Transcriptome profiling to discover putative genes associated with paraquat resistance in goosegrass (Eleusine indica L.).
Transcriptome profiling to discover putative genes associated with paraquat resistance in goosegrass (Eleusine indica L.).
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转录组分析发现与牛筋草 (Eleusine indica L.) 百草枯抗性相关的推定基因
DOI：
10.1371/journal.pone.0099940
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Chen Y
中科院分区：
文献类型：
--
作者：
An J;Shen X;Ma Q;Yang C;Liu S;Chen Y
背景牛牛草（Eleusine indica L.）是世界上一种严重的一年生杂草，已经对包括百草枯（一种非选择性除草剂）在内的多种除草剂产生了抗性。杂草对百草枯的抗性机制目前尚不完全清楚。为了进一步研究牛筋草对百草枯抗性的分子机制，我们对经过或未经百草枯处理的牛筋草的敏感和抗性生物型进行了转录组分析。结果 RNA-seq 文库生成了 194,716,560 个有效读数，平均长度为 91.29 bp。从头组装分析产生了 158,461 个转录本，平均长度为 1153.74 bp 和 100,742 个 unigenes，平均长度为 712.79 bp。其中，25,926 个 unigene 被分配给包含三个主要类别的 65 个 GO 术语。共有13,809个unigenes和1,208个酶委托编号被分配到314个预测的KEGG代谢途径，12,719个unigenes被分为25个KOG分类。此外，我们的结果显示，在百草枯处理实验中，53 个与活性氧清除相关的基因、10 个与多胺相关的基因和 18 个与运输相关的基因存在差异表达。与多胺和运输相关的基因可能是潜在的候选基因，可以进一步研究它们以确认它们在牛筋草的百草枯抗性中的作用。结论 这是首次使用 Illumina 平台对 E. indica 进行大规模转录组测序。从组装的序列中鉴定出涉及百草枯抗性的潜在基因。转录组数据可为进一步分析基因表达和功能基因组学研究提供参考，并将有助于牛筋草对百草枯抗性的分子水平研究。
Background Goosegrass (Eleusine indica L.), a serious annual weed in the world, has evolved resistance to several herbicides including paraquat, a non-selective herbicide. The mechanism of paraquat resistance in weeds is only partially understood. To further study the molecular mechanism underlying paraquat resistance in goosegrass, we performed transcriptome analysis of susceptible and resistant biotypes of goosegrass with or without paraquat treatment. Results The RNA-seq libraries generated 194,716,560 valid reads with an average length of 91.29 bp. De novo assembly analysis produced 158,461 transcripts with an average length of 1153.74 bp and 100,742 unigenes with an average length of 712.79 bp. Among these, 25,926 unigenes were assigned to 65 GO terms that contained three main categories. A total of 13,809 unigenes with 1,208 enzyme commission numbers were assigned to 314 predicted KEGG metabolic pathways, and 12,719 unigenes were categorized into 25 KOG classifications. Furthermore, our results revealed that 53 genes related to reactive oxygen species scavenging, 10 genes related to polyamines and 18 genes related to transport were differentially expressed in paraquat treatment experiments. The genes related to polyamines and transport are likely potential candidate genes that could be further investigated to confirm their roles in paraquat resistance of goosegrass. Conclusion This is the first large-scale transcriptome sequencing of E. indica using the Illumina platform. Potential genes involved in paraquat resistance were identified from the assembled sequences. The transcriptome data may serve as a reference for further analysis of gene expression and functional genomics studies, and will facilitate the study of paraquat resistance at the molecular level in goosegrass.
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