title: Exploring single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes in the jellyfish (Rhopilema esculentum) by transcriptome sequencing.
abstract: In this study, single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes (DEGs) in the oral parts, gonads, and umbrella parts of the jellyfish Rhopilema esculentum were analyzed by RNA-Seq technology. A total of 76.4 million raw reads and 72.1 million clean reads were generated from deep sequencing. Approximately 119,874 tentative unigenes and 149,239 transcripts were obtained. A total of 1,034,708 SNP markers were detected in the three tissues. For microsatellite mining, 5088 SSRs were identified from the unigene sequences. The most frequent repeat motifs were mononucleotide repeats, which accounted for 61.93%. Transcriptome comparison of the three tissues yielded a total of 8841 DEGs, of which 3560 were up-regulated and 5281 were down-regulated. This study represents the greatest sequencing effort carried out for a jellyfish and provides the first high-throughput transcriptomic resource for jellyfish.
authors.affiliation: Liaoning Ocean and Fisheries Science Research Institute, Heishijiao Street No. 50, Dalian, Liaoning Province 116023, China. Electronic address: yunfengli@126.com.
authors.forename: Yunfeng
authors.initials: Y
authors.lastname: Li
authors.affiliation: Liaoning Ocean and Fisheries Science Research Institute, Heishijiao Street No. 50, Dalian, Liaoning Province 116023, China. Electronic address: zunchunz@hotmail.com.
authors.forename: Zunchun
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Liaoning Ocean and Fisheries Science Research Institute, Heishijiao Street No. 50, Dalian, Liaoning Province 116023, China. Electronic address: merlin.t.024@live.com.
authors.forename: Meilin
authors.initials: M
authors.lastname: Tian
authors.affiliation: Dalian Ocean University, Heishijiao Street No. 52, Dalian, Liaoning Province 116023, China. Electronic address: tianyi@dlou.edu.cn.
authors.forename: Yi
authors.initials: Y
authors.lastname: Tian
authors.affiliation: Liaoning Ocean and Fisheries Science Research Institute, Heishijiao Street No. 50, Dalian, Liaoning Province 116023, China. Electronic address: ebuma@sina.com.
authors.forename: Ying
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Liaoning Ocean and Fisheries Science Research Institute, Heishijiao Street No. 50, Dalian, Liaoning Province 116023, China. Electronic address: lnlylsl@126.com.
authors.forename: Shilei
authors.initials: S
authors.lastname: Li
authors.affiliation: Liaoning Ocean and Fisheries Science Research Institute, Heishijiao Street No. 50, Dalian, Liaoning Province 116023, China. Electronic address: cnliu51@tom.com.
authors.forename: Weidong
authors.initials: W
authors.lastname: Liu
authors.affiliation: Liaoning Ocean and Fisheries Science Research Institute, Heishijiao Street No. 50, Dalian, Liaoning Province 116023, China. Electronic address: chongbohe@163.com.
authors.forename: Chongbo
authors.initials: C
authors.lastname: He
mesh_terms: D000818:Animals; D015870:Gene Expression; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D009928:Organ Specificity; D020641:Polymorphism, Single Nucleotide; D037401:Scyphozoa / Q000235:genetics*; D059467:Transcriptome
keywords: Different gene expressions; Gene annotation; Molecular marker; Rhopilema esculentum; Transcriptome sequencing