De novo assembly and characterization of the Barnyardgrass (Echinochloa crus-galli) transcriptome using next-generation pyrosequencing.
De novo assembly and characterization of the Barnyardgrass (Echinochloa crus-galli) transcriptome using next-generation pyrosequencing.
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使用下一代焦磷酸测序技术对稗草（稗草）转录组进行从头组装和表征
DOI：
10.1371/journal.pone.0069168
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Li YF
中科院分区：
文献类型：
--
作者：
Yang X;Yu XY;Li YF
稗草（Echinochloacrus-galli）是危害水稻生产的重要杂草。这种杂草的除草剂抗性的快速进化使其成为使用除草剂最难管理的杂草之一。由于稗草的全基因组序列数据有限，我们使用454 GS-FLX平台对易感和抗性稗草生物型的转录组进行了测序。结果454次焦磷酸测序得到371,281个原始片段，平均长度为341.8 bp，总长度为126.89 Mb（SRX 160526）。从头组装产生了10，142个重叠群（约5.92 Mb），平均长度为583 bp，以及68，940个单体（约22.13 Mb），平均长度为321 bp。获得了约244，653个GO术语分配给生物过程，细胞组分和分子功能类别。共有6，092个重叠群和单例，具有2，515个酶委员会编号，被分配给151个预测的KEGG代谢途径。使用Illumina测序的数字丰度分析在易感、抗性、除草剂处理的易感和除草剂处理的抗性稗草生物型中鉴定了78，124个转录本。从这些分析中，8个除草剂靶位点基因组和4个非靶位点基因组中确定的抗性生物型。这些基因可能是与稗草抗除草剂相关的候选基因，可用于进一步的功能基因组学研究。利用PCR和RACE技术鉴定了C4光合作用相关基因RbcS、RbcL、NADP-me和MDH。结论这是首次大规模的E. crus-galli使用454 GS-FLX平台进行。从组装的序列中鉴定了参与除草剂抗性进化的潜在候选基因。该转录组数据可作为进一步基因表达和功能基因组学研究的参考，并将有助于在分子水平上研究该物种以及其他杂草的除草剂抗性。
Background Barnyardgrass (Echinochloa crus-galli) is an important weed that is a menace to rice cultivation and production. Rapid evolution of herbicide resistance in this weed makes it one of the most difficult to manage using herbicides. Since genome-wide sequence data for barnyardgrass is limited, we sequenced the transcriptomes of susceptible and resistant barnyardgrass biotypes using the 454 GS-FLX platform. Results 454 pyrosequencing generated 371,281 raw reads with an average length of 341.8 bp, which made a total length of 126.89 Mb (SRX160526). De novo assembly produced 10,142 contigs (∼5.92 Mb) with an average length of 583 bp and 68,940 singletons (∼22.13 Mb) with an average length of 321 bp. About 244,653 GO term assignments to the biological process, cellular component and molecular function categories were obtained. A total of 6,092 contigs and singletons with 2,515 enzyme commission numbers were assigned to 151 predicted KEGG metabolic pathways. Digital abundance analysis using Illumina sequencing identified 78,124 transcripts among susceptible, resistant, herbicide-treated susceptible and herbicide-treated resistant barnyardgrass biotypes. From these analyses, eight herbicide target-site gene groups and four non-target-site gene groups were identified in the resistant biotype. These could be potential candidate genes involved in the herbicide resistance of barnyardgrass and could be used for further functional genomics research. C4 photosynthesis genes including RbcS, RbcL, NADP-me and MDH with complete CDS were identified using PCR and RACE technology. Conclusions This is the first large-scale transcriptome sequencing of E. crus-galli performed using the 454 GS-FLX platform. Potential candidate genes involved in the evolution of herbicide resistance were identified from the assembled sequences. This transcriptome data may serve as a reference for further gene expression and functional genomics studies, and will facilitate the study of herbicide resistance at the molecular level in this species as well as other weeds.
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影响因子：
1.4
作者：
Malik, Mayank S.;Burgos, Nilda R.;Talbert, Ronald E.
通讯作者：
Talbert, Ronald E.
DOI：
10.1038/nrg2934
发表时间：
2011-02
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
9.2
作者：
Christin, Pascal-Antoine;Salamin, Nicolas;Besnard, Guillaume
通讯作者：
Besnard, Guillaume
影响因子：
11.6
作者：
Bouchenak-Khelladi, Yanis;Verboom, G. Anthony;Savolainen, Vincent
通讯作者：
Savolainen, Vincent
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL