Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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

Affiliations
Free PMC article

De Novo Assembly of a Tadpole Shrimp (Triops Newberryi) Transcriptome and Preliminary Differential Gene Expression Analysis

Rebekah L Horn et al. Mol Ecol Resour. .
Free PMC article

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.

Figures

Figure 1
Figure 1
The gene ontology (GO) categories (y-axis) present in the Triops newberryi transcriptome. The number of read counts (log scale) used to infer expression level is on the x-axis. The percentage of read counts that fall into biological processes, molecular function and cellular components are on the right.

Similar articles

See all similar articles

Cited by 4 articles

Associated data

LinkOut - more resources

Feedback