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Jiang C, Liu S, Yang Y, Cui W, Xu S, Rasoamananto I, Lavitra T, Zhang L, Sun L. Population genomic analysis reveals a polygenic sex determination system in Apostichopus japonicus. iScience 2024; 27:110852. [PMID: 39381746 PMCID: PMC11458978 DOI: 10.1016/j.isci.2024.110852] [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: 05/05/2024] [Revised: 08/16/2024] [Accepted: 08/28/2024] [Indexed: 10/10/2024] Open
Abstract
The sea cucumber Apostichopus japonicus, a key species in Chinese aquaculture, plays a significant evolutionary role within the Echinodermata phylum. However, the sex determination mechanism in this species remains poorly understood. Here, we conducted extensive sex surveys and sampling of eight wild populations, investigating the sex-related SNPs and insertion or deletions (indels) through bulk segregation analysis (BSA) and genome-wide association study (GWAS) analysis. Our findings suggest that A. japonicus employs a polygenic sex determination (PSD) system, with solute carrier family 8 (SLC8A) being the candidate gene for sex determination, encoding sodium-calcium exchanger (NCX1). The analysis of normalized sequencing depth reveals variations across chromosomes 6, 13, 14, 16, and 18, supporting the PSD system. We also identified 541.656 kb of male-specific sequences and screened five markers (C77185, C98086, C64977, C125, and C876) for molecular sex identification. Overall, this study provides new insights into A. japonicus sex determination, highlighting a complex multi-gene mechanism rather than a simple XX/XY system.
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Affiliation(s)
- Chunxi Jiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujia Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Wei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Irène Rasoamananto
- Institut Halieutique et des Sciences Marines (IH.SM), University of Toliara, Toliara, Madagascar
| | - Thierry Lavitra
- Institut Halieutique et des Sciences Marines (IH.SM), University of Toliara, Toliara, Madagascar
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Liu X, Sun L, Li Z, Zhao H, Yang Y. Development of Reliable Male-Specific Molecular Markers for Genetic Sex Identification in Sea Cucumber Apostichopus japonicus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10364-2. [PMID: 39215885 DOI: 10.1007/s10126-024-10364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Apostichopus japonicus is an important marine aquaculture species in China, with high nutritional and economic value. In A. japonicus, there is no obvious sexual dimorphism in external appearance, and sex differentiation primarily relies on the observation of mature gonads after dissection, which leads to difficulties in sex identification. The confusion in sex identification greatly reduces breeding efficiency in the sea cucumber industry. Therefore, developing a reliable sex-specific marker is crucial. In this study, we identified 586 male-specific sequences through whole-genome assembly and sequence alignment, but did not identify any female-specific sequences, inferring an XY-type sex determination system in sea cucumbers. We developed a set of male-specific molecular markers to establish an accurate, stable, and widely adaptable genetic sex identification technique for A. japonicus. The male-specific molecular markers were validated with 100% accuracy in sea cucumber populations from six different geographical regions in China. In conclusion, this study provides further evidence for the XY-type sex determination system in A. japonicus and establishes an effective genetic sex identification method for multi-geographic populations, which benefits future study on reproductive biology and has significant implications in sea cucumber aquaculture industry.
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Affiliation(s)
- Xinghai Liu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences & Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ziming Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Hongyuan Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences & Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
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Cheng C, Wu F, Xu Y, Ren C, Chen T, Li S, Shen P, Jiang F. Proteome analysis provides insights into sex differences in Holothuria Scabra. PLoS One 2024; 19:e0301884. [PMID: 39208133 PMCID: PMC11361572 DOI: 10.1371/journal.pone.0301884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Sex-determining mechanism is still ambiguous for sea cucumber Holothuria scabra which only manifests gonochorism in gonad. In this study, proteomic analysis was employed to delineate sex-related proteins and genes in gonads of H. scabra, subsequently validated through Quantitative real-time polymerase chain reaction (qRT-PCR). A total of 5,313 proteins were identified via proteome sequencing. Among these, 817 proteins exhibited expression in both the ovary and testis, with 445 proteins displaying up-regulation and 372 proteins showing down-regulation (ovary vs testis). Furthermore, 136 and 69 proteins were identified as ovary-specific and testis-specific Differentially Abundant Proteins (DAPs), respectively. And 9 DAP coding genes which play crucial role in ovary and testis were verified by qRT-PCR. Notably, 24 ovary-bias proteins enriched in ribosome pathway strongly indicated the crucial role of ribosome in ovary. This study serves to furnish novel evidence pertaining to sex differences in H. scabra.
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Affiliation(s)
- Chuhang Cheng
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
- College of Life Science and Technology of Guangxi University, Nanning, China
| | - FeiFei Wu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Yizhi Xu
- School of Biological Sciences, University of Edinburgh, Edinburgh, England
| | - 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
| | - Ting Chen
- 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
| | - Shella Li
- BASIS International School, Guangzhou, China
| | - Peihong Shen
- College of Life Science and Technology of Guangxi University, Nanning, China
| | - Fajun Jiang
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
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Zhong S, Liu X, Ma X, Chen X, Jiang Y, Zeng M, Zhao L, Huang L, Huang G, Zhao Y, Liu H, Qiao Y. Chromosomal-level genome assembly and annotation of the tropical sea cucumber Holothuria scabra. Sci Data 2024; 11:474. [PMID: 38724539 PMCID: PMC11082199 DOI: 10.1038/s41597-024-03340-x] [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: 12/12/2023] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
Holothuria scabra, a commercially valuable yet ecologically vulnerable tropical holothuroid, has experienced a severe decline in its wild populations, especially in China. Genomic resources are crucial for the development of effective genomic breeding projects and stock conservation strategies to restore these natural populations. Until now, a high-quality, chromosome-level reference genome for H. scabra has not been available. Here, we employed Oxford Nanopore and Hi-C sequencing technologies to assemble and annotate a high-quality, chromosome-level reference genome of H. scabra. The final genome comprised 31 scaffolds with a total length of 1.19 Gb and a scaffold N50 length of 53.52 Mb. Remarkably, 1,191.67 Mb (99.95%) of the sequences were anchored to 23 pseudo-chromosomes, with the longest one spanning 79.75 Mb. A total of 34,418 protein-coding genes were annotated in the final genome, with BUSCO analysis revealing 98.01% coverage of metazoa_odb10 genes, marking a significant improvement compared to the previous report. These chromosome-level sequences and annotations will provide an essential genomic basis for further investigation into molecular breeding and conservation management of H. scabra.
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Affiliation(s)
- Shengping Zhong
- Guangxi Key Laboratory of Marine Drugs, Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China.
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, 536000, China.
| | - Xujia Liu
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, 536000, China.
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, 530007, China.
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536000, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530007, China
| | - Yan Jiang
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, 536000, China
| | - Mengqing Zeng
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, 536000, China
| | - Longyan Zhao
- Guangxi Key Laboratory of Marine Drugs, Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Lianghua Huang
- Guangxi Key Laboratory of Marine Drugs, Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Guoqiang Huang
- Guangxi Key Laboratory of Marine Drugs, Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530007, China
| | - Hongtao Liu
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, 570100, China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536000, China.
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Perillo M, Sepe RM, Paganos P, Toscano A, Annunziata R. Sea cucumbers: an emerging system in evo-devo. EvoDevo 2024; 15:3. [PMID: 38368336 PMCID: PMC10874539 DOI: 10.1186/s13227-023-00220-0] [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: 05/29/2023] [Accepted: 12/24/2023] [Indexed: 02/19/2024] Open
Abstract
A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.
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Affiliation(s)
- Margherita Perillo
- Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA, 02543, USA.
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Rosa Maria Sepe
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Periklis Paganos
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Alfonso Toscano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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6
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Wang Y, Liu X, Zheng Y, Yang Y, Chen M. Endocrine regulation of reproductive biology in echinoderms: An evolutionary perspective from closest marine invertebrate relatives to chordates. Mol Cell Endocrinol 2024; 580:112105. [PMID: 37952726 DOI: 10.1016/j.mce.2023.112105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/27/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023]
Abstract
Echinoderms are a phylum of invertebrate deuterostomes, which contain echinoids, asteroids, holothuroids, crinoids, and ophiuroids. Echinoderms have special evolutionary position and unique characteristics, including pentamerous radial body structure, elaborate calcareous endoskeletons, and versatile water vascular system. Echinoderms exhibit extraordinarily diverse reproductive modes: asexual reproduction, sexual reproduction, sexual reversal, etc. Endocrine regulation plays important well-known roles in sex differentiation, gonadal development and maturation, gametogenesis, and reproductive behavior in vertebrates. However, the entire picture of reproductive endocrinology in echinoderms as an evolutionary model of the closest marine invertebrate relatives to chordates has not been revealed. Here, we reviewed previous and recent research progress on reproductive endocrinology in echinoderms, mainly including two sections: Sex steroids in echinoderms and neuropeptide regulation in echinoderm reproduction. This review introduces a variety of endocrine regulatory mechanisms in reproductive biology of echinoderms. It discusses the vertebrate-like sex steroids, putative steroidogenic pathway and metabolism, and reproduction-related neuropeptides. The review will provide a deeper understanding about endocrine regulatory mechanisms of gonadal development in lower deuterostomes and the application of endocrine control in economic echinoderm species in aquaculture.
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Affiliation(s)
- Yixin Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xinghai Liu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yingqiu Zheng
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yujia Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
| | - Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
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7
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Shen X, Hu J, Yáñez JM, Bastos Gomes G, Poon ZWJ, Foster D, Alarcon JF, Shao L, Guo X, Shao Y, Huerlimann R, Li C, Goulden E, Anderson K, Fan G, Domingos JA. Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers. Gigascience 2024; 13:giae034. [PMID: 38995143 PMCID: PMC11240236 DOI: 10.1093/gigascience/giae034] [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: 10/30/2023] [Revised: 04/19/2024] [Accepted: 05/22/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Cobia (Rachycentron canadum) is the only member of the Rachycentridae family and exhibits considerable sexual dimorphism in growth rate. Sex determination in teleosts has been a long-standing basic biological question, and the molecular mechanisms of sex determination/differentiation in cobia are completely unknown. RESULTS Here, we reported 2 high-quality, chromosome-level annotated male and female cobia genomes with assembly sizes of 586.51 Mb (contig/scaffold N50: 86.0 kb/24.3 Mb) and 583.88 Mb (79.9 kb/22.5 Mb), respectively. Synteny inference among perciform genomes revealed that cobia and the remora Echeneis naucrates were sister groups. Further, whole-genome resequencing of 31 males and 60 females, genome-wide association study, and sequencing depth analysis identified 3 short male-specific regions within a 10.7-kb continuous genomic region on male chromosome 18, which hinted at an undifferentiated sex chromosome system with a putative XX/XY mode of sex determination in cobia. Importantly, the only 2 genes within/between the male-specific regions, epoxide hydrolase 1 (ephx1, renamed cephx1y) and transcription factor 24 (tcf24, renamed ctcf24y), showed testis-specific/biased gene expression, whereas their counterparts cephx1x and ctf24x, located in female chromosome 18, were similarly expressed in both sexes. In addition, male-specific PCR targeting the cephx1y gene revealed that this genomic feature is conserved in cobia populations from Panama, Brazil, Australia, and Japan. CONCLUSION The first comprehensive genomic survey presented here is a valuable resource for future studies on cobia population structure and dynamics, conservation, and evolutionary history. Furthermore, it establishes evidence of putative male heterogametic regions with 2 genes playing a potential role in the sex determination of the species, and it provides further support for the rapid evolution of sex-determining mechanisms in teleost fish.
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Affiliation(s)
- Xueyan Shen
- Tropical Futures Institute, James Cook University Singapore, 387380, Singapore
| | - Jie Hu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808 Santiago, Chile
| | - Giana Bastos Gomes
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | | | | | | | - Libin Shao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xinyu Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yunchang Shao
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
- Geogia Tech Shenzhen Institute (GTSI), Tianjin University, Shen Zhen 518067, China
| | - Roger Huerlimann
- Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, 904-0495, Japan
| | - Chengze Li
- Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, 904-0495, Japan
| | - Evan Goulden
- Department of Agriculture and Fisheries, Queensland Government, Bribie Island Research Centre, Woorim, QLD 4507, Australia
| | - Kelli Anderson
- Department of Agriculture and Fisheries, Queensland Government, Bribie Island Research Centre, Woorim, QLD 4507, Australia
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jose A Domingos
- Tropical Futures Institute, James Cook University Singapore, 387380, Singapore
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville QLD 4811, Australia
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8
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Wei Y, Huang D, Ye Z, Jiang Z, Ge L, Ren Y, Wang J, Xu X, Yang J, Wang T. Comparative transcriptome analysis reveals key genes and pathways related to gonad development in the sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101144. [PMID: 37769382 DOI: 10.1016/j.cbd.2023.101144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023]
Abstract
The sea cucumber Apostichopus japonicus is an economically important marine species in China, and understanding the mechanisms underlying its gonad development is crucial for successful reproduction and breeding. In this study, we performed transcriptome comparisons and analyses of A. japonicus gonadal and non-gonadal tissues to identify genes and molecular pathways associated with gonadal development. We also supplemented the annotation of the A. japonicus genome. Collectively, results revealed a total of 941 ovary-specific genes and 2499 testis-specific genes through different expression analysis and WGCNA analysis. The most enriched pathways in ovary and testis were "DNA replication" and "purine metabolism", respectively. Additionally, we identified key candidate gene modules that control gonad development and germ cell maturation, with CDT1 and DYNC2LI1 serving as hub genes. Our findings provide important insights into the gonadal development system of A. japonicus and offer valuable references for further research on reproductive biology in this marine invertebrate species.
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Affiliation(s)
- Ying Wei
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Dexiang Huang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Zhiqing Ye
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Zhijing Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Lifei Ge
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Yucheng Ren
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Jixiu Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Xiuwen Xu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Jingwen Yang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Tianming Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China.
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9
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Sun L, Jiang C, Su F, Cui W, Yang H. Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus. Sci Data 2023; 10:454. [PMID: 37443361 PMCID: PMC10344927 DOI: 10.1038/s41597-023-02368-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. In this study, we produced a high-quality chromosome-level genome of A. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. The assembled A. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb and scaffold N50 size of 29.65 Mb. A total of 99.9% of the assembly was anchored to 23 chromosomes. In total, 19,828 genes were annotated, and 97.2% of BUSCO genes were fully represented. This high-quality genome of A. japonicus will not only aid in the development of sustainable aquaculture practices, but also lay a foundation for a deeper understanding of their genetic makeup, evolutionary history, and ecological adaptation.
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Affiliation(s)
- Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chunxi Jiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Su
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Identification of sex-specific splicing via comparative transcriptome analysis of gonads from sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101031. [PMID: 36371882 DOI: 10.1016/j.cbd.2022.101031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Alternative splicing (AS) is an essential post-transcriptional regulation mechanism for sex differentiation and gonadal development, which has rarely been reported in marine invertebrates. Sea cucumber (Apostichopus japonicus) is an economically important marine benthic echinoderm with a potential XX/XY sex determination mechanism, whose molecular mechanism in the gonadal differentiation has not been clearly understood. In this study, we analyzed available RNA-seq datasets of male and female gonads to explore if AS mechanism exerts an essential function in sex differentiation and gonadal development of A. japonicus. In our results, a total of 20,338 AS events from 7219 alternatively spliced genes, and 189 sexually differential alternative splicing (DAS) events from 156 genes were identified in gonadal transcriptome of sea cucumber. Gene Ontology analysis indicated that these DAS genes were significantly enriched in spermatogenesis-related GO terms. Maximal Clique Centrality (MCC) was then applied for protein-protein interaction (PPI) analysis to search for protein interactions and hub DAS gene. Among all DAS genes, we identified 10 DAS genes closely related to spermatogenesis and (or) sperm motility and a hub gene dnah1. Thus, this study revealed that alternative isoforms were generated from certain genes in female and male gonads through alternative splicing, which may provide direct evidence that alternative splicing mechanisms participate in female and male gonads. These results suggested a novel perspective for explaining the molecular mechanisms underlying gonadal differentiation between male and female sea cucumbers.
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Díaz-Martínez JP, Mejía-Gutiérrez LM, Islas-Villanueva V, Benítez-Villalobos F. Trioecy is maintained as a time-stable mating system in the pink sea urchin Toxopneustes roseus from the Mexican Pacific. Sci Rep 2022; 12:21408. [PMID: 36496463 PMCID: PMC9741619 DOI: 10.1038/s41598-022-26059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022] Open
Abstract
Trioecy is a sexual system that consists of the co-occurrence of females, males and hermaphrodites in a population and is common in plants; however, in animals it is uncommon and poorly understood. In echinoderms, trioecy had never been recorded until now. Frequencies of females, males, and hermaphrodites were evaluated and gametogenic development was histologically characterized in a population of Toxopneustes roseus inhabiting the Mexican Pacific. Trioecy in this population is functional and temporally stable, since the three sexes coexisted in each sampling month. The hermaphrodites presented similar gametogenic development as the females and males and participated during the spawning season, contributing to the population's reproductive process. Trioecy is considered an evolutionarily transitory state, and it is extremely difficult to explain its presence in a species. We hypothesize that continuous ocean warming represents a threat to the survival of this population of T. roseus, since its early developmental stages, which represent a population bottleneck, are more vulnerable to high temperatures than other sea urchins inhabiting the area, while its population density is significantly lower. These conditions generate a strongly stressed environment, which is the determining factor that maintains the stability of trioecy in the species in which it has been studied.
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Affiliation(s)
- Julia Patricia Díaz-Martínez
- Programa de Posgrado en Ecología Marina, División de Estudios de Posgrado, Universidad del Mar Campus Puerto Ángel, Cd. Universitaria S/N, 70902, Oaxaca, Mexico
| | - Leobarda Margarita Mejía-Gutiérrez
- Programa de Posgrado en Ecología Marina, División de Estudios de Posgrado, Universidad del Mar Campus Puerto Ángel, Cd. Universitaria S/N, 70902, Oaxaca, Mexico
| | - Valentina Islas-Villanueva
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Av. de los Insurgentes Sur 1582, 03940, Mexico, Mexico
- Instituto de Genética, Universidad del Mar Campus Puerto Ángel, Cd. Universitaria S/N, 70902, Oaxaca, Mexico
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