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Li X, Cao T, Liu H, Fu L, Wang Q. Identification and expression analysis of Sox family genes in echinoderms. BMC Genomics 2024; 25:655. [PMID: 38956468 PMCID: PMC11218330 DOI: 10.1186/s12864-024-10547-0] [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: 04/03/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous developmental processes. Echinoderms occupy a pivotal position in many research fields, such as neuroscience, sex determination and differentiation, and embryonic development. However, to date, no comprehensive study has been conducted to characterize and analyze Sox genes in echinoderms. In the present study, the evolution and expression of Sox family genes across 11 echinoderms were analyzed using bioinformatics methods. The results revealed a total of 70 Sox genes, with counts ranging from 5 to 8 across different echinoderms. Phylogenetic analysis revealed that the identified Sox genes could be categorized into seven distinct classes: the SoxB1 class, SoxB2 class, SoxC class, SoxD class, SoxE class, SoxF class and SoxH class. Notably, the SoxB1, SoxB2, and SoxF genes were ubiquitously present in all the echinoderms studied, which suggests that these genes may be conserved in echinoderms. The spatiotemporal expression patterns observed for Sox genes in the three echinoderms indicated that various Sox members perform distinct functional roles. Notably, SoxB1 is likely involved in echinoderm ovary development, while SoxH may play a crucial role in testis development in starfish and sea cucumber. In general, the present investigation provides a molecular foundation for exploring the Sox gene in echinoderms, providing a valuable resource for future phylogenetic and genomic studies.
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Affiliation(s)
- Xiaojing Li
- Yantai Vocational College, Yantai, 264003, China
| | - Tiangui Cao
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Hui Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Longhai Fu
- Yantai Vocational College, Yantai, 264003, China
| | - Quanchao Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
- Key Laboratory of Ecological Warning, Protection & Restoration for Bohai Sea, Ministry of Natural Resources, Qingdao, 266061, China.
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Zhang Q, Huang J, Fu Y, Chen J, Wang W. Genome-wide identification and expression profiles of sex-related gene families in the Pacific abalone Haliotis discus hannai. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101205. [PMID: 38364653 DOI: 10.1016/j.cbd.2024.101205] [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: 11/01/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
In recent years, members of the Dmrt family, TGF-β superfamily and Sox family have been recognized as crucial genes for sex determination/differentiation across diverse animal species. Nevertheless, knowledge regarding the abundance and potential functions of these genes in abalone remains limited. In this study, a total of 5, 10, and 7 members of the Dmrt family, the TGF-β superfamily and the Sox family, respectively, were identified in the Pacific abalone Haliotis discus hannai. Sequence characteristics, phylogenetic relationships and spatiotemporal expression profiles of these genes were investigated. Notably, HdDmrt-04 (Dmrt1/1L-like) emerged as a potential mollusc-specific gene with a preponderance for expression in the testis. Interestingly, none of the TGF-β superfamily members exhibited specific or elevated expression in the gonads, highlighting the need for further investigation into their role in abalone sex differentiation. The Sox proteins in H. discus hannai were categorized into 7 subfamilies: B1, B2, C, D, E, F, and H. Among them, HdSox-07 (SoxH-like) was observed to play a crucial role in testis development, while HdSox-03 (SoxB1-like) and HdSox-04 (SoxC-like) probably cooperate in abalone ovary development. Taken together, the results of the present study suggested that HdDmrt-04 and HdSox-07 can be used as male-specific markers for gonad differentiation in H. discus hannai and imply conservation of their functions across invertebrates and vertebrates. Our findings provide new insights into the evolution and genetic structure of the Dmrt family, the TGF-β superfamily and the Sox family in abalone and pave the way for a deeper understanding of sex differentiation in gastropods.
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Affiliation(s)
- Qian Zhang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Jianfang Huang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Yangtao Fu
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China
| | - Jianming Chen
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China.
| | - Wei Wang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China.
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Wang J, Nie H. Genome-wide identification and expression analysis of Sox gene family in the Manila clam (Ruditapes philippinarum). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101244. [PMID: 38749209 DOI: 10.1016/j.cbd.2024.101244] [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: 04/03/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/27/2024]
Abstract
Sox transcription factors are vital in numerous fundamental biological processes. In this study, nine Sox gene family members were discovered in the Ruditapes philippinarum genome, classified into the SoxB1, SoxB2, SoxC, SoxD, SoxE, and SoxF groups, marking the first genome-wide identification of this gene family in R. philippinarum. Analyses of phylogeny, exon-intron structures, and domains bolster the support for their categorization and annotation. Furthermore, transcriptomic analyses across various developmental stages revealed that RpSox4, RpSox5, RpSox9, and RpSox11 were significantly expressed in the D-larval stage. Additionally, investigations into transcriptomes of clams with different shell colors indicated that most sox genes exhibited their highest expression levels in orange clams, followed by zebra, white zebra, and white clams, and the results of transcriptomes analysis in different tissues indicated that 8 Sox genes (except RpSox17) were highly expressed in the mantle tissue. Moreover, qPCR was used to detect the expression of Sox gene in R. philippinarum at different developmental periods, different shell colors and different tissues, and the results showed consistency with those of the transcriptomes. This study's findings lay the groundwork for additional exploration into the role of the Sox gene in melanin production in R. philippinarum shells.
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Affiliation(s)
- Jiadi Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China.
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Abdullah M, Rehman MSU, Rehman MSNU, AlKahtane AA, Al-Hazani TM, Hassan FU, Rehman SU. Genome-Wide Identification, Evolutionary and Mutational Analysis of the Buffalo Sox Gene Family. Animals (Basel) 2023; 13:2246. [PMID: 37508024 PMCID: PMC10376873 DOI: 10.3390/ani13142246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes from the whole buffalo genome, using comparative genomic and evolutionary analyses. All the buffalo Sox genes were divided into nine sub-groups, and each gene had a specific number of exons and introns, which contributed to different gene structures. Molecular phylogeny revealed more sequence similarity of buffalo Sox genes with those of cattle. Furthermore, evolutionary analysis revealed that the HMG domain remained conserved in the all members of the Sox gene family. Similarly, all the genes are under strong purifying selection pressure; seven segmental duplications occurred from 9.65 to 21.41 million years ago (MYA), and four potential recombination breakpoints were also predicted. Mutational analysis revealed twenty non-synonymous mutations with potential effects on physiological functions, including embryonic development and cell differentiation in the buffalo. The present study provides insights into the genetic architecture of the Sox gene family in buffalo, highlights the significance of mutations, and provides their potential utility for marker-assisted selection for targeted genetic improvement in buffalo.
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Affiliation(s)
- Muhammad Abdullah
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muhammad Saif-Ur Rehman
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | | | - Abdullah A AlKahtane
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Tahani Mohamed Al-Hazani
- Biology Department, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj 11940, Saudi Arabia
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
- Department of Breeding and Genetics, Cholistan University of Veterinary and Animal Sciences, Bahawalpur 63100, Pakistan
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
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Liu BZ, Cong JJ, Su WY, Hao ZL, Sun ZH, Chang YQ. Identification and functional analysis of Dmrt1 gene and the SoxE gene in the sexual development of sea cucumber, Apostichopus japonicus. Front Genet 2023; 14:1097825. [PMID: 36741310 PMCID: PMC9894652 DOI: 10.3389/fgene.2023.1097825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
Members of the Doublesex and Mab-3-related transcription factor (Dmrt) gene family handle various vital functions in several biological processes, including sex determination/differentiation and gonad development. Dmrt1 and Sox9 (SoxE in invertebrates) exhibit a very conserved interaction function during testis formation in vertebrates. However, the dynamic expression pattern and functional roles of the Dmrt gene family and SoxE have not yet been identified in any echinoderm species. Herein, five members of the Dmrt gene family (Dmrt1, 2, 3a, 3b and 5) and the ancestor SoxE gene were identified from the genome of Apostichopus japonicus. Expression studies of Dmrt family genes and SoxE in different tissues of adult males and females revealed different expression patterns of each gene. Transcription of Dmrt2, Dmrt3a and Dmrt3b was higher expressed in the tube feet and coelomocytes instead of in gonadal tissues. The expression of Dmrt1 was found to be sustained throughout spermatogenesis. Knocking-down of Dmrt1 by means of RNA interference (RNAi) led to the downregulation of SoxE and upregulation of the ovarian regulator foxl2 in the testes. This indicates that Dmrt1 may be a positive regulator of SoxE and may play a role in the development of the testes in the sea cucumber. The expression level of SoxE was higher in the ovaries than in the testes, and knocking down of SoxE by RNAi reduced SoxE and Dmrt1 expression but conversely increased the expression of foxl2 in the testes. In summary, this study indicates that Dmrt1 and SoxE are indispensable for testicular differentiation, and SoxE might play a functional role during ovary differentiation in the sea cucumber.
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Min Y, Li Q, Yu H. Heme-Peroxidase 2 Modulated by POU2F1 and SOX5 is Involved in Pigmentation in Pacific Oyster (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:263-275. [PMID: 35275290 DOI: 10.1007/s10126-022-10098-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Color polymorphism is frequently observed in molluscan shellfish, while the molecular regulation of shell pigmentation is not well understood. Peroxidase is a key enzyme involved in melanogenesis. Here, we identified a heme-peroxidase 2 gene (CgHPX2), and characterized the expression patterns and transcriptional regulation of CgHPX2 in the Pacific oyster Crassostrea gigas. Tissues expression analysis showed that CgHPX2 was a mantle-specific gene and primarily expressed in the edge mantle in black shell color oyster compared with white shell oyster. In situ hybridization showed that strong signals for CgHPX2 were detected in the both inner and outer surface of the outer fold of mantle in the black shell color oyster, whereas positive signals in white shell oyster were mainly localized in the outer surface of the outer fold of mantle. In the embryos and larvae, a high expression level of CgHPX2 was detected in the trochophore stage in both black and white shell color oysters. The temporal localization of CgHPX2 was mainly detected in the shell gland and edge mantle of trochophore and calcified shell larvae, respectively. In addition, a 2227 bp of 5' flanking region sequence of CgHPX2 was cloned, which contained a presumed core promoter region and many potential transcription factor binding sites. Further luciferase assay experiment confirmed that POU domain, class 2, transcription factor 1 (POU2F1), and SRY-box transcription factor 5 (SOX5) were involved in transcriptional regulation of CgHPX2 gene through binding to its specific promoter region. After CgPOU2F1 and CgSOX5 RNA interference, the CgHPX2 gene expression was significantly decreased. These results suggested that CgPOU2F1 and CgSOX5 might be two important transcription factors that positively regulated the expression of CgHPX2 gene, improving our understanding of the transcriptional regulation of molluscan shell pigmentation.
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Affiliation(s)
- Yue Min
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education College of Fisheries, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education College of Fisheries, Ocean University of China, Qingdao, 266003, China
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Liu F, Zhou L, Zhang J, Wang Y, Wang Z, Liu X, Cai M. Genome-wide identification and transcriptome-based expression profiling of the Sox gene family in the spinyhead croaker (Collichthys lucidus). JOURNAL OF FISH BIOLOGY 2022; 100:15-24. [PMID: 34553785 DOI: 10.1111/jfb.14913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Sox genes encode transcription factors with a high-mobility group (HMG) box, playing critical roles in the initiation and maintenance of a variety of developmental processes, such as sex determination and differentiation. In the present study, we identified 26 Sox genes in the genome of spinyhead croaker Collichthys lucidus (Richardson, 1844) with homology-based analysis of the HMG box. The transcriptome-based expression profiles revealed that the expression of the Sox gene in gonads began to differ between sexes when the body length was 2.74 ± 0.24 cm. At that time, three Sox genes (Sox11b, Sox8a and Sox19) were significantly upregulated, accompanied by the downregulation of 12 Sox genes in the ovary, and six Sox genes were temporarily significantly upregulated in the testis. Afterwards, the expression profile of Sox genes changed only with a small amplitude in both the ovary and testis. For adult tissues, huge differences were observed in the expression profiles of Sox genes between ovaries and testes, as well as small differences in somatic tissues between sexes. These results provide clues to further decipher the role of Sox genes in the processes of sex determination and differentiation in spinyhead croaker and other teleosts.
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Affiliation(s)
- Fujiang Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Li Zhou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Jing Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Xiande Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Mingyi Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
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Furukawa F, Doshimo Y, Sodeyama G, Adachi K, Mori K, Mori Y, Inadama R, Koyama M, Funayama S, Oda T, Furukawa S, Moriyama S, Kimura S, Kaneko T, Okumura SI. Hemocyte migration and expression of four Sox genes during wound healing in Pacific abalone, Haliotis discus hannai. FISH & SHELLFISH IMMUNOLOGY 2021; 117:24-35. [PMID: 34274420 DOI: 10.1016/j.fsi.2021.07.011] [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: 05/17/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
In molluscs, migration of hemocytes and epithelial cells is believed to play central roles in wound healing. Here, we assessed cellular and molecular mechanisms of wound healing in Pacific abalone, a marine gastropod. Light and electron microscopy in the wounds showed early accumulation of putative hemocytes, collagen deposition by fibroblasts, and further coverage of this tissue by migration of adjacent epithelial cells. Cell labelling technique allowed us to track hemocytes, which migrated to wound surface within 24 h. The migrated cells first expressed PCNA and SoxF weakly, and then the epithelial cells expressed abundant PCNA and SoxB1, SoxB2, and SoxC. These findings imply that abalone SoxF is involved in hemocyte migration or their differentiation into fibroblasts, and suggest that the migrated epithelia acquire stem cell-like property and undergo active proliferation. This study is the first to show direct evidence of hemocyte migration to wounds and expression of Sox genes in molluscan wound healing.
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Affiliation(s)
- Fumiya Furukawa
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
| | - Yumi Doshimo
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Gin Sodeyama
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Kenta Adachi
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan; Takehara Station, Setouchi Field Science Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Takehara, Hiroshima 725-0024, Japan
| | - Kazuma Mori
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Yuichi Mori
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Ryota Inadama
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Mugen Koyama
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Shohei Funayama
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Takuji Oda
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | | | - Shunsuke Moriyama
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Satoshi Kimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Toyoji Kaneko
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Sei-Ichi Okumura
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
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Broquard C, Saowaros SA, Lepoittevin M, Degremont L, Lamy JB, Morga B, Elizur A, Martinez AS. Gonadal transcriptomes associated with sex phenotypes provide potential male and female candidate genes of sex determination or early differentiation in Crassostrea gigas, a sequential hermaphrodite mollusc. BMC Genomics 2021; 22:609. [PMID: 34372770 PMCID: PMC8353863 DOI: 10.1186/s12864-021-07838-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 06/24/2021] [Indexed: 01/08/2023] Open
Abstract
Background In the animal kingdom, mollusca is an important phylum of the Lophotrochozoa. However, few studies have investigated the molecular cascade of sex determination/early gonadal differentiation within this phylum. The oyster Crassostrea gigas is a sequential irregular hermaphrodite mollusc of economic, physiological and phylogenetic importance. Although some studies identified genes of its sex-determining/−differentiating pathway, this particular topic remains to be further deepened, in particular with regard to the expression patterns. Indeed, these patterns need to cover the entire period of sex lability and have to be associated to future sex phenotypes, usually impossible to establish in this sequential hermaphrodite. This is why we performed a gonadal RNA-Seq analysis of diploid male and female oysters that have not changed sex for 4 years, sampled during the entire time-window of sex determination/early sex differentiation (stages 0 and 3 of the gametogenetic cycle). This individual long-term monitoring gave us the opportunity to explain the molecular expression patterns in the light of the most statistically likely future sex of each oyster. Results The differential gene expression analysis of gonadal transcriptomes revealed that 9723 genes were differentially expressed between gametogenetic stages, and 141 between sexes (98 and 43 genes highly expressed in females and males, respectively). Eighty-four genes were both stage- and sex-specific, 57 of them being highly expressed at the time of sex determination/early sex differentiation. These 4 novel genes including Trophoblast glycoprotein-like, Protein PML-like, Protein singed-like and PREDICTED: paramyosin, while being supported by RT-qPCR, displayed sexually dimorphic gene expression patterns. Conclusions This gonadal transcriptome analysis, the first one associated with sex phenotypes in C. gigas, revealed 57 genes highly expressed in stage 0 or 3 of gametogenesis and which could be linked to the future sex of the individuals. While further study will be needed to suggest a role for these factors, some could certainly be original potential actors involved in sex determination/early sex differentiation, like paramyosin and could be used to predict the future sex of oysters. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07838-1.
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Affiliation(s)
- Coralie Broquard
- Normandie University, UNICAEN, CNRS, BOREA, 14000, Caen, France.,Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Esplanade de la Paix, CS 14032, 14032, Cedex 05, Caen, France.,Ifremer, RBE-SG2M-LGPMM, La Tremblade, France
| | - Suwansa-Ard Saowaros
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Mélanie Lepoittevin
- Normandie University, UNICAEN, CNRS, BOREA, 14000, Caen, France.,Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Esplanade de la Paix, CS 14032, 14032, Cedex 05, Caen, France
| | | | | | | | - Abigail Elizur
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Anne-Sophie Martinez
- Normandie University, UNICAEN, CNRS, BOREA, 14000, Caen, France. .,Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Esplanade de la Paix, CS 14032, 14032, Cedex 05, Caen, France.
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Wei H, Li W, Liu T, Li Y, Liu L, Shu Y, Zhang L, Wang S, Xing Q, Zhang L, Bao Z. Sexual Development of the Hermaphroditic Scallop Argopecten irradians Revealed by Morphological, Endocrine and Molecular Analysis. Front Cell Dev Biol 2021; 9:646754. [PMID: 33796533 PMCID: PMC8007870 DOI: 10.3389/fcell.2021.646754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022] Open
Abstract
Simultaneous or functional hermaphrodites possessing both ovary and testis at the same time are good materials for studying sexual development. However, previous research on sex determination and differentiation was mainly conducted in gonochoristic species and studies on simultaneous hermaphrodites are still limited. In this study, we conducted a combined morphological, endocrine and molecular study on the gonadal development of a hermaphroditic scallop Argopecten irradians aged 2–10 month old. Morphological analysis showed that sex differentiation occurred at 6 months of age. By examining the dynamic changes of progesterone, testosterone and estradiol, we found testosterone and estradiol were significantly different between the ovaries and testes almost throughout the whole process, suggesting the two hormones may be involved in scallop sex differentiation. In addition, we identified two critical sex-related genes FoxL2 and Dmrt1L, and investigated their spatiotemporal expression patterns. Results showed that FoxL2 and Dmrt1L were female- and male-biased, respectively, and mainly localized in the germ cells and follicular cells, indicating their feasibility as molecular markers for early identification of sex. Further analysis on the changes of FoxL2 and Dmrt1L expression in juveniles showed that significant sexual dimorphic expression of FoxL2 occurred at 2 months of age, earlier than that of Dmrt1L. Moreover, FoxL2 expression was significantly correlated with estradiol/testosterone ratio (E2/T). All these results indicated that molecular sex differentiation occurs earlier than morphological sex differentiation, and FoxL2 may be a key driver that functions through regulating sex steroid hormones in the scallop. This study will deepen our understanding of the molecular mechanism underlying sex differentiation and development in spiralians.
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Affiliation(s)
- Huilan Wei
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Wanru Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Tian Liu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Liangjie Liu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Ya Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Lijing Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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11
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Yao C, Wan H, Zhang Z, Lin J, Wang Y. Genome-wide identification and expression profile of the sox gene family in different tissues and during embryogenesis in the Pacific white shrimp (Litopenaeus vannamei). Gene 2020; 763:144956. [DOI: 10.1016/j.gene.2020.144956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/22/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
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12
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Huang X, Wu C, Gong K, Chen Q, Gu Q, Qin H, Zhao C, Yu T, Yang L, Fu W, Wang Y, Qin Q, Liu S. Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus. Front Genet 2020; 11:804. [PMID: 32849805 PMCID: PMC7399338 DOI: 10.3389/fgene.2020.00804] [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: 04/22/2020] [Accepted: 07/06/2020] [Indexed: 11/29/2022] Open
Abstract
The Sox gene family encoded transcription factors that played key roles in developmental processes in vertebrates. To further understand the evolutionary fate of the Sox gene family in teleosts, the Sox genes were comprehensively characterized in fish of different ploidy levels, including blunt snout bream (2n = 48, Megalobrama amblycephala, BSB), goldfish (2n = 100, Carassius auratus red var., 2nRCC), and autotetraploid C. auratus (4n = 200, 4nRCC). The 4nRCC, which derived from the whole genome duplication (WGD) of 2nRCC, were obtained through the distant hybridization of 2nRCC (♀) × BSB (♂). Compared with the 26 Sox genes in zebrafish (2n = 50, Danio rerio), 26, 47, and 92 putative Sox genes were identified in the BSB, 2nRCC, and 4nRCC genomes, respectively, and classified into seven subfamilies (B1, B2, C, D, E, F, and K). Comparative analyses showed that 89.36% (42/47) of Sox genes were duplicated in 2nRCC compared with those in BSB, while 97.83% (90/92) of Sox genes were duplicated in 4nRCC compared with those in 2nRCC, meaning the Sox gene family had undergone an expansion in BSB, 2nRCC, and 4nRCC, respectively, following polyploidization events. In addition, potential gene loss, genetic variations, and paternal parent SNP locus insertion occurred during the polyploidization events. Our data provided new insights into the evolution of the Sox gene family in polyploid vertebrates after several rounds of WGD events.
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Affiliation(s)
- Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Kaijun Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qian Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qianhong Gu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Wen Fu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
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13
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Zhang J, Yu P, Liu T, Qiao D, Hu Q, Su S. Identification and functional analysis of SOX transcription factors in the genome of the Chinese soft-shell turtle (Pelodiscus sinensis). Comp Biochem Physiol B Biochem Mol Biol 2020; 242:110407. [PMID: 31923463 DOI: 10.1016/j.cbpb.2020.110407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/27/2019] [Accepted: 12/10/2019] [Indexed: 11/28/2022]
Abstract
SOX transcription factors play an irreplaceable role in biological developmental processes. Sox genes have been identified in a wide variety of species; however, their identification and functional analysis in the genome of the Chinese soft-shell turtle (Pelodiscus sinensis) have not been performed. In the present study, the Chinese soft-shell turtle genome was found to contain 17 Sox genes, which were categorized into seven groups according to their phylogenetic relationships. Gene structure and protein motif analysis of the Sox genes showed that within the same phylogenetic group, their exon-intron number and motif structure of the Sox family were relatively conserved, but diverged in the comparison between different groups. Sexual dimorphism expression analysis for the Sox genes displayed that Sox8 and Sox9 were upregulated in the testis, while Sox3, Sox7, Sox11, and Sox13 were upregulated in the ovary. A correlation network analysis of SOX transcription factors with their target genes analysis showed that Sox3 correlated negatively with Sox9 and gata4. Sox11 and Sox7 correlated negatively with gata4. Sox8 and Sox9 correlated positively with gata4. Therefore, the genome-wide identification and functional analysis of the Sox gene family will be useful to further reveal the functions of Sox genes in the Chinese soft-shell turtle.
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Affiliation(s)
- Jun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
| | - Peng Yu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Tiantian Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dan Qiao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Qingtao Hu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Shiping Su
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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14
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Yang J, Hu Y, Han J, Xiao K, Liu X, Tan C, Zeng Q, Du H. Genome-wide analysis of the Chinese sturgeon sox gene family: identification, characterisation and expression profiles of different tissues. JOURNAL OF FISH BIOLOGY 2020; 96:175-184. [PMID: 31713865 DOI: 10.1111/jfb.14199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
The sox family is assumed to be responsible for a number of developmental systems. Genome sequencing technology makes it possible to scan sox genes and conduct characteristic analyses of different species. In fish, full characterisation of sox genes at the genome-wide level has been reported for pufferfish Takifugu rubripes, medaka Oryzias latipes, tilapia Oreochromis niloticus and channel catfish Ictalurus punctatus. However, no systematic investigation of the sox family in sturgeons (Acipenseridae) has been reported to date. This study conducted genome-wide identification of the sox genes in the Chinese sturgeon Acipenser sinensis and profiled their tissue distribution between male and female individuals. In total, 19 sox genes were identified, including soxb1, b2, c, d, e, f and h, in the Chinese sturgeon. Genomic structure analysis indicated relatively conserved exon-intron structures in each sox group and phylogenetic analysis supported the previous classification of the sox family. Most of the sox genes showed a tissue-specific expression pattern, indicating the possible involvement of Chinese sturgeon sox genes at different developmental processes such as cardiac and gonadal development. This study provides a comprehensive resource of Chinese sturgeon sox genes and enables a better understanding of the evolution and function of the sox family.
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Affiliation(s)
- Jing Yang
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Yacheng Hu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Jilu Han
- China Three Gorges Corporation, Yichang, China
| | - Kan Xiao
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Xueqing Liu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Chun Tan
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Qingkai Zeng
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Hejun Du
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
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15
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Zhu C, Zhang L, Ding H, Pan Z. Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea. PeerJ 2019; 7:e7770. [PMID: 31660260 PMCID: PMC6814067 DOI: 10.7717/peerj.7770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022] Open
Abstract
The Asian clam, Corbicula fluminea, is a commonly consumed small freshwater bivalve in East Asia. However, available genetic information of this clam is still limited. In this study, the transcriptome of female C. fluminea was sequenced using the Illumina HiSeq 2500 platform. A total of 89,563 unigenes were assembled with an average length of 859 bp, and 36.7% of them were successfully annotated. Six members of Sox gene family namely SoxB1, SoxB2, SoxC, SoxD, SoxE and SoxF were identified. Based on these genes, the divergence time of C. fluminea was estimated to be around 476 million years ago. Furthermore, a total of 3,117 microsatellites were detected with a distribution density of 1:12,960 bp. Fifty of these microsatellites were randomly selected for validation, and 45 of them were successfully amplified with 31 polymorphic ones. The data obtained in this study will provide useful information for future genetic and genomic studies in C. fluminea.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai'an, Jiangsu, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Lei Zhang
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China.,Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai'an City, Huai'an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an, China
| | - Huaiyu Ding
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai'an, Jiangsu, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Zhengjun Pan
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai'an, Jiangsu, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China
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16
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Wan H, Han K, Jiang Y, Zou P, Zhang Z, Wang Y. Genome-Wide Identification and Expression Profile of the Sox Gene Family During Embryo Development in Large Yellow Croaker, Larimichthys crocea. DNA Cell Biol 2019; 38:1100-1111. [DOI: 10.1089/dna.2018.4586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Haifu Wan
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Kunhuang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Yonghua Jiang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Pengfei Zou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Ziping Zhang
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
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17
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Phenotypic Stability of Sex and Expression of Sex Identification Markers in the Adult Yesso Scallop Mizuhopecten yessoensis throughout the Reproductive Cycle. Animals (Basel) 2019; 9:ani9050277. [PMID: 31137722 PMCID: PMC6562885 DOI: 10.3390/ani9050277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 02/03/2023] Open
Abstract
Simple Summary Bivalve sex is thought to fluctuate depending on environmental conditions. So far, there has been no investigation on the phenotypic stability of sex in the commercially important Yesso scallop Mizuhopecten yessoensis. The present study revealed that the sex of the Yesso scallop is stable after initial sex differentiation and that this species maintains a sex-stable maturation system throughout its life. In addition, gonad differentiation for each sex was precisely characterized by using molecular markers throughout the maturational cycle. Abstract The objective of the present study was to analyze the phenotypic stability of sex after sex differentiation in the Yesso scallop, which is a gonochoristic species that has been described as protandrous. So far, no study has investigated in detail the sexual fate of the scallop after completion of sex differentiation, although bivalve species often show annual sex change. In the present study, we performed a tracking experiment to analyze the phenotypic stability of sex in scallops between one and two years of age. We also conducted molecular marker analyses to describe sex differentiation and gonad development. The results of the tracking experiment revealed that all scallops maintained their initial sex phenotype, as identified in the last reproductive period. Using molecular analyses, we characterized my-dmrt2 and my-foxl2 as sex identification markers for the testis and ovary, respectively. We conclude by proposing that the Yesso scallop is a sex-stable bivalve after its initial sex differentiation and that it maintains a sex-stable maturation system throughout its life. The sex-specific molecular markers identified in this study are useful tools to assess the reproductive status of the Yesso scallop.
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18
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Li Y, Zhang L, Li R, Zhang M, Li Y, Wang H, Wang S, Bao Z. Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis. BMC Genomics 2019; 20:288. [PMID: 30975074 PMCID: PMC6460854 DOI: 10.1186/s12864-019-5661-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/31/2019] [Indexed: 12/15/2022] Open
Abstract
Background Reverse transcription quantitative PCR (RT-qPCR) is widely used for gene expression analysis in various organisms. Its accuracy largely relies on the stability of reference genes, making reference gene selection a vital step in RT-qPCR experiments. However, previous studies in mollusks only focused on the reference genes widely used in vertebrates. Results In this study, we conducted the transcriptome-wide identification of reference genes in the bivalve mollusk Mizuhopecten yessoensis based on 60 transcriptomes covering early development, adult tissues and gonadal development. A total of 964, 1210 and 2097 candidate reference genes were identified, respectively, resulting in a core set of 568 genes. Functional enrichment analysis showed that these genes are significantly overrepresented in Gene Ontology (GO) terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to ribosomes, energy production, etc. Six genes (RS23, EF1A, NDUS4, SELR1, EIF3F, and OLA1) were selected from the candidate genes for RT-qPCR validation, together with 6 commonly used reference genes (ACT, CYTC, HEL, EF1B, GAPDH and RPL16). Stability analyses using geNorm, NormFinder and the comparative delta-Ct method revealed that the new candidate reference genes are more stable than the traditionally used genes, and ACT and CYTC are not recommended under either of the three circumstances. There was a significant correlation between the Ct of RT-qPCR and the log2(TPM) of RNA-Seq data (Ct = − 0.94 log2(TPM) + 29.67, R2 = 0.73), making it easy to estimate the Ct values from transcriptome data prior to RT-qPCR experiments. Conclusion Our study represents the first transcriptome-wide identification of reference genes for early development, adult tissues, and gonadal development in the Yesso scallop and will benefit gene expression studies in other bivalve mollusks. Electronic supplementary material The online version of this article (10.1186/s12864-019-5661-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Ruojiao Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Meiwei Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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19
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Li Y, Zhang L, Li Y, Li W, Guo Z, Li R, Hu X, Bao Z, Wang S. Dynamics of DNA Methylation and DNMT Expression During Gametogenesis and Early Development of Scallop Patinopecten yessoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:196-205. [PMID: 30680591 DOI: 10.1007/s10126-018-09871-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
DNA methylation reprograms during gametogenesis and embryo development, which is essential for germ cell specification and genomic imprinting in mammals. Corresponding process remains poorly investigated in molluscs. Here, we examined global DNA methylation level in the gonads of scallop Patinopecten yessoensis during gametogenesis and in embryos/larvae at different stages. DNA methylation level fluctuates during gametogenesis and early development, peaking at proliferative stage of ovary, growing stage of testis, and in blastulae. To understand the mechanisms underlying these changes, we conducted genome-wide characterization of DNMT family and investigated their expression profiles based on transcriptomes and in situ hybridization. Three genes were identified, namely PyDNMT1, PyDNMT2, and PyDNMT3. Expression of PyDnmt3 agrees with DNA methylation level during oogenesis and early development, suggesting PyDNMT3 may participate in de novo DNA methylation that occurs mainly at proliferative stage of ovary and testis, and in blastulae and gastrulae. PyDnmt1 expression is positively correlated with DNA methylation level during spermatogenesis, and is higher at maturation stage of ovary and in 2-8 cell embryos than other stages, implying possible involvement of PyDNMT1 in DNA methylation maintenance during meiosis and embryonic development. This study will facilitate better understanding of the developmental epigenetic reprogramming in bivalve molluscs.
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Affiliation(s)
- Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Wanru Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Zhenyi Guo
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Ruojiao Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China.
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20
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Ujiié Y, Kimoto K, Ishimura T. Advanced approach to analyzing calcareous protists for present and past pelagic ecology: Comprehensive analysis of 3D-morphology, stable isotopes, and genes of planktic foraminifers. PLoS One 2019; 14:e0213282. [PMID: 30845272 PMCID: PMC6405064 DOI: 10.1371/journal.pone.0213282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/18/2019] [Indexed: 11/18/2022] Open
Abstract
Marine protists play an important role in oceanic ecosystems and biogeochemical cycles. However, the difficulties in culturing pelagic protists indicate that their ecology and behavior remain poorly understood; phylogeographic studies based on single-cell genetic analyses have often shown that they are highly divergent at the biological species level, with variable geographic distributions. This indicates that their ecology could be complex. On the other hand, the biomineral (calcareous) shells of planktic foraminifers are widely used in geochemical analyses to estimate marine paleoenvironmental characteristics (i.e., temperature), because the shell chemical composition reflects ambient seawater conditions. Among the pelagic protists, planktic foraminifers are ideal study candidates to develop a combined approach of genetic, morphological, and geochemical methods, thus reflecting environmental and ecological characteristics. The present study precisely tested whether the DNA extraction process physically and chemically affects the shells of the planktic foraminifer Globigerinoides ruber. We used a nondestructive method for analyzing physical changes (micro-focus X-ray computed tomography (MXCT) scanning) to compare specimens at the pre- and post-DNA extraction stages. Our results demonstrate that DNA extraction has no significant effect on shell density and thickness. We measured stable carbon and oxygen isotopes on the shell of each individual in a negative control or one of two DNA-extracted groups and detected no significant differences in isotopic values among the three groups. Moreover, we evaluated isotopic variations at the biological species level with regard to their ecological characteristics such as depth habitat, life stages, and symbionts. Thus, our examination of the physiochemical effects on biomineral shells through DNA extraction shows that morphological and isotopic analyses of foraminifers can be combined with genetic analysis. These analytical methods are applicable to other shell-forming protists and microorganisms. In this study, we developed a powerful analytical tool for use in ecological and environmental studies of modern and past oceans.
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Affiliation(s)
- Yurika Ujiié
- Center for Advanced Marine Core Research, Kochi University, Nankoku, Japan
- * E-mail:
| | - Katsunori Kimoto
- Research and Development Center for Global Change, JAMSTEC, Yokosuka, Japan
| | - Toyoho Ishimura
- National Institute of Technology, Ibaraki College, Hitachinaka, Japan
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Tapia-Morales S, López-Landavery EA, Giffard-Mena I, Ramírez-Álvarez N, Gómez-Reyes RJE, Díaz F, Galindo-Sánchez CE. Transcriptomic response of the Crassostrea virginica gonad after exposure to a water-accommodation fraction of hydrocarbons and the potential implications in reproduction. Mar Genomics 2018; 43:9-18. [PMID: 30409725 DOI: 10.1016/j.margen.2018.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/06/2018] [Accepted: 10/20/2018] [Indexed: 11/26/2022]
Abstract
The Crassostrea virginica oyster has biological and economic importance in the Gulf of Mexico, an area with a high extraction and production of hydrocarbons. Exposure to hydrocarbons affects the reproductive processes in bivalves. In C. virginica, the effect of hydrocarbons on the gonad of the undifferentiated organism has not been evaluated to determine the possible damage during the maturation process. To evaluate this effect, RNA-seq data was generated from C. virginica gonads exposed to a 200 μg/L of hydrocarbons at different exposure times (7, 14 and 21 days) and a control treatment (without hydrocarbons). The analysis of the gonad transcriptome showed the negative effect of hydrocarbons on maturation, with a sub-expression of 22 genes involved in different stages of this process. Additionally, genes in the immune system were down-regulated, which may indicate that exposure to hydrocarbons causes immunosuppression in bivalves. A group of oxidative stress genes was also reduced. These data contribute to a better understanding of the effect of hydrocarbons on the reproductive process in bivalves and, at the same time, allow us to identify possible biomarkers associated with hydrocarbon contamination in the gonad of C. virginica.
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Affiliation(s)
- S Tapia-Morales
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico; Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Laboratorio de Patología Experimental Acuícola, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - E A López-Landavery
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - I Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Laboratorio de Patología Experimental Acuícola, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - N Ramírez-Álvarez
- Universidad Autónoma de Baja California, Instituto de Investigaciones Oceanológicas, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - R J E Gómez-Reyes
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - F Díaz
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - C E Galindo-Sánchez
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico.
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Li R, Zhang L, Li W, Zhang Y, Li Y, Zhang M, Zhao L, Hu X, Wang S, Bao Z. FOXL2 and DMRT1L Are Yin and Yang Genes for Determining Timing of Sex Differentiation in the Bivalve Mollusk Patinopecten yessoensis. Front Physiol 2018; 9:1166. [PMID: 30246781 PMCID: PMC6113668 DOI: 10.3389/fphys.2018.01166] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/03/2018] [Indexed: 01/24/2023] Open
Abstract
Sex determination and differentiation have long been a research hotspot in metazoans. However, little is known about when and how sex differentiation occurs in most mollusks. In this study, we conducted a combined morphological and molecular study on sex differentiation in the Yesso scallop Patinopecten yessoensis. Histological examination on gonads from 5- to 13-month-old juveniles revealed that the morphological sex differentiation occurred at 10 months of age. To determine the onset of molecular sex differentiation, molecular markers were screened for early identification of sex. The gonadal expression profiles of eight candidate genes for sex determination or differentiation showed that only two genes displayed sexually dimorphic expression, with FOXL2 being abundant in ovaries and DMRT1L in testes. In situ hybridization revealed that both of them were detected in germ cells and follicle cells. We therefore developed LOG10(DMRT1L/FOXL2) for scallop sex identification and confirmed its feasibility in differentiated individuals. By tracing its changes in 5- to 13-month-old juveniles, molecular sex differentiation time was determined: some scallops differentiate early in September when they are 7 months old, and some do late in December when they are 10 months old. Two kinds of coexpression patterns were found between FOXL2 and DMRT1L: expected antagonism after differentiation and unexpected coordination before differentiation. Our results revealed that scallop sex differentiation co-occurs with the formation of follicles, and molecular sex differentiation is established prior to morphological sex differentiation. Our study will assist in a better understanding of the molecular mechanism underlying bivalve sex differentiation.
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Affiliation(s)
- Ruojiao Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wanru Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Yang Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Meiwei Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Liang Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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