Exploring single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes in the jellyfish (Rhopilema esculentum) by transcriptome sequencing
| Autor: | Ying Dong, Weidong Liu, Zunchun Zhou, Yi Tian, Li Yunfeng, Shilei Li, Chongbo He, Meilin Tian |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Jellyfish Scyphozoa Gene Expression UniGene Single-nucleotide polymorphism Aquatic Science 010502 geochemistry & geophysics Polymorphism Single Nucleotide 01 natural sciences Deep sequencing Transcriptome 03 medical and health sciences biology.animal Genetics Animals SNP 0105 earth and related environmental sciences Rhopilema esculentum biology High-Throughput Nucleotide Sequencing 030104 developmental biology Organ Specificity Microsatellite Microsatellite Repeats |
| Zdroj: | Marine Genomics. 34:31-37 |
| ISSN: | 1874-7787 |
| DOI: | 10.1016/j.margen.2017.01.007 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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