Central Asia revealed as a key area in evolution of Eremurus (Asphodelaceae)

Eremurus was described at the beginning of the 19th century.However,due to limited sampling and the small number of gene markers to date,its phylogeny and evolution are largely unknown.In this study,we analyzed plastomes from 27 species belonging to 2 subgenera and 3 sections of Eremurus,which are found in Central Asia(its center of diversity)and China.We also analyzed nuclear DNA ITS of 33 species,encompassing all subgenera and sections of the genus in Central Asia,southwest Asia and China.Our findings revealed that the genus was monophyletic,although both subgenera Eremurus and Henningia were found to be paraphyletic.Both plastome and nrDNA-based phylogenetic trees had three clades that did not reflect the current taxonomy of the genus.Our biogeographical and time-calibrated trees suggest that Eremurus originated in the ancient Tethyan area in the second half of the Eocene.Diversification of Eremurus occurred from the early Oligocene to the late Miocene.Paratethys Sea retreat and several orogenetic events,such as the progressive uplift of the Qinghai-Tibet Plateau and surrounding mountain belts(Altai,Pamir,Tian Shan),caused serious topographic and climate(aridification)changes in Central Asia that may have triggered a split of clades and speciation.In this transformed Central Asia,speciation proceeded rapidly driven mainly by vicariance caused by numerous mountain chains and specialization to a variety of climatic,topographic and soil conditions that exist in this region.

Phylogenomics of Allium section Cepa(Amaryllidaceae)provides new insights on domestication of onion

Allium sect.Cepa(Amaryllidaceae)comprises economically important plants,yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent.Until now,phylogenetic studies of the section have been based on a few genes.In this study,we sequenced the complete chloroplast genome(plastomes)of four central Asian species of sect.Cepa:Allium oschaninii,A.praemixtum,A.pskemense and A.galanthum.Their chloroplast(cp)genomes included 114 unique genes of which 80 coded proteins.Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies.Our plastome-based phylogenetic tree of Allium sect.Cepa revealed two separate clades:one comprising the central Asian species A.oschaninii,A.praemixtum,and A.pskemense,and another comprising A.galanthum,A.altaicum,and two cultivated species,A.cepa and A.fistulosum.These findings contradict previously reported phylogenies that relied on ITS and morphology.Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A.galanthum and A.cepa followed by chloroplast capture;however,this is impossible to prove without additional data.Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion.Among the chloroplast genes,rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.