title: Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for 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.
authors: Key Laboratory for Ecological Environment in Coastal Areas (SOA), National Marine Environmental Monitoring Center, Dalian 116023, China.
authors: Qing
authors: Q
authors: Yang
authors: Department of Reconstructive Sciences, Center for Regenerative Medicine and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA.
authors: Fanyue
authors: F
authors: Sun
authors: Harbin University of Science and Technology, Rongcheng Campus, Rongcheng 264300, China.
authors: Zhi
authors: Z
authors: Yang
authors: Key Laboratory for Ecological Environment in Coastal Areas (SOA), National Marine Environmental Monitoring Center, Dalian 116023, China.
authors: Hongjun
authors: H
authors: Li
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D033342:Copepoda / Q000235:genetics*; D055669:Ecological and Environmental Phenomena; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D063990:Gene Ontology; D056426:Genetic Loci; D005819:Genetic Markers; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D009691:Nucleic Acid Denaturation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D012333:RNA, Messenger