Highly rearranged gene orders and rapid evolutionary rates in the mitochondrial genomes of Apodida (Echinodermata: Holothuroidea)

doi:10.3389/fmars.2023.1219437

	Highly rearranged gene orders and rapid evolutionary rates in the mitochondrial genomes of Apodida (Echinodermata: Holothuroidea)
	Sun, Shao'e 1,2,3,4; Ni, Gang 5; Wang, Wansheng 5; Sha, Zhongli1,2,3,4 ; Xiao, Ning 1,2,3,4; Xiaoqi, Zeng 5
	2023-08-30
发表期刊	FRONTIERS IN MARINE SCIENCE
卷号	10 页码:15
通讯作者	Sha, Zhongli([email protected])
摘要	Mitochondrial genome (mitogenome) is a frequently-used tool for phylogenetic and evolutionary studies among metazoans, however, it was still poorly represented in some invertebrate groups, including holothurians. Apodida is one of the most ancient orders of Holothuroidea, with unique characteristics in lacking tube feet and the respiratory tree. Here, we sequenced six mitogenomes from the holothurian order Apodida (Synaptidae and Chiridotidae) and compared them with other available holothurian mitogenomes. The apodan mitogenomes present positive GC skews and negative AT skews, a pattern diametrically opposite to that found in the mitogenomes of other holothurians. The amino acid genetic distances of the 13 protein-coding genes (PCGs) were the highest between Apodida and other holothurians. The mitochondrial gene orders within Apodida were extensively rearranged at the species level, and also were unique from the arrangement patterns of other holothurians. Phylogenetic relationships based on two different criteria: (i) nucleotides sequences with all codon positions (PCG123) and (ii) Neutral Transitions Excluded model (NTE) confirmed the monophyly and basal position of the order Apodida with a long branch. The NTE phylogeny generated a low variation of branch length, but it did not ameliorate the long branch length of Apodida. The divergence time estimation suggested that the Apodida originated in the Middle Carboniferous, implying that they survived the extinction event that occurred in the boundary of the Permian and Triassic. The NTE dataset revealed younger age than that generated by PCG123 dataset. Apodida is accompanied by a faster evolutionary rate than other holothurians (0.0069 vs 0.0043 subs/s/my). The absence of tube feet and the respiratory tree may play an important role in the dramatic evolutionary changes of apodan mitogenomes.
关键词	mitochondrial genome Holothuroidea Apodida gene order phylogenetic relationships evolutionary rate
DOI	10.3389/fmars.2023.1219437
收录类别	SCI
语种	英语
资助项目	Ministry of Science and Technology of China[2021YFF0502801]; Young Talent Program of Ocean University of China[862201013143]; National Key R&D Program of China[2022YFC3102403]
WOS研究方向	Environmental Sciences & Ecology ; Marine & Freshwater Biology
WOS类目	Environmental Sciences ; Marine & Freshwater Biology
WOS记录号	WOS:001064594000001
出版者	FRONTIERS MEDIA SA
WOS关键词	NUCLEOTIDE SUBSTITUTION ; PHYLOGENETIC INFERENCE ; MULTIPLE REVERSALS ; MAXIMUM-LIKELIHOOD ; CONSEQUENCES ; MITOGENOMICS ; PATTERNS ; METAZOA ; TRENDS ; BIAS
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/181772
专题	海洋生物分类与系统演化实验室
通讯作者	Sha, Zhongli
作者单位	1.Chinese Acad Sci, Inst Oceanol, Dept Marine Organism Taxon & Phylogeny, Qingdao, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao, Peoples R China 4.Univ Chinese Acad Sci, Coll Biol Sci, Beijing, Peoples R China 5.Ocean Univ China, Minist Educ, Key Lab Mariculture, Qingdao, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Sun, Shao'e,Ni, Gang,Wang, Wansheng,et al. Highly rearranged gene orders and rapid evolutionary rates in the mitochondrial genomes of Apodida (Echinodermata: Holothuroidea)[J]. FRONTIERS IN MARINE SCIENCE,2023,10:15.
APA	Sun, Shao'e,Ni, Gang,Wang, Wansheng,Sha, Zhongli,Xiao, Ning,&Xiaoqi, Zeng.(2023).Highly rearranged gene orders and rapid evolutionary rates in the mitochondrial genomes of Apodida (Echinodermata: Holothuroidea).FRONTIERS IN MARINE SCIENCE,10,15.
MLA	Sun, Shao'e,et al."Highly rearranged gene orders and rapid evolutionary rates in the mitochondrial genomes of Apodida (Echinodermata: Holothuroidea)".FRONTIERS IN MARINE SCIENCE 10(2023):15.