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First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima.
Sarker, Kishor Kumar; Lu, Liang; Huang, Junman; Zhou, Tao; Wang, Li; Hu, Yun; Jiang, Lei; Naher, Habibon; Baki, Mohammad Abdul; Sarker, Anirban; Li, Chenhong.
  • Sarker KK; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.
  • Lu L; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
  • Huang J; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.
  • Zhou T; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
  • Wang L; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.
  • Hu Y; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
  • Jiang L; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.
  • Naher H; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
  • Baki MA; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.
  • Sarker A; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
  • Li C; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.
BMC Genom Data ; 23(1): 22, 2022 03 28.
Article in English | MEDLINE | ID: covidwho-1793989
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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Full text: Available Collection: International databases Database: MEDLINE Main subject: Conservation of Natural Resources / Transcriptome Type of study: Prognostic study Limits: Animals Language: English Journal: BMC Genom Data Year: 2022 Document Type: Article Affiliation country: S12863-022-01043-z

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Conservation of Natural Resources / Transcriptome Type of study: Prognostic study Limits: Animals Language: English Journal: BMC Genom Data Year: 2022 Document Type: Article Affiliation country: S12863-022-01043-z