1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Zhong S, Zhao L, Huang G, Liu Y, Huang L. The first complete mitochondrial genome of Phyrella fragilis (Mitsukuri & Ohshima in Ohshima, 1912) (Dendrochirotida: Phyllophoridae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2979-2980. [PMID: 34553066 PMCID: PMC8451628 DOI: 10.1080/23802359.2021.1976687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Echinoderms (Echinodermata) are morphologically diverse and ecologically important groups of marine invertebrate, many of which are key components of local benthic ecosystem. However, due to morphological plasticity and limited molecular phylogenetic studies, the taxonomic histories in echinoderms have not been completely resolved. The phylogenetic relationships of Phyllophoridae genera and species remain controversial and many species are incorrectly assigned within genus Phyrella. In this study, we report the first complete mitochondrial genome of Phyrella from Phyrella fragilis. The mitogenome has 15,910 base pairs (64.32% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study will provide useful genetic data for future phylogenetic and taxonomic classification of Phyllophoridae.
Collapse
Affiliation(s)
- Shengping Zhong
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China.,Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd, Beihai, China
| | - Longyan Zhao
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang 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
| | - Lianghua Huang
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
| |
Collapse
|
4
|
Zhong S, Qiao Y, Zhao L, Huang G, Liu Y, Huang L. Characterization and phylogenetic analysis of the complete mitochondrial genome of Actinopyga lecanora (Jaeger, 1833) (Holothuriida: Holothuriidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2801-2802. [PMID: 34514132 PMCID: PMC8425705 DOI: 10.1080/23802359.2021.1970641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The white-bottomed sea cucumber, Actinopyga lecanora, is a valuable inshore fisheries resource which is famous for its high nutrition and pharmacological compounds. However, due to morphological plasticity and limited molecular phylogenetic studies, the taxonomic histories in the genus Actinopyga have not been completely resolved yet. Moreover, there remains a complex of cryptic species within Actinopyga, many of which are incorrectly assigned within the family Holothuriidae. In this study, we report the complete mitochondrial genome of A. lecanora. The mitogenome has 15,568 base pairs (63.40% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study offers useful mitogenome data for future phylogenetic and taxonomic classification of Holothuriidae.
Collapse
Affiliation(s)
- Shengping Zhong
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China.,Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd, Beihai, China
| | - Ying Qiao
- Ministry of Natural Resources, Fourth institute of Oceanography, Beihai, China
| | - Longyan Zhao
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang 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
| | - Lianghua Huang
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
| |
Collapse
|
5
|
Yang Q, Lu Z, Yang F, Wu J, Zhang Z, Lin Q, Zhou C. The complete mitochondrial genome of the sea cucumber: Colochirus robustus (Cucumariidae: Dendrochirotida) and phylogenetic analysis. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1735968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Fuyuan Yang
- 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
| | - Zhe Zhang
- 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
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| |
Collapse
|