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类群与杂草类物种。尽管已有多项基于分子标记的研究，但受限于少数关键性状、表型可塑性、基因流与杂交事件的影响，学界仍难以厘清该属整体的分类学与系统发育关系。本研究针对代表35个苋属物种的94份种质库保藏材料，通过测序分型（GBS）技术推断苋属的系统发育关系，并测定了各材料的基因组大小。单核苷酸多态性（SNPs）分别通过从头组装法与基于参考基因组的方法完成鉴定，所用参考基因组分别为远缘物种甜菜（Beta vulgaris）以及近缘物种尾穗苋（Amaranthus hypochondriacus）。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，以及通过多物种溯祖模型计算得到的物种树，均支持此前将该属划分为3个亚属的分类学处理，但苋属A. Acnida亚属包含两个高度分化的演化支。对苋属（A. Amaranthus）亚属内的Hybridus复合群的分析，为栽培籽粒苋的演化历史提供了新的认知。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分明。野生与栽培苋属材料并未按照物种划分聚类，而是依据其源自中南美洲的地理起源进行分组。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A. quitensis可能还参与了南美洲栽培籽粒苋（A. caudatus）的演化过程。本研究还测定了各物种的基因组大小，观测到除两个类群外，基因组大小变异程度较低，且这两个类群存在近期多倍化的证据。除上述两个类群外，各物种基因组大小较为相近，表明多倍化在苋属的演化历史中并未发挥主要作用。