High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies.
High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies.
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对夏威夷 Parhyale mRNA 和 microRNA 进行高通量测序，以帮助比较发育研究。
DOI：
10.1371/journal.pone.0033784
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Aboobaker AA
中科院分区：
文献类型：
--
作者：
Blythe MJ;Malla S;Everall R;Shih YH;Lemay V;Moreton J;Wilson R;Aboobaker AA
了解动物形态多样性的遗传和进化基础需要使用新模式生物进行比较发育研究。这就需要开发用于遗传学研究的工具以及生成待研究生物体的序列信息。下一代测序技术的发展使得能够快速且经济高效地生成序列信息。由于先进分子工具的发展，夏威夷 P. hawaiensis 已成为一种选择的模式生物，因此夏威夷 P. hawaiensis 遗传信息将有助于推动该生物体的功能研究。在这里，我们展示了使用下一代测序平台生成的转录组和 miRNA 集合。我们从从胚胎到胚带阶段构建的夏威夷 P. hawaiensis cDNA 文库中生成了大约 170 万个读数。这些读数被组装成包含 163,501 个转录本的数据集。使用 Annot8r 和 pfam2go 的组合注释，将基因本体分类分配给 20,597 个转录本。 Annot8r 用于为我们的转录数据集提供 KEGG 同源性。总共定义了 25,292 个 KEGG 通路分配，并通过针对 NCBI nr 蛋白质数据库的相互爆炸进一步确认。这已经鉴定出许多参与发育的关键保守信号通路的夏威夷 P. hawaiensis 基因直系同源物。我们还从 P. hawaiensis 中生成了小 RNA 序列，鉴定了 55 个保守的 miRNA。未通过与 mirBase 严格比较注释的测序小 RNA 用于在水蚤中搜索可能的新 miRNA。使用保守的方法，我们鉴定了 51 个可能保守于水蚤基因组中的 miRNA 候选者，它们可能是潜在的甲壳类/节肢动物特异性 miRNA。我们的研究展示了在没有基因组测序的新模型生物中发现的基因和 miRNA。我们的工作提供的数据对于夏威夷 P. hawaiensis 社区以及更广泛的进化发育生物学界来说非常有价值。
Understanding the genetic and evolutionary basis of animal morphological diversity will require comparative developmental studies that use new model organisms. This necessitates development of tools for the study of genetics and also the generation of sequence information of the organism to be studied. The development of next generation sequencing technology has enabled quick and cost effective generation of sequence information. Parhyale hawaiensis has emerged as a model organism of choice due to the development of advanced molecular tools, thus P. hawaiensis genetic information will help drive functional studies in this organism. Here we present a transcriptome and miRNA collection generated using next generation sequencing platforms. We generated approximately 1.7 million reads from a P. hawaiensis cDNA library constructed from embryos up to the germ band stage. These reads were assembled into a dataset comprising 163,501 transcripts. Using the combined annotation of Annot8r and pfam2go, Gene Ontology classifications was assigned to 20,597 transcripts. Annot8r was used to provide KEGG orthology to our transcript dataset. A total of 25,292 KEGG pathway assignments were defined and further confirmed with reciprocal blast against the NCBI nr protein database. This has identified many P. hawaiensis gene orthologs of key conserved signalling pathways involved in development. We also generated small RNA sequences from P. hawaiensis, identifying 55 conserved miRNAs. Sequenced small RNAs that were not annotated by stringent comparison to mirBase were used to search the Daphnia pulex for possible novel miRNAs. Using a conservative approach, we have identified 51 possible miRNA candidates conserved in the Daphnia pulex genome, which could be potential crustacean/arthropod specific miRNAs. Our study presents gene and miRNA discovery in a new model organism that does not have a sequenced genome. The data provided by our work will be valuable for the P. hawaiensis community as well as the wider evolutionary developmental biology community.
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影响因子：
3.7
作者：
Bai X;Mamidala P;Rajarapu SP;Jones SC;Mittapalli O
通讯作者：
Mittapalli O
DOI：
10.1073/pnas.0903105106
发表时间：
2009-08-18
影响因子：
11.1
作者：
Liubicich, Danielle M.;Serano, Julia M.;Patel, Nipam H.
通讯作者：
Patel, Nipam H.
DOI：
10.1126/science.1197761
发表时间：
2011-02-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Colbourne JK;Pfrender ME;Gilbert D;Thomas WK;Tucker A;Oakley TH;Tokishita S;Aerts A;Arnold GJ;Basu MK;Bauer DJ;Cáceres CE;Carmel L;Casola C;Choi JH;Detter JC;Dong Q;Dusheyko S;Eads BD;Fröhlich T;Geiler-Samerotte KA;Gerlach D;Hatcher P;Jogdeo S;Krijgsveld J;Kriventseva EV;Kültz D;Laforsch C;Lindquist E;Lopez J;Manak JR;Muller J;Pangilinan J;Patwardhan RP;Pitluck S;Pritham EJ;Rechtsteiner A;Rho M;Rogozin IB;Sakarya O;Salamov A;Schaack S;Shapiro H;Shiga Y;Skalitzky C;Smith Z;Souvorov A;Sung W;Tang Z;Tsuchiya D;Tu H;Vos H;Wang M;Wolf YI;Yamagata H;Yamada T;Ye Y;Shaw JR;Andrews J;Crease TJ;Tang H;Lucas SM;Robertson HM;Bork P;Koonin EV;Zdobnov EM;Grigoriev IV;Lynch M;Boore JL
通讯作者：
Boore JL
影响因子：
3
作者：
Guerra-Assunção JA;Enright AJ
通讯作者：
Enright AJ
影响因子：
4.4
作者：
Ewen-Campen B;Shaner N;Panfilio KA;Suzuki Y;Roth S;Extavour CG
通讯作者：
Extavour CG