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With the development of molecular sequencing approaches, many taxonomic and phylogenetic problems of the genus Allium L. have been solved; however, the phylogenetic relationships of some subgenera or sections, such as section Bromatorrhiza, remain unresolved, which has greatly impeded our full understanding of the species relationships among the major clades of Allium. In this study, the complete chloroplast (cp) genomes of nine species in the Allium sect. Bromatorrhiza were determined using the Illumina paired-end sequencing, the NOVOPlasty de novo assembly strategy, and the PGA annotation method. The results showed that the cp genome exhibited high conservation and revealed a typical circular tetrad structure. Among the sect. Bromatorrhiza species, the gene content, SSRs, codon usage, and RNA editing site were similar. The genome structure and IR regions' fluctuation were investigated while genes, CDSs, and non-coding regions were extracted for phylogeny reconstruction. Evolutionary rates (Ka/Ks values) were calculated, and positive selection analysis was further performed using the branch-site model. Five hypervariable regions were identified as candidate molecular markers for species authentication. A clear relationship among the sect. Bromatorrhiza species were detected based on concatenated genes and CDSs, respectively, which suggested that sect. Bromatorrhiza is monophyly. In addition, there were three genes with higher Ka/Ks values (rps2, ycf1, and ycf2), and four genes (rpoC2, atpF, atpI, and rpl14) were further revealed to own positive selected sites. These results provide new insights into the plastome component, phylogeny, and evolution of Allium species. [ABSTRACT FROM AUTHOR]

The Qinghai-Tibet Plateau (QTP) has been biogeographically divided into the eastern monsoonal and the western continental climatic zones along the 500 mm isohyet. However, this biogeographic hypothesis has been rarely tested using a phylogeographic approach. The members of the genus Allium subgenus Cyathophora coincidentally distribute across this biogeographical divide. Intriguingly, Allium fasciculatum of subgenus Amerallium co-occurs in the distribution range of subgenus Cyathophora. To illuminate the role of this biogeographic divide on the genetic divergence, we genotyped 466 individuals of 52 populations of subgenus Cyathophora and 110 individuals of 19 populations of A. fasciculatum using three chloroplast DNA fragments, whole nrITS and nine nuclear microsatellite loci, supplemented with the present environmental space and paleo-distribution modeling. Our phylogeographical evidence recovered the concordant east–west genetic breaks both for subgenus Cyathophora and A. fasciculatum along the 500 mm isohyet. The divergence time estimations and environmental niche differentiations suggested this east–west genetic breaks could have been triggered by the climatic-induced vicariance during the early Pleistocene. Noticeably, this split within subgenus Cyathophora could have been deepened by the morphological vicariance from the eastern umbel to the western spicate, while that within A. fasciculatum could have been obscured due to the pollen flows from the east to west caused by the postglacial expansion. The genetic structures and ecological niche modelings (ENMs) recovered the distinct responses to the Quaternary climatic oscillations for species constricted to different climatic zones, further highlighting the profound effect of the climatic differences and tectonic uplifts on the genetic diversification. Overall, our findings offer strong evidence for the existence of a biogeographic divide between the eastern monsoonal and the west continental climatic zones of the QTP nearly along the 500 mm isohyet. [ABSTRACT FROM AUTHOR]

• 4 chloroplast genomes of Curcuma were newly sequenced and assembled. • Multiple SSRs and highly variable regions were identified. • Curcuma has gene introgression with related taxa. • Chloroplast genes of Curcuma may had undergone positive selection pressure in evolution. Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA , psbD , PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast. [ABSTRACT FROM AUTHOR]