Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain
The mud crab Scylla paramamosain is a species with significant sexual dimorphism in growth rate and body size, of which the females are of higher economic and nutritional values than the males. Accordingly, there is an urgent need to explore the molecular mechanism underlying sex determination and g...
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-03-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2021.658091/full |
| _version_ | 1818929009751228416 |
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| author | Wenxiao Cui Wenxiao Cui Qin Yang Qin Yang Yin Zhang Yin Zhang Ardavan Farhadi Ardavan Farhadi Huan Fang Huan Fang Huaiping Zheng Huaiping Zheng Shengkang Li Shengkang Li Yueling Zhang Yueling Zhang Mhd Ikhwanuddin Mhd Ikhwanuddin Hongyu Ma Hongyu Ma |
| author_facet | Wenxiao Cui Wenxiao Cui Qin Yang Qin Yang Yin Zhang Yin Zhang Ardavan Farhadi Ardavan Farhadi Huan Fang Huan Fang Huaiping Zheng Huaiping Zheng Shengkang Li Shengkang Li Yueling Zhang Yueling Zhang Mhd Ikhwanuddin Mhd Ikhwanuddin Hongyu Ma Hongyu Ma |
| author_sort | Wenxiao Cui |
| collection | DOAJ |
| description | The mud crab Scylla paramamosain is a species with significant sexual dimorphism in growth rate and body size, of which the females are of higher economic and nutritional values than the males. Accordingly, there is an urgent need to explore the molecular mechanism underlying sex determination and gonadal differentiation. The single-molecule long-read technology combining with RNA sequencing was employed to construct a full-length transcriptome for gonads of S. paramamosain. In total, 1,562,819 FLNC reads were obtained from 1,813,758 reads of inserts (ROIs). Among them, the 10,739 fusion isoforms corresponded to 23,634 reads and were involved in 5,369 genes in the reference annotation. According to the criteria for new transcripts, a total of 213,809 isoforms were recognized as novel transcripts and then matched against Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), NR, Swissprot, and KOG databases. We also identified 22,313 SSRs, 169,559 lncRNAs, and 25,451 SNPs. Additionally, 349,854 alternative splicing (AS) events from 8,430 gene models were detected, and 5,129 polyadenylation sites were profiled from 3,090 genes. GO and KEGG annotation indicated that AS and APA probably play important roles in the gonadal development and maturation. Besides, the DEGs associated with gonadal development and maturation were identified and analyzed based on the RNA-Seq data. |
| first_indexed | 2024-12-20T03:37:59Z |
| format | Article |
| id | doaj.art-44eb18eae87544d6837b3ddfeaf1df27 |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-12-20T03:37:59Z |
| publishDate | 2021-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-44eb18eae87544d6837b3ddfeaf1df272022-12-21T19:54:49ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452021-03-01810.3389/fmars.2021.658091658091Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosainWenxiao Cui0Wenxiao Cui1Qin Yang2Qin Yang3Yin Zhang4Yin Zhang5Ardavan Farhadi6Ardavan Farhadi7Huan Fang8Huan Fang9Huaiping Zheng10Huaiping Zheng11Shengkang Li12Shengkang Li13Yueling Zhang14Yueling Zhang15Mhd Ikhwanuddin16Mhd Ikhwanuddin17Hongyu Ma18Hongyu Ma19Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaInstitute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, MalaysiaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, ChinaSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, ChinaThe mud crab Scylla paramamosain is a species with significant sexual dimorphism in growth rate and body size, of which the females are of higher economic and nutritional values than the males. Accordingly, there is an urgent need to explore the molecular mechanism underlying sex determination and gonadal differentiation. The single-molecule long-read technology combining with RNA sequencing was employed to construct a full-length transcriptome for gonads of S. paramamosain. In total, 1,562,819 FLNC reads were obtained from 1,813,758 reads of inserts (ROIs). Among them, the 10,739 fusion isoforms corresponded to 23,634 reads and were involved in 5,369 genes in the reference annotation. According to the criteria for new transcripts, a total of 213,809 isoforms were recognized as novel transcripts and then matched against Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), NR, Swissprot, and KOG databases. We also identified 22,313 SSRs, 169,559 lncRNAs, and 25,451 SNPs. Additionally, 349,854 alternative splicing (AS) events from 8,430 gene models were detected, and 5,129 polyadenylation sites were profiled from 3,090 genes. GO and KEGG annotation indicated that AS and APA probably play important roles in the gonadal development and maturation. Besides, the DEGs associated with gonadal development and maturation were identified and analyzed based on the RNA-Seq data.https://www.frontiersin.org/articles/10.3389/fmars.2021.658091/fullScylla paramamosainfull-length transcriptomegonadalternative splicingalternative polyadenylationdifferentially expressed genes |
| spellingShingle | Wenxiao Cui Wenxiao Cui Qin Yang Qin Yang Yin Zhang Yin Zhang Ardavan Farhadi Ardavan Farhadi Huan Fang Huan Fang Huaiping Zheng Huaiping Zheng Shengkang Li Shengkang Li Yueling Zhang Yueling Zhang Mhd Ikhwanuddin Mhd Ikhwanuddin Hongyu Ma Hongyu Ma Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain Frontiers in Marine Science Scylla paramamosain full-length transcriptome gonad alternative splicing alternative polyadenylation differentially expressed genes |
| title | Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain |
| title_full | Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain |
| title_fullStr | Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain |
| title_full_unstemmed | Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain |
| title_short | Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain |
| title_sort | integrative transcriptome sequencing reveals the molecular difference of maturation process of ovary and testis in mud crab scylla paramamosain |
| topic | Scylla paramamosain full-length transcriptome gonad alternative splicing alternative polyadenylation differentially expressed genes |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2021.658091/full |
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