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首页> 外文期刊>Acta Horticulturae >The chloroplast genome as a tool for exploring genetic relationships among globe artichoke, leafy cardoons and wild artichokes
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The chloroplast genome as a tool for exploring genetic relationships among globe artichoke, leafy cardoons and wild artichokes

机译：叶绿体基因组作为探索朝鲜蓟，绿叶菜心菜和野生洋蓟之间遗传关系的工具

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The main aim of this work was to isolate the entire chloroplast (cp) genome sequences of Cynara taxa, in order to retrieve the most useful resources for phylogenetic and population studies. Twenty-two samples were analysed, of which 18 belonged to thethree taxa of C. cardunculus L., and the remaining to four wild species (C. syriaca, C. cornigera, C. baetica, and C. humilis). First, we obtained reads by whole-genome and a BAG clone of the 'Brindisino' globe artichoke by means of high-throughput sequencing. This genome was assembled, its size was 152,529 bp and it consisted of two single-copy regions separated by a pair of inverted repeats of 25,155 bp. The large and the small single-copy regions spanned 83,578 and 18,641 bp, respectively. For the other genotypes, a long-range PCR approach was employed for producing partially overlapping amplicons. These fragments were high-throughput sequenced and reads were assembled for each genotype using de novo and reference-guided methods. No structural differences regarding gene content and order were highlighted among all analysed genotypes. A conserved structure was also observed among other eight Asteraceae species analysed. Cynara cp genome consists of 114 unique genes, including 30 tRNA, 4 rRNA, and 80 predicted protein-coding genes. The comparative analysis among all newly sequenced genomes allowed the discovery of a large number of informative loci, in terms of variable microsatellites, INDELS, and SNPs. The Cynara complete cp sequence allowed theplacing of this genus in the Asteraceae family tree and, thanks to the set of samples considered helped clarify the phylogenetic relationships within this genus.
机译：这项工作的主要目的是分离整个Cynara类群的叶绿体（cp）基因组序列，以便检索用于系统发育和种群研究的最有用资源。分析了22个样品，其中18个属于C. cardunculus L.的三个分类，其余为四个野生物种（C. syriaca，C。cornigera，C。baetica和C. humilis）。首先，我们通过高通量测序获得了全基因组的读物和'Brindisino'朝鲜蓟的BAG克隆。该基因组已组装，其大小为152,529 bp，由两个单拷贝区域组成，这些区域由一对25,155 bp的反向重复序列隔开。大和小单拷贝区域分别跨越83,578和18,641 bp。对于其他基因型，采用长距离PCR方法生产部分重叠的扩增子。对这些片段进行高通量测序，并使用从头和参考指导的方法对每种基因型的读段进行组装。在所有分析的基因型之间，没有突出显示关于基因含量和顺序的结构差异。在分析的其他八种菊科物种中也观察到了保守的结构。 Cynara cp基因组由114个独特基因组成，包括30个tRNA，4个rRNA和80个预测的蛋白质编码基因。所有新测序的基因组之间的比较分析允许发现大量的信息位点，包括可变微卫星，INDELS和SNP。 Cynara完整的cp序列使得该属可以放置在菊科家族树中，而且由于所考虑的样本集有助于阐明该属的系统发生关系。

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