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Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, Jiang L, Naher H, Baki MA, Sarker A, Li C. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima. BMC Genom Data 2022; 23:22. [PMID: 35346024 PMCID: PMC8960216 DOI: 10.1186/s12863-022-01043-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/18/2022] [Indexed: 11/10/2022] Open
Abstract
Objectives American shad (Alosa sapidissima) is an important migratory fish under Alosinae and has long been valued for its economic, nutritional and cultural attributes. Overfishing and barriers across the passage made it vulnerable to sustain. To protect this valuable species, aquaculture action plans have been taken though there are no published genetic resources prevailing yet. Here, we reported the first de novo assembled and annotated transcriptome of A. sapidissima using blood and brain tissues. Data description We generated 160,481 and 129,040 non-redundant transcripts from brain and blood tissues. The entire work strategy involved RNA extraction, library preparation, sequencing, de novo assembly, filtering, annotation and validation. Both coding and non-coding transcripts were annotated against Swissprot and Pfam datasets. Nearly, 83% coding transcripts were functionally assigned. Protein clustering with clupeiform and non-clupeiform taxa revealed ~ 82% coding transcripts retained the orthologue relationship which improved confidence over annotation procedure. This study will serve as a useful resource in future for the research community to elucidate molecular mechanisms for several key traits like migration which is fascinating in clupeiform shads.
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Affiliation(s)
- Kishor Kumar Sarker
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Liang Lu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Junman Huang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Tao Zhou
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Li Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Yun Hu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Lei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Habibon Naher
- Department of Zoology, Jagannath University, Dhaka, 1100, Bangladesh
| | | | - Anirban Sarker
- Department of Zoology, Jagannath University, Dhaka, 1100, Bangladesh
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China. .,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
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Andrews SN, Dadswell MJ, Buhariwalla CF, Linnansaari T, Curry RA. Looking for Striped Bass in Atlantic Canada: The Reconciliation of Local, Scientific, and Historical Knowledge. Northeast Nat (Steuben) 2019. [DOI: 10.1656/045.026.0105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Samuel N. Andrews
- Canadian Rivers Institute, Department of Biology and Forestry and Environmental Management, Universi
| | | | - Colin F. Buhariwalla
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Pictou, NS B0K 1H0,
| | - Tommi Linnansaari
- Canadian Rivers Institute, Department of Biology and Forestry and Environmental Management, Universi
| | - R. Allen Curry
- Canadian Rivers Institute, Department of Biology and Forestry and Environmental Management, Universi
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