Data from: Development of chloroplast genomic resources for Cynara

In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera, and C. syriaca). One complete cp genome was isolated using short reads from a whole genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy, combined with a reference based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes (“Brindisino” artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short “variable” cp regions. The evaluation of the molecular resources obtained from this study led us to support the “super-barcode” theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level.

本研究以20份基因型材料的完整叶绿体（chloroplast, cp）基因组为基础，依托高通量测序技术，为菜蓟属（Cynara）开发了全新的叶绿体基因组资源。本研究的目标物种涵盖7份球茎洋蓟、2份栽培刺菜蓟、8份野生洋蓟，以及另外3个野生菜蓟属物种（C. baetica、C. cornigera与C. syriaca）。本研究通过全基因组测序项目的短读长序列组装得到1条完整的叶绿体基因组，其余基因组则通过长距聚合酶链式反应（long-range PCR）获得，本文一并提供其扩增引物对。本研究采用从头组装结合参考组装的策略，成功重构了所有叶绿体基因组。本研究将新测序的20份基因型与从公共数据库中获取的另外2份菜蓟属叶绿体基因组（"Brindisino"洋蓟与C. humilis）进行比较分析，结果显示菜蓟属中共存在126个简约信息位点与258个独态位点，总计384个变异位点。本研究共检测到39个简单序列重复（simple sequence repeat, SSR）位点与34个插入缺失（insertion-deletion, INDEL）事件。经数据分析后，本研究设计了37对SSR扩增引物，并在菜蓟属基因型材料中验证了这些分子标记的有效性。相较于仅使用简约信息位点或仅使用短片段叶绿体变异区域开展的系统发育分析，基于全部叶绿体变异位点构建的系统发育树获得了最优的分辨效果。本研究对获得的分子资源进行评估后，支持"超级条形码（super-barcode）"理论，并认为菜蓟属完整叶绿体序列可作为可靠且极具价值的分子标记，用于探究物种多样性及种内变异分析。