoporphyra seriata complete organellar genomes. With the results, this study provides useful genetic information regarding taxonomic discrepancies, the reconstruction of phylogenetic trees, and the evolution of red algae. Moreover, the species-specific markers can be used as fast and easy methods to identify a target species.
期刊介绍：
Genes & Genomics is an official journal of the Korean Genetics Society (http://kgenetics.or.kr/). Although it is an official publication of the Genetics Society of Korea, membership of the Society is not required for contributors. It is a peer-reviewed international journal publishing print (ISSN 1976-9571) and online version (E-ISSN 2092-9293). It covers all disciplines of genetics and genomics from prokaryotes to eukaryotes from fundamental heredity to molecular aspects. The articles can be reviews, research articles, and short communications.
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