Structural Features and Phylogenetic Implications of Crinoid Echinoderms Based on Thirteen Novel Mitochondrial Genomes

• Published in: Journal of marine science and engineering Vol. 12; no. 3; p. 361
• Main Authors: Xu, Qinzeng, Lu, Min, Sun, Yuyao, Li, Zhong, Li, Yixuan, Dong, Yue, Hu, Xuying, Zhang, Qian, Liu, Bing, He, Xuebao
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.02.2024
• Subjects: Amino acids; Bayesian analysis; Benthic communities; Benthos; Biodiversity; Codon; Codon bias; crinoids; echinoderm; Echinodermata; Evolution; Evolutionary biology; Gene order; Genes; Genomes; Genomics; Marine ecosystems; Marine invertebrates; Mitochondria; mitochondrial genome; mitochondrial structure character; Morphology; Nucleotides; Phylogenetics; Phylogeny; Positive selection; Probability theory; Protein biosynthesis; Protein synthesis; Proteins; Software; Statistical inference; Stop codon; Taxonomy; Topology; United Kingdom
• ISSN: 2077-1312; 2077-1312
• DOI: 10.3390/jmse12030361

Crinoids, as integral echinoderms, play a crucial ecological role in benthic communities, serving as significant indicators reflecting the health of marine ecosystems. However, the phylogenetic relationships within crinoids are unclear. More molecular data can help to facilitate biodiversity assessment and elucidate evolutionary relationships by the phylogenetic tree. In this study, 13 complete mitochondrial genomes of the Crinoidea class were sequenced, annotated, and compared with other same class species available on NCBI. The results reveal five different gene order patterns among these mitochondrial genomes, indicating that crinoids have undergone gene rearrangements during evolution. The complete mitochondrial genome length of crinoids ranges from 15,772 bp to 16,850 bp. High A + T content, ranging from 64.5% to 74.2%, was observed. Additionally, our analysis of protein-coding genes highlights a preference for A + T nucleotides, along with specific start and stop codon usage, offering insights into codon bias and its implications for protein synthesis and function. The phylogenetic topology shows that the stalkless crinoid and stalked crinoid are distinct, and the phylogenetic trees generated based on maximum likelihood and Bayesian inference are almost identical at the family and order topology levels. The phylogenetic relationships of each family were fully clarified in four orders. A total of eleven positive selection sites were detected within six genes: cytb, nad2, nad3, nad4, nad4L and nad5. This study reveals the phylogenetic relationships of crinoid species, the mitochondrial gene differences, and the selective pressure on the evolution of stalked crinoids. This study significantly enhanced the crinoid mitochondrial genome database and contributed to a better understanding of the phylogenetic relationships among crinoid echinoderms.