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. 2025 Feb 25;15(1):6723.
doi: 10.1038/s41598-025-85642-7.

Comprehensive analysis of Metacrinus rotundus full length transcriptome

Zhong Li  1   2 , Yue Dong  1   2 , Xuebao He  3 , Chen Han  2   4 , Xiaomei Liao  2 , Jing Mo  2 , Qian Zhang  2 , Xuelei Zhang  2 , Zongling Wang  2 , Qinzeng Xu  5
Affiliations

Comprehensive analysis of Metacrinus rotundus full length transcriptome

Zhong Li et al. Sci Rep. .

Abstract

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.

Keywords: Single-molecule real-time; Stalked crinoid; Transposable elements.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests. Supplemental material: The supplemental material related to this article can be found online at:

Figures

Fig. 1
Fig. 1
Sampling photographs of Metacrinus rotundus.
Fig. 2
Fig. 2
Phylogenetic tree of Metacrinus rotundus.
Fig. 3
Fig. 3
FL transcripts annotation of Metacrinus rotundus. (A) Annotation number in Swiss-Prot, KEGG, NT, Pfam, NR, and KOG databases. (B) Homologous species annotation. The species identified by homology search against the NCBI NR databases. (C) KEGG annotation result.
Fig. 4
Fig. 4
Wayne diagram of lncRNAs predicted based on CPAT, CPC2, Uniport and NR.
Fig. 5
Fig. 5
Overview of SSRs isolated from FL transcripts of Metacrinus rotundus. (A) The number of SSRs with different repeats and motifs. (B) The dominant motifs of dinucleotide, trinucleotide and tetranucleotide SSRs.
Fig. 6
Fig. 6
Comparison of SSRs among three species of echinoderms.
Fig. 7
Fig. 7
Transcriptional factor prediction of Metacrinus rotundus full-length transcriptome.
Fig. 8
Fig. 8
Comparison of TFs among three species of echinoderms.
See this image and copyright information in PMC

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