Comprehensive Transcriptome Study to Develop Molecular Resources of the CopepodCalanus sinicusfor Their Potential Ecological Applications

Abstract

Calanus sinicus Brodsky (Copepoda, Crustacea) is a dominant zooplanktonic species widely distributed in the margin seas of the Northwest Pacific Ocean. In this study, we utilized an RNA-Seq-based approach to develop molecular resources for C. sinicus. Adult samples were sequenced using the Illumina HiSeq 2000 platform. The sequencing data generated 69,751 contigs from 58.9 million filtered reads. The assembled contigs had an average length of 928.8 bp. Gene annotation allowed the identification of 43,417 unigene hits against the NCBI database. Gene ontology (GO) and KEGG pathway mapping analysis revealed various functional genes related to diverse biological functions and processes. Transcripts potentially involved in stress response and lipid metabolism were identified among these genes. Furthermore, 4,871 microsatellites and 110,137 single nucleotide polymorphisms (SNPs) were identified in the C. sinicus transcriptome sequences. SNP validation by the melting temperature (T m)-shift method suggested that 16 primer pairs amplified target products and showed biallelic polymorphism among 30 individuals. The present work demonstrates the power of Illumina-based RNA-Seq for the rapid development of molecular resources in nonmodel species. The validated SNP set from our study is currently being utilized in an ongoing ecological analysis to support a future study of C. sinicus population genetics.

Glutathione S-Transferase (GST) Gene Diversity in the Crustacean Calanus finmarchicus – Contributors to Cellular Detoxification

“…PRJNA234316 ). Yang et al [ 58 ] reported 31 GST proteins in the de novo transcriptome of the calanoid Calanus sinicus , but to date, these data are not publicly accessible. None of these studies included annotations by GST class or subclass, or protein structural analyses.…”

“…However, in general, it appears that the number of GST genes in these copepod species exceeds 30 based on automated annotations of TSA data (e.g. [ 58 ]).…”

Prevalence and proliferation of antibiotic resistance genes in the subtropical mangrove wetland ecosystem of South China Sea

“…Based on previous studies, adapter sequences were removed using SeqPrep v1.33. Moreover, sequences <100 bp and those with quality <20 as well as reads containing an N base were removed using Sickle v1.2; then, clean reads were created (Yang, Sun, Yang, & Li, ). Nonbacteria sequences (algae, protist, etc) were also cleaned by local Blastn program against NR database (V20151204) from NCBI with evalue 1e‐10 (Camacho et al, ).…”

“…The red labels are the sampling sites that located at the north bank of the estuary, the A, B, C, and D are mangrove sampling sites, and the E is a sandy beach site outside the mangrove. The yellow labels are the south bank sites, all of them are sandy beach sites Z <20 as well as reads containing an N base were removed using Sickle v1.2; then, clean reads were created (Yang, Sun, Yang, & Li, 2014).…”

Development of molecular resources for the Chinese horseshoe crab Tachypleus tridentatus

“…The total RNA concentration and integrity were determined using an Agilent 2100 Bioanalyzer and a NanoDrop spectrophotometer (Thermo Scientific), respectively. RNA-seq library construction and sequencing (Illumina) were performed as described by Yang et al (2014). After the mRNA was enriched by beads with Oligo(dT) primers, the mRNA was dissected into short fragments.…”