Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, Republic of Korea.
Plant Genomics Laboratory, Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon, Republic of Korea.
Genes Genomics. 2024 Mar;46(3):355-365. doi: 10.1007/s13258-023-01472-9. Epub 2023 Nov 23.
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).
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.
We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.
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.
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.
许多属于红藻门的红藻物种被人类作为营养和药物的原料食用。随着海藻市场的增长，紫菜物种的重要性日益增加。红藻物种的分类发生了重大变化，近年来这种分类的准确性有了显著提高。在这里，我们报告了三种紫菜（条斑紫菜、坛紫菜和正红紫菜）叶绿体（cp）和线粒体（mt）的完整圆形基因组。
本研究旨在组装、注释和描述三种紫菜细胞器基因组的结构，进行比较基因组研究，并基于 SNP 开发分子标记。
我们分析了三种紫菜细胞器基因组的结构、重复序列、序列差异、基因重排和系统发育关系。
三种紫菜的叶绿体基因组平均包含 212 个蛋白质编码基因（PCGs），而线粒体基因组平均包含 25 个 PCGs。我们基于类红藻门（和五个作为外群的佛罗里达藻门物种）的 201 个和 23 个 PCGs（分别在 cp 和 mt 基因组中）重建了叶绿体和线粒体基因组的系统发育树。此外，还开发了 12 种用于 qRT-PCR 分析的种特异性分子标记。
这是首次报道坛紫菜完整的细胞器基因组。有了这些结果，本研究为分类差异、系统发育树重建和红藻进化提供了有用的遗传信息。此外，种特异性标记可作为鉴定目标物种的快速简便方法。
