Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared to the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of post-zygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values.

尽管菊科（Compositae）仅拥有向日葵和生菜这两种主要粮食作物，但该科内诸多其他物种已被人类开发利用，并经历了不同程度的驯化。本研究借助下一代测序技术，为菊科作物及其野生近缘种构建了15套参考转录组组装结果。这些数据为解析植物驯化过程中的演化与基因组学效应提供了研究基础。具体而言，本研究对苦苣（Cichorium endivia）、菊苣（Cichorium intybus）、窄叶松果菊（Echinacea angustifolia）、一年生艾菊（Iva annua）、菊芋（Helianthus tuberosus）、大丽花（Dahlia hybrida）、假蒲公英毛莲（Leontodon taraxacoides）和田春黄菊（Glebionis segetum）进行了Illumina测序，同时对糙籽芥（Guizotia scabra）、甜叶菊（Stevia rebaudiana）、银胶菊（Parthenium argentatum）及雪莲果（Smallanthus sonchifolius）开展了454测序。Illumina测序读段通过Trinity软件进行组装，454测序读段则采用MIRA与CAP3软件完成组装。本研究通过对一组超保守同源基因（UCOs）进行BLASTX分析，评估了各转录组的覆盖度，成功检索到88%~98%的目标基因。研究发现，454组装结果的重叠群（contig）长度与测序读长呈正相关，且454组装的重叠群整体长度显著长于Illumina组装结果。这一结果表明更长的测序读长有助于组装得到更完整的转录本。最后，本研究比较了菊科作物与其野生近缘种间同源基因的同义位点（Ks）分化程度，发现当祖先类群为自交不亲和时，同源基因的分化程度更高。同时，本研究还观察到，存在合子后隔离证据的类群对之间，同源基因的分化程度同样更高。针对菊苣与苦苣等亲缘关系较远的同属类群，本研究在Ks值分布中检测到了基因渐渗的特征信号。