Full-length transcriptome assembly of black amur bream (Megalobrama terminalis) as a reference resource.
Alternative splicing
Black amur bream
Isoform sequencing
Transcriptomic analysis
Journal
Molecular biology reports
ISSN: 1573-4978
Titre abrégé: Mol Biol Rep
Pays: Netherlands
ID NLM: 0403234
Informations de publication
Date de publication:
29 Oct 2024
29 Oct 2024
Historique:
received:
17
09
2024
accepted:
23
10
2024
medline:
29
10
2024
pubmed:
29
10
2024
entrez:
29
10
2024
Statut:
epublish
Résumé
The genus Megalobrama holds significant economic value in China, with M. terminalis (Black Amur bream) ranking second in production within this group. However, lacking comprehensive genomic and transcriptomic data has impeded research progress. This study aims to fill this gap through an extensive transcriptomic analysis of M. terminalis. We utilized PacBio Isoform Sequencing to generate 558,998 subreads, totaling 45.52 Gb, which yielded 22,141 transcripts after rigorous filtering and clustering. Complementary Illumina short-read sequencing corrected 967,114 errors across these transcripts. Our analysis identified 12,426 non-redundant isoforms, with 11,872 annotated in various databases. Functional annotation indicated 11,841 isoforms matched entries in the NCBI non-redundant protein sequences database. Gene Ontology analysis categorized 10,593 isoforms, revealing strong associations with cellular processes and binding functions. Additionally, 8203 isoforms were mapped to pathways in the Kyoto Encyclopedia of Genes and Genomes, highlighting significant involvement in immune system processes and complement cascades. We notably identified key immune molecules such as alpha-2-macroglobulin and complement component 3, each with multiple isoforms, underscoring their potential roles in the immune response. Our analysis also uncovered 853 alternative splicing events, predominantly involving retained introns, along with 672 transcription factors and 426 long non-coding RNAs. The high-quality reference transcriptome generated in this study provides a valuable resource for comparative genomic studies within the Megalobrama genus, supporting future research to enhance aquaculture stocks.
Sections du résumé
BACKGROUND
BACKGROUND
The genus Megalobrama holds significant economic value in China, with M. terminalis (Black Amur bream) ranking second in production within this group. However, lacking comprehensive genomic and transcriptomic data has impeded research progress. This study aims to fill this gap through an extensive transcriptomic analysis of M. terminalis.
METHODS AND RESULTS
RESULTS
We utilized PacBio Isoform Sequencing to generate 558,998 subreads, totaling 45.52 Gb, which yielded 22,141 transcripts after rigorous filtering and clustering. Complementary Illumina short-read sequencing corrected 967,114 errors across these transcripts. Our analysis identified 12,426 non-redundant isoforms, with 11,872 annotated in various databases. Functional annotation indicated 11,841 isoforms matched entries in the NCBI non-redundant protein sequences database. Gene Ontology analysis categorized 10,593 isoforms, revealing strong associations with cellular processes and binding functions. Additionally, 8203 isoforms were mapped to pathways in the Kyoto Encyclopedia of Genes and Genomes, highlighting significant involvement in immune system processes and complement cascades. We notably identified key immune molecules such as alpha-2-macroglobulin and complement component 3, each with multiple isoforms, underscoring their potential roles in the immune response. Our analysis also uncovered 853 alternative splicing events, predominantly involving retained introns, along with 672 transcription factors and 426 long non-coding RNAs.
CONCLUSIONS
CONCLUSIONS
The high-quality reference transcriptome generated in this study provides a valuable resource for comparative genomic studies within the Megalobrama genus, supporting future research to enhance aquaculture stocks.
Identifiants
pubmed: 39470845
doi: 10.1007/s11033-024-10056-z
pii: 10.1007/s11033-024-10056-z
doi:
Substances chimiques
Fish Proteins
0
Protein Isoforms
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1101Subventions
Organisme : Science & Technology Innovation Program of Hangzhou Academy of Agricultural Sciences
ID : 2022HNCT-01
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature B.V.
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