De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus

摘要

Background: The menhaden, Bervoortia tyrannus, is one of the most important fish within the oceanicecosystem and a crucial species supporting major fisheries along the Atlantic and Gulf coasts. However, little isknown about menhaden from a genetic aspect. The objective of this project is to apply high throughput sequencingto the testes of menhaden to provide the genetic tools required to further study their population dynamicsResult: We applied Illumina Next Seq 500 technology to two different testes and used Velvet/Oases to performthe de novo assembly that resulted in the construction of 254,462 contigs. Applying BLASTX to annotate the contigsagainst the non-redundant protein database resulted in 46.89% matches. To validate the accuracy of the assembly,the reads were mapped back to transcripts (RMBT) with a percentage of 87.83%. To experimentally verify theassembly results, primers were designed based on the assembled transcriptome, and PCR products were verifiedby Sanger sequencing. To enhance the functional categorization of the annotated contigs, they were furtherclassified using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Clusters ofOrthologous Groups (COG) databases.Conclusion: This research is the first report of an annotated overview of the testes transcriptomes in B. tyrannus,resulting in the most comprehensive genetic resource available for menhaden to date. This work can provide arepository for future gene expression analysis, functional studies, and reproductive investigations in B. tyrannus.This will enhance the capabilities of population monitoring and can be used as a benchmark in comparative studiesin other fish models. Overall, this research will open new opportunities and bring new insights for researchersstudying B. tyrannus.