BackgroundAs part of nation-wide project to infer the genetic variation of the native flora in Kazakhstan, a study was attempted to assess phylogenetic relationships of endemic and rare Allium species. In total, 20 Allium species were collected in field trips in five different regions of Kazakhstan during 2015–2016. Most species (9) were collected in the southern part of the country along of Karatau mountains, followed by Altai mountains (5) in eastern Kazakhstan. The ITS and matK DNA regions were applied in order to assess the taxonomic relationships among species. The major goal of the study was to assess the taxonomic position of five endemic and rare species from Allium subgenus Reticulatobulbosa collected in Karatau mountains of Southern Kazakhstan.ResultsThe 20 collected Allium species were assessed using morphological traits and a DNA barcoding approach. The morphological analyses of four different species in subgenus Reticulatobulbosa inferred similarities of A. inconspicuum and A. barszchewskii (both from section Companulata) that were separated from A. oreoscordum and A. oreoprasoides (section Nigrimontana) by several traits, including form of bulbs and leaves, presence of bracts, shape of perianth lobes and style. The Neighbor-Joining method was applied to generate ITS and matK phylogenetic trees for two groups of populations: 1) 20 Allium species collected within the project, and 2) 50 Allium worldwide species.ConclusionsThe analyses of nucleotide sequences of ITS and matK robustly confirmed the monophyletic origin of the Allium species. The variability in 20 local Allium species in ITS was 6.6 higher than in matK, therefore the topology of the ITS tree was better resolved. The taxonomy of Allium species largely coincided with a recent classification of this genus. Analyses of both ITS and matK suggest that A. oreoscordum is genetically close to A. oreoprasoides in section Nigrimontana of subgenus Reticulatobulbosa. This result was also confirmed using morphological description of individual plants of four species in subgenus Reticulatobulbosa. The study is another contribution to taxonomy clarification in Allium.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1194-0) contains supplementary material, which is available to authorized users.

The article presents the results of studies on distribution, ecological preferences and floristic composition of communities with the participation of the rare northern Tian-Shan endemic Tulipa tarda Stapf. As a result of the analysis of our own materials, data from herbaria, literature and some Internet sources, a point map of the distribution of the species in Kazakhstan was compiled. Based on the descriptions of 13 geobotanical plots, the altitudinal distribution range of the species (1100-1900 m above sea level) was determined, and relative indifference of the species to the steepness and exposure of slopes, as well as its confinement to multicomponent plant communities, mainly of the steppe and semi-steppe type, were established. According to our results combined with two descriptions from the adjacent territory of Kyrgyzstan, the flora of communities with the participation of T. tarda comprises 199 species of higher plants from 140 genera and 45 families. The 16 most species rich families (from Asteraceae to Crassulaceae) comprise 78% of the entire flora of the surveyed communities. The floristic core of the communities consists of only 13 species, most of which are steppe and petro-lithophilic ecological elements. The communities with the participation of Tulipa tarda include eight species listed in the Red Book of Kazakhstan, which stresses the need for special protection of not only of the species under study, but also of all plant communities with its participation.

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The Aconitum L. is a diverse genus consisting of more than 300 species all over the World, including 11 species grown in Kazakhstan. The phylogeny of the genus was mostly studied by using internal transcribed sequences (ITS) of the nuclear genome and maturase K (matK) of the chloroplast genome. Therefore, in this study it was decided to assess the phylogenetic position of three local species A. leucostomum, A. soongoricum and A. apetalum, by using ITS and matK. The application of Maximum-Likelihood (ML) method suggested that the A. soongoricum belong to subgenus Aconitum, and A. leucostomum and A. apetalum to the subgenus Lycoctonum, which was congruent to previous taxanomic studies for this genus. The Median-Joining network using ITS suggested that A. sachalinense belongs to the group of processors of the genus among species that were involved in the analysis. The study is the first attempt to understand phylogenetic relationship of three species of Aconitum grown in Kazakhstan.

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