Li Zhong, Dong Yue, He Xuebao, Han Chen, Liao Xiaomei, Mo Jing, Zhang Qian, Zhang Xuelei, Wang Zongling, Xu Qinzeng
College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, MNR, Qingdao, 266061, China.
Sci Rep. 2025 Feb 25;15(1):6723. doi: 10.1038/s41598-025-85642-7.
Modern stalked crinoids, an important group of echinoderms, represent the ancestral mode of crinoids, and studying their evolution is key to understanding the evolution of echinoderms. In this study, we selected Metacrinus rotundus, a species of modern stalked crinoids, for investigation. We generated M. rotundus transcripts using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 160,849 full-length (FL) transcripts were captured by Iso-Seq, with a mean length of 2,470 bp. Of these FL transcripts, 110,859 were well-annotated based on public database. A portion of transcripts remained unannotated, representing potential novel genes for M. rotundus. Additionally, we identified 71,740 long-noncoding RNA (LncRNAs), 57,548 simple sequence repeats (SSRs), and 3,486 hypothetical transcript factors (TFs). By comparing Holothuroid and Echinoid, M. rotundus have a higher proportion of zf-CCCH and TF_Otx within TFs, as well as trinucleotide SSRs within SSRs. Notably, transposable elements (TEs) make up a large proportion of the full-length transcriptome of M. rotundus, with RNA transposons being the largest class of annotated TEs. Our study enhances understanding of the characteristics of M. rotundus transcriptome and provides a valuable genetic resource for further studies on adaptive evolution in this species, as well as in other crinoids.
现代有柄海百合是棘皮动物的一个重要类群，代表了海百合的原始模式，研究它们的进化是理解棘皮动物进化的关键。在本研究中，我们选择了现代有柄海百合的一种——罗氏海百合进行调查。我们使用太平洋生物科学公司的单分子实时（SMRT）长读长测序技术生成了罗氏海百合的转录本。通过Iso-Seq共捕获了160,849个全长（FL）转录本，平均长度为2470 bp。在这些FL转录本中，基于公共数据库有110,859个得到了良好注释。一部分转录本仍未注释，代表了罗氏海百合潜在的新基因。此外，我们鉴定出71,740个长链非编码RNA（LncRNAs）、57,548个简单序列重复（SSRs）和3,486个假定的转录因子（TFs）。通过与海参和海胆进行比较，罗氏海百合在转录因子中zf-CCCH和TF_Otx的比例较高，在简单序列重复中三核苷酸SSR的比例也较高。值得注意的是，转座元件（TEs）在罗氏海百合全长转录组中占很大比例，其中RNA转座子是注释的TEs中最大的一类。我们的研究增进了对罗氏海百合转录组特征的理解，并为该物种以及其他海百合的适应性进化进一步研究提供了宝贵的遗传资源。
