Patil Maheshkumar Prakash, Woo Hee-Eun, Kim Young-Ryun, Kim Jong-Oh, Kim Kyunghoi
Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513, Republic of Korea.
Institute of Sustainable Earth and Environment Dynamics (SEED), Pukyong National University, 365 Sinseon-Ro, Nam-Gu, Busan, 48547, Republic of Korea.
Biochem Genet. 2025 Feb 25. doi: 10.1007/s10528-025-11063-w.
Red algae are widely used as a source of health-promoting bioactive compounds and dietary fibers in health foods. The identification and classification of red algal species based on morphological and molecular characteristics is challenging because of the similarity of the thallus and its high degree of plasticity and because complete mitochondrial genomes have only been reported for a few species. In this study, the complete mitochondrial genome sequencing of the red macroalga Chondracanthus tenellus (Harvey) (Hommersand et al., Hydrobiologia 260:105-120, 1993)) (Rhodophyta, Gigartinales) was performed for the first time. Additionally, we aimed to reconstruct the phylogenetic relationships of the species within the order Gigartinales using complete mitochondrial genome sequences. Genomic DNA was extracted, analyzed by whole-genome sequencing (WGS), and assembled using NOVOPlasty. The mitochondrial genome sequence was annotated, and both a genome map and a phylogenetic tree were constructed using maximum likelihood analysis. The mitochondrial genome was 25,928 bp in length, had strongly biased [AT] content (72.08%), and comprised 3 rRNAs, 23 tRNAs, and 24 protein-coding genes (PCGs). In comparison with the mitochondrial genome of other red algae, that of C. tenellus lacks rpl5 and rpl20. Based on a phylogenetic study of the complete mitochondrial genome, C. tenellus belongs to the family Gigartinaceae and is monophyletic with other species of the order Gigartinales. This is the first report of C. tenellus complete mitochondrial genome; its characteristics are consistent with those of other red algae. The study of genomic data will be beneficial for future comparative genomics, phylogenetics, and evolutionary studies.
红藻作为保健食品中促进健康的生物活性化合物和膳食纤维的来源被广泛使用。基于形态学和分子特征对红藻物种进行鉴定和分类具有挑战性，这是因为藻体相似且可塑性高，而且仅报道了少数物种的完整线粒体基因组。在本研究中，首次对红大型海藻细弱软骨藻（哈维）（霍默桑德等人，《水生生物学》260:105 - 120，1993年）（红藻门，杉藻目）进行了完整线粒体基因组测序。此外，我们旨在利用完整线粒体基因组序列重建杉藻目内物种的系统发育关系。提取基因组DNA，通过全基因组测序（WGS）进行分析，并使用NOVOPlasty进行组装。对线粒体基因组序列进行注释，并使用最大似然分析构建基因组图谱和系统发育树。线粒体基因组长度为25,928 bp，[AT]含量严重偏向（72.08%），包含3个rRNA、23个tRNA和24个蛋白质编码基因（PCG）。与其他红藻的线粒体基因组相比，细弱软骨藻的线粒体基因组缺少rpl5和rpl20。基于对完整线粒体基因组的系统发育研究，细弱软骨藻属于杉藻科，与杉藻目的其他物种是单系的。这是细弱软骨藻完整线粒体基因组的首次报道；其特征与其他红藻一致。基因组数据的研究将有利于未来的比较基因组学、系统发育学和进化研究。
