De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae).
De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae).
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DOI：
10.1371/journal.pone.0042605
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Hendrickx F
中科院分区：
文献类型：
--
作者：
Van Belleghem SM;Roelofs D;Van Houdt J;Hendrickx F
盐沼甲虫Pogonus chalceus代表了一个独特的机会，了解和研究扩散多态性的起源和进化，因为在扩散相关性状（例如翅膀发育，身体大小和代谢）中显着的种群间分歧已被证明在强大的基因流中持续存在。测序和组装P. chalceus的转录组是开发大规模遗传信息的第一步，这将使我们能够进一步研究这些自然种群中扩散性状的重复表型进化。我们使用Illumina HiSeq 2000对转录组的37个G碱基进行测序，并使用Trinity短读组装程序进行从头转录组组装。这导致65，766个重叠群，聚类成39，393个独特的转录物（单基因）。12，987个子集显示与NCBI数据库中已知蛋白质的相似性（BLAST），7，589个被分配基因本体（GO）。利用同源性搜索，我们确定了所有报道的基因参与翅发育，保幼激素和蜕皮激素途径赤拟谷盗。约有一半（56.7%）的独特组装基因之间共享的三个生命阶段（三龄幼虫，蛹，成虫）。我们在这些单基因中发现了38，141个单核苷酸多态性（SNP）。在这些SNPs中，26，823个（70.3%）在预测的开放阅读框架（ORF）中发现，6，998个（18.3%）是非同义的。组装的转录组和SNP数据是必要的基因组资源，为进一步研究的发展途径，遗传机制和代谢后果的适应性分歧在自然种群的扩散能力。
The salt marsh beetle Pogonus chalceus represents a unique opportunity to understand and study the origin and evolution of dispersal polymorphisms as remarkable inter-population divergence in dispersal related traits (e.g. wing development, body size and metabolism) has been shown to persist in face of strong homogenizing gene flow. Sequencing and assembling the transcriptome of P. chalceus is a first step in developing large scale genetic information that will allow us to further study the recurrent phenotypic evolution in dispersal traits in these natural populations. We used the Illumina HiSeq2000 to sequence 37 Gbases of the transcriptome and performed de novo transcriptome assembly with the Trinity short read assembler. This resulted in 65,766 contigs, clustering into 39,393 unique transcripts (unigenes). A subset of 12,987 show similarity (BLAST) to known proteins in the NCBI database and 7,589 are assigned Gene Ontology (GO). Using homology searches we identified all reported genes involved in wing development, juvenile- and ecdysteroid hormone pathways in Tribolium castaneum. About half (56.7%) of the unique assembled genes are shared among three life stages (third-instar larva, pupa, and imago). We identified 38,141 single nucleotide polymorphisms (SNPs) in these unigenes. Of these SNPs, 26,823 (70.3%) were found in a predicted open reading frame (ORF) and 6,998 (18.3%) were nonsynonymous. The assembled transcriptome and SNP data are essential genomic resources for further study of the developmental pathways, genetic mechanisms and metabolic consequences of adaptive divergence in dispersal power in natural populations.
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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：
6.4
作者：
Hendrickx, Frederik;Maelfait, Jean-Pierre;Bugter, Rob
通讯作者：
Bugter, Rob
影响因子：
2.7
作者：
BOER, PJD
通讯作者：
BOER, PJD
影响因子：
56.9
作者：
Abouheif, E;Wray, GA
通讯作者：
Wray, GA
影响因子：
5.8
作者：
Danecek, Petr;Auton, Adam;Durbin, Richard
通讯作者：
Durbin, Richard