Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny.
Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny.
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DOI：
10.1186/1471-2164-14-263
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发表时间：
2013-04-18
期刊：
影响因子：
4.4
通讯作者：
Li W
中科院分区：
文献类型：
--
作者：
Niu SH;Li ZX;Yuan HW;Chen XY;Li Y;Li W
油松(Pinus Tabuliformis)是中国北部的一种乡土针叶树种，但作为基因组资源相对不发达，从而限制了基因的发现和育种。利用下一代测序平台获得了大规模的转录组数据，以弥补烟青霉基因组信息的缺乏。越来越多的松属转录组数据为多基因系统发育分析和研究物种分化时如何保持保守的基因和功能提供了极好的资源。在一个完整的454GS-Flx运行中，从多个组织和个人的归一化cDNA文库中获得的第一个油松杆菌转录组被测序，产生了911,302个测序读数。高质量的重叠表达序列标签(EST)被组装成46,584个推定的转录本，其中700多个SSR和92,000个SNPs/INDELs被表征。对6个针叶树种的转录组进行比较分析，得到191个同源基因，由此推断出系统发育树、进化模式和计算的基因转移率。我们还确定了938个快速进化的序列，这些序列可能有助于识别可能对正向选择做出反应而进化的基因，并可能对松树谱系中的物种形成负责。获得了大量高质量的EST，并进行了重新组装和鉴定，这代表了现有油松转录本目录的戏剧性扩展，并将逐步应用于油松育种工作。此外，这些数据将为今后油松和其他近缘物种的比较基因组学研究提供便利。
The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcriptome data were obtained using a next-generation sequencing platform to compensate for the lack of P. tabuliformis genomic information. The increasing amount of transcriptome data on Pinus provides an excellent resource for multi-gene phylogenetic analysis and studies on how conserved genes and functions are maintained in the face of species divergence. The first P. tabuliformis transcriptome from a normalised cDNA library of multiple tissues and individuals was sequenced in a full 454 GS-FLX run, producing 911,302 sequencing reads. The high quality overlapping expressed sequence tags (ESTs) were assembled into 46,584 putative transcripts, and more than 700 SSRs and 92,000 SNPs/InDels were characterised. Comparative analysis of the transcriptome of six conifer species yielded 191 orthologues, from which we inferred a phylogenetic tree, evolutionary patterns and calculated rates of gene diversion. We also identified 938 fast evolving sequences that may be useful for identifying genes that perhaps evolved in response to positive selection and might be responsible for speciation in the Pinus lineage. A large collection of high-quality ESTs was obtained, de novo assembled and characterised, which represents a dramatic expansion of the current transcript catalogues of P. tabuliformis and which will gradually be applied in breeding programs of P. tabuliformis. Furthermore, these data will facilitate future studies of the comparative genomics of P. tabuliformis and other related species.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
影响因子：
4.4
作者：
Garzón-Martínez GA;Zhu ZI;Landsman D;Barrero LS;Mariño-Ramírez L
通讯作者：
Mariño-Ramírez L
影响因子：
3.4
作者：
Gernandt, DS;López, GG;Liston, A
通讯作者：
Liston, A
DOI：
10.1073/pnas.1132171100
发表时间：
2003-06-10
影响因子：
11.1
作者：
Kirst, M;Johnson, AF;Sederoff, R
通讯作者：
Sederoff, R
过渡 - 转换偏差不是普遍的：蚱hopper假基因的反词。
影响因子：
4.5
作者：
Keller, Irene;Bensasson, Douda;Nichols, Richard A.
通讯作者：
Nichols, Richard A.