Transcriptome sequencing and de novo analysis of the copepod Calanus sinicus using 454 GS FLX.
Transcriptome sequencing and de novo analysis of the copepod Calanus sinicus using 454 GS FLX.
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使用 454 GS FLX 对桡足类 Calanus sinicus 进行转录组测序和从头分析
DOI：
10.1371/journal.pone.0063741
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Sun S
中科院分区：
文献类型：
--
作者：
Ning J;Wang M;Li C;Sun S
背景尽管桡足类物种丰富，具有重要的经济意义，但关于桡足类的基因组信息仍然有限。尤其是东亚沿海的优势种--中华哲水蚤，其基因组资源十分匮乏。在本研究中，我们进行了从头转录组测序，以产生大量的桡足类动物中华绒毛虫的表达序列标签。结果以桡足目幼虫和成虫为基本材料进行转录组测序。使用454焦磷酸测序，共获得1,470,799个读数，组装成56,809个高质量表达序列标签。根据它们与已知蛋白质的序列相似性，识别了大约14,000个不同的基因，包括所有主要保守信号通路的成员。在这些基因中也发现了与生长、脂肪代谢、蜕皮和滞育有关的转录本。在中华绒螯蟹幼虫和成虫中发现了与几个过程相关的差异表达基因。我们检测到284,154个单核苷酸多态(SNPs)，为基因功能研究提供了资源。结论我们的数据为中华绒毛虫提供了最全面的转录组资源。这一资源使我们能够识别与主要生理过程相关的基因和编码区的SNPs，这有助于对差异基因表达的定量分析。这些数据应该为未来对该物种和相关物种的遗传和基因组研究提供基础。
Background Despite their species abundance and primary economic importance, genomic information about copepods is still limited. In particular, genomic resources are lacking for the copepod Calanus sinicus, which is a dominant species in the coastal waters of East Asia. In this study, we performed de novo transcriptome sequencing to produce a large number of expressed sequence tags for the copepod C. sinicus. Results Copepodid larvae and adults were used as the basic material for transcriptome sequencing. Using 454 pyrosequencing, a total of 1,470,799 reads were obtained, which were assembled into 56,809 high quality expressed sequence tags. Based on their sequence similarity to known proteins, about 14,000 different genes were identified, including members of all major conserved signaling pathways. Transcripts that were putatively involved with growth, lipid metabolism, molting, and diapause were also identified among these genes. Differentially expressed genes related to several processes were found in C. sinicus copepodid larvae and adults. We detected 284,154 single nucleotide polymorphisms (SNPs) that provide a resource for gene function studies. Conclusion Our data provide the most comprehensive transcriptome resource available for C. sinicus. This resource allowed us to identify genes associated with primary physiological processes and SNPs in coding regions, which facilitated the quantitative analysis of differential gene expression. These data should provide foundation for future genetic and genomic studies of this and related species.
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影响因子：
3.7
作者：
Gregory R;Darby AC;Irving H;Coulibaly MB;Hughes M;Koekemoer LL;Coetzee M;Ranson H;Hemingway J;Hall N;Wondji CS
通讯作者：
Wondji CS
影响因子：
4.4
作者：
Eichner C;Frost P;Dysvik B;Jonassen I;Kristiansen B;Nilsen F
通讯作者：
Nilsen F
影响因子：
64.8
作者：
Beaugrand, G;Brander, KM;Reid, PC
通讯作者：
Reid, PC
DOI：
10.1071/it9941461
发表时间：
1994-01-01
期刊：
Invertebrate Taxonomy
影响因子：
--
作者：
Hulsemann, Kuni
通讯作者：
Hulsemann, Kuni
影响因子：
2.6
作者：
HUMES, AG
通讯作者：
HUMES, AG