1
|
He Y, Zhao H, Wang Y, Qu C, Gao X, Miao J. A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis. BMC Genomics 2024; 25:689. [PMID: 39003448 PMCID: PMC11245801 DOI: 10.1186/s12864-024-10607-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis. RESULTS The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers. CONCLUSIONS These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.
Collapse
Affiliation(s)
- Yingying He
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China
| | - Hancheng Zhao
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yongxin Wang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, China
| | - Changfeng Qu
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China
| | | | - Jinlai Miao
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China.
| |
Collapse
|
2
|
Ogawa A, Hiruta SF, Aung MM, Fujita T. Complete mitochondrial genome of a sea cucumber, Euapta godeffroyi (Echinodermata, Holothuroidea, Apodida, Synaptidae). Mitochondrial DNA B Resour 2022; 7:1457-1459. [PMID: 35965644 PMCID: PMC9367668 DOI: 10.1080/23802359.2022.2107462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We determined the complete mitochondrial genome sequence of a holothurian Euapta godeffroyi belonging to the order Apodida. The complete mitogenome of E. godeffroyi was 16,410 bp in length and consisted of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The orders of PCGs and rRNAs did not match those of any recorded holothurian mitogenomes. The maximum likelihood (ML) phylogenetic tree placed E. godeffroyi as the sister group to chiridotid species and supported the monophyly of the order Apodida.
Collapse
Affiliation(s)
- Akito Ogawa
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-Cutting-Edge Science and Technology Avant-grade Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Japan
| | - Shimpei F. Hiruta
- The Mt. Fuji Institute for Nature and Biology, Showa University, Fujiyoshida, Japan
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Japan
| | - Mu Mu Aung
- Forest Research Institute, Forest Department, Ministry of Natural Resources and Environmental Conservation, Yezin, Myanmar
| | - Toshihiko Fujita
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Japan
| |
Collapse
|
3
|
Li Z, Ma B, Li X, Lv Y, Jiang X, Ren C, Hu C, Luo P. The Complete Mitochondrial Genome of Stichopus naso (Aspidochirotida: Stichopodidae: Stichopus) and Its Phylogenetic Position. Genes (Basel) 2022; 13:genes13050825. [PMID: 35627210 PMCID: PMC9141342 DOI: 10.3390/genes13050825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/21/2023] Open
Abstract
The mitochondrial genome is widely used to study the molecular evolution of and perform phylogenetic analyses on animals. In this study, the complete mitochondrial genome (mitogenome) of Stichopus naso was sequenced. The mitogenome was 16,239 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The genome composition showed positive AT-skew (0.023) and negative GC-skew (−0.158). The order of the mitochondrial genes was consistent with those from the Stichopus and Isostichopus species, whereas it was different from those of other species of Aspidochirotida. The phylogenetic analysis, based on the nucleotide sequences of 13 PCGs through the methods of Bayesian inference (BI) and maximum likelihood (ML), indicated that S. naso has close relationships with S. horrens and S. monotuberculatus, and belongs to a member of Stichopodidae. Our study provides a reference mitogenome for further molecular evolution studies and phylogenetic research on sea cucumbers.
Collapse
Affiliation(s)
- Zhuobo Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Lv
- Marin College, Beibu Gulf University, Qinzhou 535011, China;
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- Correspondence:
| |
Collapse
|
4
|
Sun S, Sha Z, Xiao N. The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100839. [PMID: 33933835 DOI: 10.1016/j.cbd.2021.100839] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.
Collapse
Affiliation(s)
- Shao'e Sun
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Xiao
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| |
Collapse
|
5
|
Yang F, Zhou C, Tran NT, Sun Z, Wu J, Ge H, Lu Z, Zhong C, Zhu Z, Yang Q, Lin Q. Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers. FEBS Open Bio 2020; 10:1587-1600. [PMID: 32573974 PMCID: PMC7396427 DOI: 10.1002/2211-5463.12914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/31/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Sea cucumber species are abundant (>1400 species) and widely distributed globally. mtDNA sequencing is frequently used to identify the phylogenetic and evolutionary relationships among species. However, there are no reports on the mitochondrial genome of Phyllophorus liuwutiensis. Here, we performed mtDNA sequencing of P. liuwutiensis to examine its phylogenetic relationships with other echinoderms. Its mitochondrial genome (15 969 bp) contains 37 coding genes, including 13 protein‐coding genes, 22 tRNA genes and 2 rRNA genes. Except for one protein‐coding gene (nad6) and five tRNA genes encoded on the negative strand, all other genes were encoded on the positive strand. The mitochondrial bases of P. liuwutiensis were composed of 29.55% T, 22.16% C, 35.64% A and 12.64% G. The putative control region was 703 bp in length. Seven overlapping regions (1–10 bp) were found. The noncoding region between the genes ranged from 1 to 130 bp in length. One putative control region has been found in the P. liuwutiensis mitogenome. All of the tRNA genes were predicted to fold into a cloverleaf structure. In addition, we compared the gene arrangements of six echinoderms, revealing that the gene order of P. liuwutiensis was a new arrangement.
Collapse
Affiliation(s)
- Fuyuan Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,College of Fisheries and Life Science, Shanghai Ocean University, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Ngoc Tuan Tran
- Institute of Marine Sciences, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, China
| | - Zaiqiao Sun
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Hui Ge
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Chenhui Zhong
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhihuang Zhu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qiuhua Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,College of Fisheries and Life Science, Shanghai Ocean University, China
| |
Collapse
|
6
|
Yang Q, Lin Q, Wu J, Yang F, Ge H, Qiu D, Li Z, Lu Z, Li S, Zhou C. The complete mitochondrial genome sequence of Stichopus variegatus (Echinodermata: Holothuroidea) and phylogenetic studies of Echinodermata. Mitochondrial DNA B Resour 2019; 4:3244-3245. [PMID: 33365938 PMCID: PMC7707333 DOI: 10.1080/23802359.2019.1669502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 11/16/2022] Open
Abstract
At present, there exist some confusing issues on the species classification and phylogeny in Echinodermata. In this study, we first determined and described the complete mitochondrial genome of Stichopus variegatus. The complete mitogenome sequence had a circular mapping molecular with the total length of 16,315 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. To further validate the newly determined sequences, phylogenetic trees involving all the Holothuroidea and other Echinodermata species available in GenBank Database were constructed. These results would be used for the species identification and further phylogenetic studies of Echinodermata.
Collapse
Affiliation(s)
- Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, Guangdong, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Fuyuan Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Hui Ge
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Denggao Qiu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Zhongqin Li
- Fisheries College, Engineering Research Center on Eel Modern Industrial Technology of Ministry of Education, Jimei University, Xiamen, Fujian, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, Guangdong, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| |
Collapse
|
7
|
Cheng C, Yu Z, Ren C, Jiang X, Zhang X, Wu X, Huang W, Hu C. The complete mitochondrial genome of a tropical sea cucumber, Holothuria leucospilota. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3118-3119. [PMID: 33365879 PMCID: PMC7707314 DOI: 10.1080/23802359.2019.1668309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mitochondrial genome of Holothuria leucospilota was 15,906 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. There were four initiation codons (ATG, ATT, ATC, and ATA) for the PCGs, and the termination codon of most PCGs was TAA, except for nad4 (TAG) and nad6 (TAG). Only one PCG (nad6) and five tRNA genes (tRNASer(UCN), tRNAGln, tRNAAla, RNAVal, and tRNAAsp) were encoded on the light chain; the other genes were encoded on the heavy chain. H. leucospilota was most closely related to Holothuria scabra in a phylogenetic tree.
Collapse
Affiliation(s)
- Chuhang Cheng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zonghe Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou China.,Institution of South China Sea Ecology and Environmental Engineering (ISEE), Chinese Academy of Sciences, Guangzhou, China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou China
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou China
| | - Xin Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofen Wu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou China.,Institution of South China Sea Ecology and Environmental Engineering (ISEE), Chinese Academy of Sciences, Guangzhou, China
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou China.,Institution of South China Sea Ecology and Environmental Engineering (ISEE), Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
8
|
Yang Q, Lin Q, Wu J, Tran NT, Huang R, Sun Z, Zhu Z, Lu Z, Li S, Zhou C. Complete mitochondrial genome of Holothuria leucospilata (Holothuroidea, Holothuriidae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2751-2752. [PMID: 33365713 PMCID: PMC7706471 DOI: 10.1080/23802359.2019.1644226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete Holothuria leucospilata mitochondrial genome was determined and analyzed in this work. It had a circular mapping molecular with a total length of 15,904 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region. Phylogenetic analysis showed that H. leucospilata clustered together with Holothuria scabra and Holothuria forskali. The complete mitochondrial genome provided in this work would be used for elucidation of Holothuroidea conservation genetics and evolutionary relationships.
Collapse
Affiliation(s)
- Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Ngoc Tuan Tran
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Ruifang Huang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zaiqiao Sun
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhihuang Zhu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| |
Collapse
|
9
|
Wang G, Li X, Wang J, Zhang J, Liu W, Lu C, Guo Y, Dong B. The complete mitochondrial genome and phylogenetic analysis of Acaudina molpdioides. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1572476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Guilin Wang
- Laboratory for Morphogenesis and Evolution, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiang Li
- Laboratory for Morphogenesis and Evolution, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jinhui Wang
- East China Sea branch, State Oceanic Administration, Shanghai, China
| | - Jin Zhang
- Laboratory for Morphogenesis and Evolution, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wei Liu
- Ningde Marine Environment Monitoring Center, State Oceanic Administration, Ningde, China
- Key Laboratory of Integrated Monitoring and Applied Technology for Marine Harmful Algal Blooms, State Oceanic Administration, Shanghai, China
| | - Chao Lu
- Ningde Marine Environment Monitoring Center, State Oceanic Administration, Ningde, China
- Key Laboratory of Integrated Monitoring and Applied Technology for Marine Harmful Algal Blooms, State Oceanic Administration, Shanghai, China
| | - Yuchen Guo
- Ningde Marine Environment Monitoring Center, State Oceanic Administration, Ningde, China
- Key Laboratory of Integrated Monitoring and Applied Technology for Marine Harmful Algal Blooms, State Oceanic Administration, Shanghai, China
| | - Bo Dong
- Laboratory for Morphogenesis and Evolution, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
10
|
Mu W, Liu J, Zhang H. Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber. PLoS One 2018; 13:e0208051. [PMID: 30500836 PMCID: PMC6267960 DOI: 10.1371/journal.pone.0208051] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/09/2018] [Indexed: 01/01/2023] Open
Abstract
Complete mitochondrial genomes play important roles in studying genome evolution, phylogenetic relationships, and species identification. Sea cucumbers (Holothuroidea) are ecologically important and diverse members, living from the shallow waters to the hadal trench. In this study, we present the mitochondrial genome sequence of the sea cucumber Benthodytes marianensis collected from the Mariana Trench. To our knowledge, this is the first reported mitochondrial genome from the genus Benthodytes. This complete mitochondrial genome is 17567 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Most of these genes are coded on the positive strand except for one protein-coding gene (nad6) and five tRNA genes which are coded on the negative strand. Two putative control regions (CRs) have been found in the B. marianensis mitogenome. We compared the order of genes from the 10 available holothurian mitogenomes and found a novel gene arrangement in B. marianensis. Phylogenetic analysis revealed that B. marianensis clustered with Peniagone sp. YYH-2013, forming the deep-sea Elasipodida clade. Positive selection analysis showed that eleven residues (24 S, 45 S, 185 S, 201 G, 211 F and 313 N in nad2; 108 S, 114 S, 322 C, 400 T and 427 S in nad4) were positively selected sites with high posterior probabilities. We predict that nad2 and nad4 may be the important candidate genes for the further investigation of the adaptation of B. marianensis to the deep-sea environment.
Collapse
Affiliation(s)
- Wendan Mu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- * E-mail:
| |
Collapse
|
11
|
Mu W, Liu J, Zhang H. The first complete mitochondrial genome of the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida: Brisingidae) allows insights into the deep-sea adaptive evolution of Brisingida. Ecol Evol 2018; 8:10673-10686. [PMID: 30519397 PMCID: PMC6262923 DOI: 10.1002/ece3.4427] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/27/2018] [Accepted: 07/10/2018] [Indexed: 01/13/2023] Open
Abstract
Starfish (phylum Echinodermata) are ecologically important and diverse members of marine ecosystems in all of the world's oceans, from the shallow water to the hadal zone. The deep sea is recognized as an extremely harsh environment on earth. In this study, we present the mitochondrial genome sequence of Mariana Trench starfish Freyastera benthophila, and this study is the first to explore in detail the mitochondrial genome of a deep-sea member of the order Brisingida. Similar to other starfish, it contained 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Twenty-two of these genes are encoded on the positive strand, while the other 15 are encoded on the negative strand. The gene arrangement was identical to those of sequenced starfish. Phylogenetic analysis showed the deep-sea Brisingida as a sister taxon to the traditional members of the Asteriidae. Positive selection analysis indicated that five residues (8 N and 16 I in atp8, 47 D and 196 V in nad2, 599 N in nad5) were positively selected sites with high posterior probabilities. Compared these features with shallow sea starfish, we predict that variation specifically in atp8, nad2, and nad5 may play an important role in F. benthophila's adaptation to deep-sea environment.
Collapse
Affiliation(s)
- Wendan Mu
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jun Liu
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Haibin Zhang
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| |
Collapse
|
12
|
Zhang Z, Bao X, Dong Y, Gao X, Gao L, Li S, Liu W, Hou H, Shi J, Pu H. Complete mitochondrial genome of Parastichopus californicus (Aspidochirotida: Stichopodidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3569-70. [PMID: 26260176 DOI: 10.3109/19401736.2015.1074222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we first determined and described the complete mitogenome sequence of Parastichopus californicus, which was 16 727 bp in length. The mitochondrial genome had the canonical mitochondrial gene content, including 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The overall base composition of the heavy-strand was 31.5% A, 18 % G, 20.6% C and 29.9% T, with a high A + T content of 61.4%. ML phylogenetic tree indicated that P. californicus and P. nigripunctatus were clustered in one branch belonging to the genus Parastichopus. This conclusion was identical to the former result by the methods of morphological taxonomy.
Collapse
Affiliation(s)
- Zhenyu Zhang
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Xiangbo Bao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Ying Dong
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Xianggang Gao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Lei Gao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Shilei Li
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Weidong Liu
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Hongman Hou
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Jingyun Shi
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Hongshaung Pu
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| |
Collapse
|
13
|
Xia J, Ren C, Yu Z, Wu X, Qian J, Hu C. Complete mitochondrial genome of the sandfish Holothuria scabra (Holothuroidea, Holothuriidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4174-4175. [PMID: 25629485 DOI: 10.3109/19401736.2014.1003899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) sequence of Holothuria scabra, an economically and ecologically important tropical sea cucumber, was first sequenced and annotated. The mitochondrial DNA is 15,779 bp in length and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a 456 bp putative control region, of which gene order is identical to the echinoderm ground pattern. Comparative analyses between H. scabra and other holothurians revealed three new findings: (1) the mitogenome of H. scabra is highly compact having five regions with overlapping genes and least intergenic nucleotides among the sequenced holothurians, only accounting for 3.58% of its mitogenome; (2) the genus Holothuria mitogenomes show a pattern of high interspecies divergence at the 13 PCGs, and the genetic p-distance reaches 25.68% between H. scabra and H. forskali; (3) the incomplete stop codon T of cox2 shared with H. forskali may be a common feature in the genus Holothuria.
Collapse
Affiliation(s)
- Jianjun Xia
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Chunhua Ren
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Zonghe Yu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Xiangyun Wu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Jing Qian
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Chaoqun Hu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| |
Collapse
|
14
|
Zheng C, Nie L, Wang J, Zhou H, Hou H, Wang H, Liu J. Recombination and evolution of duplicate control regions in the mitochondrial genome of the Asian big-headed turtle, Platysternon megacephalum. PLoS One 2013; 8:e82854. [PMID: 24367563 PMCID: PMC3867392 DOI: 10.1371/journal.pone.0082854] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 10/29/2013] [Indexed: 01/24/2023] Open
Abstract
Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3' end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.
Collapse
Affiliation(s)
- Chenfei Zheng
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Liuwang Nie
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Jue Wang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Huaxing Zhou
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Huazhen Hou
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Hao Wang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Juanjuan Liu
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| |
Collapse
|
15
|
CHANG ZY. Science China Life Sciences in 2011: a Retrospect. PROG BIOCHEM BIOPHYS 2013. [DOI: 10.3724/sp.j.1206.2012.00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|