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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.
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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.
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Pu Y, Zhou Y, Liu J, Zhang H. A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation. Gigascience 2024; 13:giad107. [PMID: 38171490 PMCID: PMC10764150 DOI: 10.1093/gigascience/giad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/05/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Chiridota heheva is a cosmopolitan holothurian well adapted to diverse deep-sea ecosystems, especially chemosynthetic environments. Besides high hydrostatic pressure and limited light, high concentrations of metal ions also represent harsh conditions in hydrothermal environments. Few holothurian species can live in such extreme conditions. Therefore, it is valuable to elucidate the adaptive genetic mechanisms of C. heheva in hydrothermal environments. FINDINGS Herein, we report a high-quality reference genome assembly of C. heheva from the Kairei vent, which is the first chromosome-level genome of Apodida. The chromosome-level genome size was 1.43 Gb, with a scaffold N50 of 53.24 Mb and BUSCO completeness score of 94.5%. Contig sequences were clustered, ordered, and assembled into 19 natural chromosomes. Comparative genome analysis found that the expanded gene families and positively selected genes of C. heheva were involved in the DNA damage repair process. The expanded gene families and the unique genes contributed to maintaining iron homeostasis in an iron-enriched environment. The positively selected gene RFC2 with 10 positively selected sites played an essential role in DNA repair under extreme environments. CONCLUSIONS This first chromosome-level genome assembly of C. heheva reveals the hydrothermal adaptation of holothurians. As the first chromosome-level genome of order Apodida, this genome will provide the resource for investigating the evolution of class Holothuroidea.
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Affiliation(s)
- Yujin Pu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zhou
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
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Li Q, Xiao W, Wu P, Zhang T, Xiang P, Wu Q, Zou L, Gui M. The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales. IMA Fungus 2023; 14:7. [PMID: 37004131 PMCID: PMC10064765 DOI: 10.1186/s43008-023-00112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Apiotrichum is a diverse anamorphic basidiomycetous yeast genus, and its mitogenome characterization has not been revealed. In this study, we assembled two Apiotrichum mitogenomes and compared them with mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. The mitogenomes of Apiotrichum gracile and A. gamsii comprised circular DNA molecules, with sizes of 34,648 bp and 38,096 bp, respectively. Intronic regions were found contributed the most to the size expansion of A. gamsii mitogenome. Comparative mitogenomic analysis revealed that 6.85-38.89% of nucleotides varied between tRNAs shared by the two Apiotrichum mitogenomes. The GC content of all core PCGs in A. gamsii was lower than that of A. gracile, with an average low value of 4.97%. The rps3 gene differentiated the most among Agaricomycotina, Pucciniomycotina and Ustilaginomycotina species, while nad4L gene was the most conserved in evolution. The Ka/Ks values for cob and rps3 genes were > 1, indicating the two genes may be subjected to positive selection in Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. Frequent intron loss/gain events and potential intron transfer events have been detected in evolution of Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. We further detected large-scale gene rearrangements between the 19 mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina, and fifteen of the 17 mitochondrial genes shared by Apiotrichum varied in gene arrangements. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods using a combined mitochondrial gene dataset revealed different taxonomic assignment of two Apiotrichum species, wherein A. gamsii had a more closely relationship with Trichosporon asahii. This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenqi Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Chengdu, 610106, Sichuan, China.
| | - Mingying Gui
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Chengdu, 610106, Sichuan, China.
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Zhao B, Gao S, Zhao M, Lv H, Song J, Wang H, Zeng Q, Liu J. Mitochondrial genomic analyses provide new insights into the "missing" atp8 and adaptive evolution of Mytilidae. BMC Genomics 2022; 23:738. [PMID: 36324074 PMCID: PMC9628169 DOI: 10.1186/s12864-022-08940-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Background Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments. In addition, some bivalve species are thought to lack the mitochondrial protein-coding gene ATP synthase F0 subunit 8. Increasing studies indicated that the absence of atp8 may be caused by annotation difficulties for atp8 gene is characterized by highly divergent, variable length. Results In this study, the complete mitochondrial genomes of three marine mussels (Xenostrobus securis, Bathymodiolus puteoserpentis, Gigantidas vrijenhoeki) were newly assembled, with the lengths of 14,972 bp, 20,482, and 17,786 bp, respectively. We annotated atp8 in the sequences that we assembled and the sequences lacking atp8. The newly annotated atp8 sequences all have one predicted transmembrane domain, a similar hydropathy profile, as well as the C-terminal region with positively charged amino acids. Furthermore, we reconstructed the phylogenetic trees and performed positive selection analysis. The results showed that the deep-sea bathymodiolines experienced more relaxed evolutionary constraints. And signatures of positive selection were detected in nad4 of Limnoperna fortunei, which may contribute to the survival and/or thriving of this species in freshwater. Conclusions Our analysis supported that atp8 may not be missing in the Mytilidae. And our results provided evidence that the mitochondrial genes may contribute to the adaptation of Mytilidae to different environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08940-8.
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Affiliation(s)
- Baojun Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Shengtao Gao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Mingyang Zhao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Hongyu Lv
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Jingyu Song
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Jing Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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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.
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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
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Sun S, Xiao N, Sha Z. Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea. PeerJ 2022; 10:e13730. [PMID: 35919401 PMCID: PMC9339218 DOI: 10.7717/peerj.13730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/23/2022] [Indexed: 01/17/2023] Open
Abstract
Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser AGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser AGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
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Affiliation(s)
- Shao’e Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ning Xiao
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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Ma B, Li Z, Lv Y, E Z, Fang J, Ren C, Luo P, Hu C. Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae). Animals (Basel) 2022; 12:ani12111437. [PMID: 35681901 PMCID: PMC9179316 DOI: 10.3390/ani12111437] [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] [Received: 04/26/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 12/04/2022] Open
Abstract
Bohadschia argu is a kind of sea cucumber with high economic value; it is the only undisputed species in the genus Bohadschia. In this study, the complete mitochondrial genome (mitogenome) of B. argus was acquired through high-throughput sequencing. The mitochondrial genome of B. argus was 15,656 bp in total length and contained a putative control region (CR) and 37 typical genes of animal mitochondrial genomes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes (tRNA). The sizes of the PCGs ranged from 168 bp to 1833 bp, and all PCGs except nad6 were encoded on the heavy chain (H). Both rrnS and rrnL were also encoded on the H chain. Twenty-two tRNA genes had positive AT skew and GC skew. All tRNAs had a typical cloverleaf secondary structure except for trnI, in which an arm of dihydrouridine was missing. B. argus shared the same gene arrangement order (the echinoderm ground pattern) as other species in Aspidochirotida. Phylogenetic analysis clearly revealed that B. argus belongs as a member of the Holothuriidae, and it is closely related to members of Actinopyga and Holothuria.
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Affiliation(s)
- Bo Ma
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuobo Li
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Lv
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou 535011, China;
| | - Zixuan E
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianxiang Fang
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- Correspondence: ; Tel.: +86-18520090836
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
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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.
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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:
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Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea). Sci Rep 2022; 12:4656. [PMID: 35304532 PMCID: PMC8933410 DOI: 10.1038/s41598-022-08644-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/25/2022] [Indexed: 12/22/2022] Open
Abstract
The deep sea (> 200 m) is considered as the largest and most remote biome, which characterized by low temperatures, low oxygen level, scarce food, constant darkness, and high hydrostatic pressure. The sea stars (class Asteroidea) are ecologically important and diverse echinoderms in all of the world’s oceans, occurring from the intertidal to the abyssal zone (to about 6000 m). To date, the phylogeny of the sea stars and the relationships of deep-sea and shallow water groups have not yet been fully resolved. Here, we recovered five mitochondrial genomes of deep-sea asteroids. The A+T content of the mtDNA in deep-sea asteroids were significantly higher than that of the shallow-water groups. The gene orders of the five new mitogenomes were identical to that of other asteroids. The phylogenetic analysis showed that the orders Valvatida, Paxillosida, Forcipulatida are paraphyletic. Velatida was the sister order of all the others and then the cladeValvatida-Spinulosida-Paxillosida-Notomyotida versus Forcipulatida-Brisingida. Deep-sea asteroids were nested in different lineages, instead of a well-supported clade. The tropical Western Pacific was suggested as the original area of asteroids, and the temperate water was initially colonized with asteroids by the migration events from the tropical and cold water. The time-calibrated phylogeny showed that Asteroidea originated during Devonian-Carboniferous boundary and the major lineages of Asteroidea originated during Permian–Triassic boundary. The divergence between the deep-sea and shallow-water asteroids coincided approximately with the Triassic-Jurassic extinction. Total 29 positively selected sites were detected in fifteen mitochondrial genes of five deep-sea lineages, implying a link between deep-sea adaption and mitochondrial molecular biology in asteroids.
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Zhang L, He J, Tan P, Gong Z, Qian S, Miao Y, Zhang HY, Tu G, Chen Q, Zhong Q, Han G, He J, Wang M. The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment. Commun Biol 2022; 5:224. [PMID: 35273345 PMCID: PMC8913654 DOI: 10.1038/s42003-022-03176-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here, we report a high-quality genome of Chiridota heheva Pawson & Vance, 2004, which thrives by extracting organic components from sediment detritus and suspended material, as a reference for nonsymbiotic animal's adaptation to deep-sea reducing environments. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion. Moreover, several hypoxia-related genes (Pyruvate Kinase M2, PKM2; Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase, LHPP; Poly(A)-specific Ribonuclease Subunit PAN2, PAN2; and Ribosomal RNA Processing 9, RRP9) were subject to positive selection in the genome of C. heheva, which contributes to their adaptation to hypoxic environments.
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Affiliation(s)
- Long Zhang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jian He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Peipei Tan
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shiyu Qian
- School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yuanyuan Miao
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Han-Yu Zhang
- Hainan Key Laboratory of Marine Georesource and Prospecting, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Guangxian Tu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qi Chen
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qiqi Zhong
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Guanzhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
| | - Muhua Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
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