Data from: Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

PREMISE OF THE STUDY: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we report on the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization. METHODS: We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing, compared the coverage and quality of sequence assemblies, and developed NimbleGen microarrays for expression analyses in five taxa. Where possible, we also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression. RESULTS: Gene discovery was enhanced by sequencing from multiple tissues, normalization of cDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and Lactuca. CONCLUSIONS: Transcriptome sequencing using next generation platforms has greatly reduced the cost of genomic studies of non-model organisms, and the ESTs and microarrays reported here will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to quantify the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.研究背景：杂草会造成严重的环境与经济损失。但相较于模式植物与作物物种，杂草的基因组特征研究仍相对滞后。本研究针对11种菊科（Compositae）杂草开发了基因组工具与资源，可为后续的种群基因组学与比较基因组学分析奠定基础。鉴于有研究提出杂交可促进入侵性演化，本研究同时对这些基因组数据开展杂交信号检测分析。 研究方法：本研究通过Sanger、454及Illumina测序技术，为11种目标杂草构建了22个表达序列标签（expressed sequence tag, EST）文库；比较了序列组装的覆盖度与质量，并为5个杂草类群开发了NimbleGen基因表达微阵列。在可行情况下，本研究还通过比较同属物种直系同源基因的同义替换率（Ks）分布，来检测并量化杂交与基因渐渗现象。 研究结果：通过多组织测序、cDNA文库标准化，尤其是提升测序深度，显著提高了基因发现效率。但短读长序列组装有时无法区分高度相似的旁系同源基因。在矢车菊属（Centaurea）和向日葵属（Helianthus）中检测到了显著的基因渐渗，而在豚草属（Ambrosia）和莴苣属（Lactuca）中未发现该现象。 研究结论：基于下一代测序平台的转录组测序大幅降低了非模式生物的基因组研究成本，本研究开发的EST文库与微阵列将加速菊科杂草的进化生物学与分子生物学研究。本研究同时证实，通过直系同源基因比较可量化全基因组范围的基因渐渗程度，并识别杂交类群间发生交换的基因。