Data from: Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop

The genus Amaranthus consists of 50 to 70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joing tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus.苋属（Amaranthus）包含50至70个物种，涵盖多个兼具重要经济价值的栽培种与杂草类群。尽管已有多项基于分子标记的研究，但由于该属仅具备少量适宜性状、表型可塑性、基因流与杂交事件等特征，学界仍难以明确整个类群的分类学与系统发育关系。本研究通过对代表35个苋属物种的94份种质资源库（genebank）材料开展测序分型（genotyping by sequencing, GBS），推断了苋属的系统发育关系，并测定了各物种的基因组大小。研究分别采用从头组装（de novo）与基于参考基因组的方法调用单核苷酸多态性（Single Nucleotide Polymorphism, SNPs），并选取亲缘关系较远的甜菜（Beta vulgaris）以及近缘种皱果苋（Amaranthus hypochondriacus）作为参考基因组。两种方法得到的SNP数量与缺失数据比例存在差异，但最终构建的系统发育树高度相似。基于个体材料的距离法邻接树（neighbor joining tree）以及基于多物种溯合模型（multispecies coalescent）的物种树，均支持此前将该属划分为3个亚属的分类学处理，不过其中Acnida亚属包含两个高度分化的演化支。对苋亚属（A. Amaranthus）内的Hybridus复合群的分析，揭示了栽培籽粒苋的演化历史。该复合群包含3种栽培籽粒苋及其野生近缘种，与该亚属内其他物种界限清晰。野生与栽培苋属材料并未按照物种划分进行聚类，而是依据其南美与中美洲的地理起源聚为类群。不同地理隔离的Hybridus种群似乎是3种栽培籽粒苋的共同祖先，而南美籽粒苋（A. caudatus）的演化可能还涉及Quitensis苋（A. quitensis）的参与。本研究同时测定了各物种的基因组大小，结果显示除两个谱系外，基因组大小整体差异较小，且这两个谱系均存在近期多倍化（polyploidization）的证据。除上述两个谱系外，各物种基因组大小较为保守，表明多倍化在该属的演化历史中并未发挥主要作用。