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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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Sertić Kovačević M, Baričević A, Kružić P, Maurić Maljković M, Hamer B. Barcoding ( COI) Sea Cucumber Holothuria mammata Distribution Analysis: Adriatic Rare or Common Species? Genes (Basel) 2023; 14:2059. [PMID: 38003002 PMCID: PMC10671717 DOI: 10.3390/genes14112059] [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: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The overexploitation of the western Pacific Ocean has expanded the sea cucumber fishery into new regions to supply the Asian market. In 2013, sea cucumbers were removed from the Croatian marine protected species list, and commercial fishery took place for a short period (2017-2018) in the Eastern Adriatic Sea. However, holothuroid species are difficult to distinguish. Holothuria mammata is a species that has rarely been reported in this region and strongly resembles the common species Holothuria tubulosa. This is the first study to assess the genetic diversity of sea cucumbers in the Adriatic Sea using genetic barcoding of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). Specimens for barcoding were collected from the northern and central Adriatic, along with a specimen that had been previously identified as H. sp. cf. mammata based on its morphological characteristics. While genetic analyses showed identified this specimen as H. tubulosa, 30% of the collected specimens were genetically identified as H. mammata. These results call into question the historically accepted sea cucumber assemblage in the Adriatic Sea, which regarded H. mammata as a rare species and generally disregarded its presence in large census studies. Such species distribution data are extremely important in developing and monitoring a sustainable fishery.
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Affiliation(s)
- Maya Sertić Kovačević
- Laboratory for Marine Biology, Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia; (M.S.K.); (P.K.)
- Laboratory for Marine Nanotechnology and Biotechnology, Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia
| | - Ana Baričević
- Laboratory for Evolutionary Ecology, Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia;
| | - Petar Kružić
- Laboratory for Marine Biology, Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia; (M.S.K.); (P.K.)
| | - Maja Maurić Maljković
- Laboratory for Marine Nanotechnology and Biotechnology, Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia
- Department of Animal Breeding and Livestock Production, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Bojan Hamer
- Laboratory for Marine Nanotechnology and Biotechnology, Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia
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Badrulhisham NS, Solehin SN, Han MG, Jahari PNS, Mohd Salleh F, Mohamed Rehan A, Kamarudin KR. The mitogenome data of Holothuria ( Mertensiothuria) leucospilota (Brandt,1835) from Malaysia. Data Brief 2023; 47:108968. [PMID: 36860405 PMCID: PMC9969244 DOI: 10.1016/j.dib.2023.108968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
White threads fish Holothuria (Mertensiothuria) leucospilota (Brandt, 1835) or locally known as bat puntil is a neritic marine organism, and it is widely distributed in Indo Pacific. They serve many important roles in ecosystem services and were discovered to contain many bioactive compounds that are useful for medicinal value. However, despite its abundance in Malaysian seawater, there is still a lack of records on H. leucospilota mitochondrial genome (mitogenome) from Malaysia. The mitogenome of H. leucospilota originating from Sedili Kechil, Kota Tinggi, Johor, Malaysia, is presented here. Whole genome sequencing was successfully sequenced using Illumina NovaSEQ6000 sequencing system and the mitochondrial-derived contigs were assembled using de novo approach. The size of the mitogenome is 15,982 bp which consists of 13 protein-coding genes (PCGs), 21 transfer RNAs, and 2 ribosomal RNAs. The overall composition of nucleotide bases was estimated to be 25.8% for T, 25.9% for C, 31.8% for A and 16.5% for G (with A + T content of 57.6%). Maximum likelihood phylogenetic tree analysis revealed that the mitochondrial Protein-Coding Genes (PCGs) sequence data from our H. leucospilota is closely related to H. leucospilota from accession number MK940237 and H. leucospilota from accession number MN594790, followed by H. leucospilota from accession number MN276190, forming sister group with H. hilla (MN163001), known as Tiger tail sea cucumber. The mitogenome of H. leucospilota will be valuable for genetic research, mitogenome reference and future conservation management of sea cucumber in Malaysia. The mitogenome data of H. leucospilota from Sedili Kechil, Kota Tinggi, Johor, Malaysia is available in the GenBank database repository with accession number ON584426.
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Affiliation(s)
- Nur Sabrina Badrulhisham
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia (UTHM), Pagoh Campus, Pagoh Education Hub, Muar 84600, Johor Darul Ta'zim, Malaysia
| | - Siti Najihah Solehin
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia (UTHM), Pagoh Campus, Pagoh Education Hub, Muar 84600, Johor Darul Ta'zim, Malaysia
| | - Ming Gan Han
- Department of Biological Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Malaysia
| | - Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Aisyah Mohamed Rehan
- Department of Chemical Engineering Technology, Faculty of Engineering Technology (FTK), Universiti Tun Hussein Onn Malaysia (UTHM), Pagoh Campus, 84600 Muar, Johor Darul Ta'zim, Malaysia
| | - Kamarul Rahim Kamarudin
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia (UTHM), Pagoh Campus, Pagoh Education Hub, Muar 84600, Johor Darul Ta'zim, Malaysia
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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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Zhong S, Huang L, Liu Y, Huang G. The first complete mitochondrial genome of Actinopyga from Actinopyga echinites (Aspidochirotida: Holothuriidae). Mitochondrial DNA B Resour 2020; 5:854-855. [PMID: 33366782 PMCID: PMC7748656 DOI: 10.1080/23802359.2019.1710598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The deep-water redfish, Actinopyga echinites, is an ecologically and economically important holothuroid in China due to its valuable nutrition and pharmacological compounds. However, the taxonomy and phylogeny of the Actinopyga have been debated and misidentifications have been reported recently. Moreover, there remain considerable doubts about cryptic species complex within Actinopyga. In this study, we report the first complete mitochondrial genome of Actinopyga from A. echinites. The mitogenome has 15,619 base pairs (62.9% A + T content) and made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs), and a putative control region. This study was the first available complete mitogenome of Actinopyga and will provide useful genetic information for future phylogenetic and taxonomic classification of Holothuriidae.
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Affiliation(s)
- Shengping Zhong
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China.,Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Lianghua Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
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