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Mol Ecol Resour. 2017 Mar;17(2):161-171. doi: 10.1111/1755-0998.12555. Epub 2016 Jul 12.

De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis.

Author information

1
Biology Department, Trent University, 1600 West Bank Drive, Peterborough, ON, Canada, K9J 7B8.
2
National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.
3
Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Box 30003, MSC 4901, Las Cruces, NM, 88003, USA.

Abstract

Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.

KEYWORDS:

RNA sequencing; branchiopod; crustacean; gene regulation

PMID:
27292122
PMCID:
PMC5154786
DOI:
10.1111/1755-0998.12555
[Indexed for MEDLINE]
Free PMC Article

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