De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus
- *Corresponding Author:
- Frank J Zadlock IV
Department of Biological Science, Seton Hall University
South Orange, New Jersey, USA
Tel: (973) 313-6146
E-mail: [email protected]
Received date: November 13, 2016; Accepted date: December 05, 2016; Published date: December 08, 2016
Citation: Zadlock FJ, Rana SB, Alvi ZA, Zhang Z, Murphy W, et al. (2016) De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus. Fish Aqua J 8:186. doi:10.4172/2150-3508.1000186
Copyright: © 2016 Zadlock FJ, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Background: The menhaden, Bervoortia tyrannus, is one of the most important fish within the oceanic ecosystem and a crucial species supporting major fisheries along the Atlantic and Gulf coasts. However, little is known about menhaden from a genetic aspect. The objective of this project is to apply high throughput sequencing to the testes of menhaden to provide the genetic tools required to further study their population dynamics
Result: We applied Illumina Next Seq 500 technology to two different testes and used Velvet/Oases to perform the de novo assembly that resulted in the construction of 254,462 contigs. Applying BLASTX to annotate the contigs against 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 the assembly results, primers were designed based on the assembled transcriptome, and PCR products were verified by Sanger sequencing. To enhance the functional categorization of the annotated contigs, they were further classified using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Clusters of Orthologous 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 a repository 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 studies in other fish models. Overall, this research will open new opportunities and bring new insights for researchers studying B. tyrannus.