Comparative plastomic analysis of cultivated Dioscorea polystachya and its close relatives provides insights on the inter- and intraspecific phylogenies and potential wild origins of domestication

Dioscorea polystachya and its closely related species are original plants of the tuber crop "yam", which had been intensively use for medicinal and food purposes and widely cultivated in northern China and its surrounding areas with a long history. Many cultivars of these species are often confused with one another because of similar tuber morphology, however, conventional DNA barcoding faces practical limitations restricting the method to effectively identify closely related species. In addition, phylogenetic relationships among various cultivar groups of Chinese yam (D. polystachya) remains unclear. To solve these problems, genomic DNAs of 15 Dioscorea samples were sequenced to assemble and annotate chloroplast genomes, which were used for analyzing their structural characteristics and identifying phylogenetic relationships at the inter- and intraspecific levels. The size of chloroplast genomes of the tested samples is about 153 kb, and 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes are annotated. Phylogenetic analysis showed that D. polystachya were sister to Dioscorea japonica, and for Huaishan yams, Dioscorea persimilis did not cluster with Dioscorea alata and Dioscorea fordii. Four cultivar groups of Chinese yam were determined, namely Tiegun group, Anping group, Foshou group and Taihang complex group. Among these cultivar groups, Foshou and Taihang complex are clustered with different wild yams, respectively. Amino acid preferences are similar at the inter- and intraspecific levels, while synonymous codon usage reflects distinct patterns in the majority of cultivars of D. polystachya. There are distinct SSR variations among species, as well as four cultivar groups. Collinearity and SNP analyses show that nucleotide hypervariable regions among Dioscorea species are mainly concentrated in trnK-atpA, rps16-trnQ, atpA-atpH, rpoB-psbD, atpH-atpI, trnV-ndhC in the LSC region, and ccsA-ndhF in the SSC region, while intraspecific variation of Chinese yam is enriched in the intergenic spacers of rpoB-psbC, ndhD-ndhF, and trnQ-trnS, as well as the gene ycf1. Phylogenetic analysis supports that Huaishan yams are not of monophyletic origin and the cultivated Chinese yam has at least two wild origins of domestication, which is consistent with the historical records of these wild yams from Mt. Dabie and Mt. Taihang. The identification efficiency of the newly developed barcodes for cultivar groups based on chloroplast genome SNP screening is significantl