Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea
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 unige...
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| Format: | Article |
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PeerJ Inc.
2019-10-01
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| Online Access: | https://peerj.com/articles/7770.pdf |
| _version_ | 1827605523140182016 |
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| author | Chuankun Zhu Lei Zhang Huaiyu Ding Zhengjun Pan |
| author_facet | Chuankun Zhu Lei Zhang Huaiyu Ding Zhengjun Pan |
| author_sort | Chuankun Zhu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T06:22:56Z |
| format | Article |
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| language | English |
| last_indexed | 2024-03-09T06:22:56Z |
| publishDate | 2019-10-01 |
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| spelling | doaj.art-8ab35b73ac41401db5ecf537da67e2962023-12-03T11:34:16ZengPeerJ Inc.PeerJ2167-83592019-10-017e777010.7717/peerj.7770Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula flumineaChuankun Zhu0Lei Zhang1Huaiyu Ding2Zhengjun Pan3Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, ChinaJiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, Jiangsu, ChinaThe 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.https://peerj.com/articles/7770.pdfCorbicula flumineaTranscriptomeSox gene familyMicrosatellite |
| spellingShingle | Chuankun Zhu Lei Zhang Huaiyu Ding Zhengjun Pan Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea PeerJ Corbicula fluminea Transcriptome Sox gene family Microsatellite |
| title | Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea |
| title_full | Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea |
| title_fullStr | Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea |
| title_full_unstemmed | Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea |
| title_short | Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea |
| title_sort | transcriptome wide identification and characterization of the sox gene family and microsatellites for corbicula fluminea |
| topic | Corbicula fluminea Transcriptome Sox gene family Microsatellite |
| url | https://peerj.com/articles/7770.pdf |
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