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. 2017 Dec 28;17(Suppl 2):258.
doi: 10.1186/s12870-017-1194-0.

Taxonomic Assessment of Allium Species From Kazakhstan Based on ITS and matK Markers

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Free PMC article

Taxonomic Assessment of Allium Species From Kazakhstan Based on ITS and matK Markers

Saule Abugalieva et al. BMC Plant Biol. .
Free PMC article

Abstract

Background: As 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.

Results: The 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.

Conclusions: The 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.

Keywords: Allium taxonomy; DNA barcoding; ITS; Subgenus Reticulatobulbosa; matK.

Conflict of interest statement

Ethics approval and consent to participate

This study does not contain any research requiring ethical consent or approval.

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Not applicable.

Competing interests

The authors declare they have no competing interests.

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Figures

Fig. 1
Fig. 1
Locations of the collecting sites (open circles) in five different regions of Kazakhstan – East, South-east, South, West, and Center. Arabic figures reflect regions of collecting sites – East, South-east, South, West, and Center of Kazakhstan)
Fig. 2
Fig. 2
Neighbor-Joining phylogenetic tree resulted from analysis of the ITS sequences of twenty local Allium species and four outgroup taxa. The subgenera and sectional classification are given according to Friesen et al. [8]. The length of branches is based on Maximum Composite Likelihood and numbers at nodes shows a probability bootstrap. * is indication of local species and taxa with reference numbers representing accessions from the NCBI database
Fig. 3
Fig. 3
Neighbor-Joining phylogenetic tree resulted from analysis of the ITS sequences of twenty local, thirty worldwide Allium species and four outgroup taxa. The subgenera and section classification are given according to Friesen et al. [8]. The length of branches is based on Maximum Composite Likelihood and numbers at nodes shows a probability bootstrap. * is indication of local species and taxa with reference numbers representing accessions from the NCBI database
Fig. 4
Fig. 4
Neighbor-Joining phylogenetic tree resulted from analysis of the matK sequences of twenty local Allium species and four outgroup taxa. The subgenera and sectional classification are given according to Friesen et al. [8]. The length of branches is based on Maximum Composite Likelihood and numbers at nodes shows bootstrap support values. * is indication of local species and taxa with reference numbers representing accessions from the NCBI database
Fig. 5
Fig. 5
Neighbor-Joining phylogenetic tree resulted from analysis of the matK sequences of twenty local and thirty worldwide occurring Allium species and four outgroup taxa. The subgenera and sectional classification are given according to Friesen et al. [8]. The length of branches is based on Maximum Composite Likelihood and numbers at nodes shows bootstrap support values (%). * indicates local species and taxa with reference numbers representing accessions from the NCBI database

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