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AP 09259027 (superviser Almerekova Sh.)

Brief description of the project

(Project’s duration is 36 months, 2021-2023)

   Project title: IRN AP09259027 «Study of the genetic diversity of species of the genus Juniperus L. growing in Kazakhstan».

Kazakhstan is the ninth largest country in the world and it has a peculiar and specific wild flora. In the eastern, southeastern, and southern regions, the country is surrounded by the high mountain ranges of Altai, Tarbagatai, Dzhungarskiy Alatau, and Tien Shan. One of the important components of forests in abovementioned mountain ranges, as well as in the boron forests of Northern Kazakhstan, is the juniper, which has an important ecological role due to its water and soil protection and anti-mudflow significance. In addition, juniper is an important raw material for the production of essential oils, which are a source of pharmacological preparations. From this point of view, the development of scientific approaches for the preservation and augmentation of the genetic resources of juniper species in Kazakhstan has a high scientific and practical importance. In total, about 75 species of this genus grow in the world. Seven of them grow in Kazakhstan — Juniperus communis, J. media, J. pseudosabina, J. sabina, J. semiglobosa, J. sibirica, and J. seravschanica. However, there were no studies on geobotanical description of all 7 species of juniper, analysis of population structure and degree of genetic diversity in juniper populations, as well as molecular taxonomy of local taxa of the genus, including J. seravschanica, which is a rare species listed in the Red Book of Kazakhstan.

The project focuses on collection of populations of each species with accompanying geobotanical studies. For the collected populations, an analysis of population structure and degree of genetic diversity is carried out using informative and highly polymorphic microsatellite DNA markers (SSR, simple sequence repeats), and species analysis using DNA barcoding technology. For molecular taxonomy, ITS (internal transcribed spacers) marker of the nuclear genome is used. In addition, the project carries out a complete sequencing of the chloroplast genome of all seven species of juniper grown in Kazakhstan using new genomic technologies.

  The goal of the project: study the intra- and interspecific genetic diversity of seven juniper species in Kazakhstan based on the use of polymorphic and informative DNA markers, including the nucleotide sequences of chloroplast genomes using new generation genomic technologies.

  Expected results:

  1. The collection of 7 juniper species populations will be carried out, the species will be determined; herbariums will be compiled and digitized. The age composition, number, density of coenopopulations of J. seravschanica and the floristic composition of plant communities with its participation will be studied.
  2. Phylogenetic relationships of species in juniper genus will be studied using ITS markers of the nuclear genome.
  3. The level of intra- and interspecific genetic diversity of Juniperus species in Kazakhstan will be studied; the structure of populations will be determined. Genetic passports of juniper species.
  4. Phylogenetic relationships of juniper species based on the genetic diversity of the chloroplast genome will be studied. Molecular genetic certification of junipers species in Kazakhstan based on different classes of DNA markers has been carried out.

   Scientific Supervisor of the project:

  Shyryn Almerekova, was born in 1989, senior researcher, PhD (2018, geobotany). She has experience in the relevant field of research (botany, molecular genetics). Co-author of over 30 scientific papers; has 19 articles, including 10 articles in peer-reviewed journals indexed in the Web of Science (H-index 3, Rsearcher ID AAO-1157-2020) and/or Scopus (H-index=3, Scopus Author ID: 57196952712), and 7 papers in journals of CCES list. She trained in research centers of Hungary, Germany, Spain. ORCID https://orcid.org/0000-0002-6079-264X

  Research group: 

  Yerlan Turuspekov, candidate of biological sciences (genetics), professor (biology), head of the laboratory of molecular genetics. He has more than 100 scientific publications, including 40 in peer-reviewed international journals indexed in the Web of Science databases (H-index 12, Researcher ID: C-3458-2011) and/or having a CiteScore percentile in the Scopus database (H-index 14, Scopus Author ID: 57197860996, 29 статей в 2016-2020); 42 papers in journals of CCES list. ORCID https://orcid.org/0000-0001-8590-1745

  Moldir Ermagambetova, PhD-student on the topic of research (2020-2023), junior researcher, she has 2 years of experience in collecting and studying populations of wild plant species, microsatellite analysis, barcoding.

  Akerke Amalova, Master of science (geobotany), researcher, co-author of 5 articles (Web of Science, H-index 2, Researcher ID: AAO-1156-2020, H-index 1, Scopus Author ID: 57213623570), 4 articles in journals of CCES list). ORCID https://orcid.org/0000-0002-7903-3467

  Yuliya Genievskaya, Master of science (biotechnology), junior researcher, co-author of 10 articles peer-reviewed in Web of Science (H-index 4, Researcher ID: AAF-2410-2019) and/or Scopus (H-index 5, Scopus Author ID: 57196939730). ORCID https://orcid.org/0000-0001-5987-2952

   List of publications of the project’s participants (2015-2020)

  1. Almerekova S., Schegoleva N., Abugalieva S., Turuspekov Y. (2020).The molecular taxonomy of three endemic Central Asian species of Ranunculus (Ranunculaceae), PlosONE (IF=3.337, Q2-Multidisciplinary sciences; SJR=1.100, 89-General Agricultural&Biological Sciences). https://doi.org/10.1371/journal.pone.0240121
  2. Almerekova Sh., Mukhitdinov N., Abugalieva S. (2017). Phylogenetic study of the endemic species Oxytropis almaatensis (Fabaceae) based on nuclear ribosomal DNA ITS sequences, BMC Plant Biology (IF=4.311, Q1-Plant sciences, SJR=1.687, percentile: 92-Plant Science), 17(Sl.1):19-27. DOI: https://doi.org/1186/s12870-017-1128-x.
  3. Almerekova S., Lisztes-Szabo Z., Mukhitdinov N., Kurmanbayeva M., Abidkulova K., Sramko G. (2018). Genetic diversity and population genetic structure of the endangered Kazakh endemic Oxytropis almaatensis (Fabaceae), Acta Botanica Hungarica (SJR=0.627, percentile: 35-Plant Science). 60(3/4): 263-278. https://doi.org/10.1556/034.2018.1.
  4. Almerekova S., Abugalieva S., Mukhitdinov N. (2018). Taxonomic assessment of the Oxytropis species from South-East of Kazakhstan, Вавиловский журнал генетики и селекции (Vavilovskii Zhurnal Genetiki i Selektsii) (SJR=0.147, percentile: 31-General Agricultural and Biological Sciences). 22(2):285-290. DOI: http://dx.doi.org/10.18699/VJ18.362.
  5. Malkócs T., Almerekova S., Bereczki J., Cservenka J., Meglécz E., & Sramkó G. (2019). Isolation and characterization of 15 SSR loci for the endangered European tetraploid species Gladiolus palustris (Iridaceae), Applications in Plant Sciences (IF=1.389, Q3; SJR=0.607, percentile: 60-Plant Science). 7(5): https://doi.org/10.1002/aps3.1245
  6. Genievskaya Y., Abugalieva S., Zhubanysheva A., Turuspekov Y. (2017). Morphological description and DNA barcoding study of sand rice (Aqriophyllum squarrosum, Chenopodiaceae) collected in Kazakhstan, BMC Plant Biology (IF=4.311, Q1-Plant sciences, SJR=1.687, percentile: 92-Plant Science). 17(S1):1-8. https://doi.org/10.1186/s12870-017-1132-1.
  7. Abugalieva S., Volkova L., Genievskaya Y., Ivaschenko A., Kotukhov Y., Sakauova G., Turuspekov Y. (2017). Taxonomic assessment of Allium species from Kazakhstan based on ITS and matK markers, BMC Plant Biology (IF=4.311, Q1-Plant sciences, SJR=1.687, percentile: 92-Plant Science). 17(2):51-60. DOI: https://doi.org/10.1186/s12870-017-1194-0.
  8. Turuspekov , Genievskaya Y., Baibulatova A., Zatybekov A., Kotuhov Y., Imanbayeva A., Abugalieva S. (2018). Phylogenetic taxonomy of Artemisia L. species from Kazakhstan based on matK analyses, Proceeding of the Latvian Academy of Sciences. Section B (SJR=0.137, percentile: 24). 72(1):29-37. DOI: https://doi.org/10.1515/prolas-2017-0068.
  9. Zhang J., Zhao J., Zhou, Q., Hu J., Ma Y., Zhao X., Zhao P., Turuspekov Y., Xie Zh., Chen G. (2018). The agronomic performance of sand rice (Agriophyllum squarrosum), a potential semi-arid crop species // Genetic Resources and Crop Evolution (SJR 0,524, IF 1,13). 65, 2293–2301. https://doi.org/10.1007/s10722-018-0689-3
  10. Turuspekov Y., Abugalieva S., Ermekbayev K., Sato K. (2014). Genetic characterization of wild barley populations (Hordeum vulgare spontaneum) from Kazakhstan based on genome wide SNP analysis // Breeding Science. 64:399-403. https://doi.org/10.1270/jsbbs.64.399

 

  Results for 2021:

  1. Thirteen populations of species pseudosabina (2 populations), J. sabina (2), J. communis (2), J. seravschanica (3), J. semiglobosa (2) and J. sibirica (2 populations) were collected in northern, eastern, southeastern and southern Kazakhstan. The species were identified; the herbarium material was compiled and digitized. The cenopopulation characteristics of the Red Data Book species J. seravschanica were determined and the floristic composition with its participation was studied.
  2. The study of phylogenetic relationships of species in juniper genus has been begun using ITS markers of the nuclear genome. We analyzed 22 samples of 6 juniper species ( seravschanica, J. semiglobosa, J. sabina, J. pseudosabina, J. sibirica, and J. communis); sequencing (determination of nucleotide sequences) of DNA of each population’s representatives was carried out. The analysis of phylogenetic relationships and haplotype networks of Juniperus species based on the ITS marker was carried out using statistical programs. Ten ITS nucleotide sequences (ID: OK325616, OK325617, OK325618, OK325619, OK325620, OK325621, OK325622, OK325623, OK325624, OK325625) for species J. seravschanica, J.sibirica, and J. sabina from different populations were deposited.
  3. The genotyping of the collected populations of juniper species has been begun using 16 microsatellite DNA markers. At this stage of work, the most informative loci were JT_30, JT_04, and Jce04.
  4. Whole genome sequencing of the chloroplast genome of juniper species sabina, J. sibirica и J. seravschanica has been begun using the Illumina platform: NovaSeq 6000. The complete chloroplast genome of J. sabina consists of 92 protein coding genes, 27 tRNA genes, and 2 rRNA genes. The chloroplast genome of J. sibirica is represented by 91 protein-coding genes, it contains 26 tRNA and 2 rRNA genes. The chloroplast genome of the species J. seravschanica from the Red Book consists of 88 protein-coding genes, 27 tRNA genes, and 2 rRNA genes; the genome size is 127,823 bp.

  Publications (2021):

  International conference abstracts:

  1. Turuspekov Y. «Genetic diversity of wild plants species in Kazakhstan». The 5th symposium on Euroasian Biodiversity. 2021. p. 18. ISBN: 978-625-409-945-8
  2. Yermagambetova M., Almerekova S., Abugalieva S. «Genetic structure analysis of Juniperus seravshanica using polymorphic microsatellite markers». The 5th symposium on Euroasian Biodiversity. 2021. p. 187. ISBN: 978-625-409-945-8
  3. Yermagambetova M., Abugalieva S, Almerekova S.. Distribution of the Juniperus species in the Ugam and Talas ridges on the Western Tien Shan Mountains. International scientific-practical conference « Biodiversity conservation aspects». – Almaty, 2021, 63-65 p.

   Reports at conferences, seminars (presentation forms):

  1. Turuspekov Y. – plenary report at an international scientific and practical conference « The 5th Symposium on EuroAsian Biodiversity (SEAB-2021)». http://seab2021.mu.edu.tr/en/speakers-7295
  2. Yermagambetova M. – oral presentation at an international scientific and practical conference « The 5th Symposium on EuroAsian Biodiversity (SEAB-2021)».
  3. Turuspekov Y. – plenary report at an international scientific and practical conference «Biodiversity conservation aspects». https://www.kaznu.kz/ru/18975/news/one/27070/

Results for 2022:

  1. The work on the collection of populations of juniper species growing in Kazakhstan is was completed. A total of 29 populations of pseudosabina (2 populations), J. sabina (4), J. communis (1), J. seravschanica (11), J. semiglobosa (4), J. sibirica (4), J. media (1) and J. turkestanica (=J. pseudosabina) (2) in northern, eastern, southeastern, and southern Kazakhstan and in the mountain regions of Uzbekistan and Kyrgyzstan. Cenopopulation characteristics (study of age composition, abundance, density) of the Red Data Book species J. seravschanica were revealed. The floristic composition of plant communities with the participation of J. seravschanica was also studied.
  2. The analysis of phylogenetic relationships and haplotype networks of species of the genus Juniperus was continued. Nucleotide sequences of Kazakhstan’s juniper species were aligned with 85 juniper accessions and one outgroup sample of Cupressus sempervirens from NCBI. As a result of the phylogenetic tree analysis, juniper samples were divided into 2 large clusters corresponding to 2 sections of the genus — Juniperus and Sabina. Haplotype network analysis identified 81 haplotypes, including an outgroup pattern. The results of clustering in the phylogenetic tree constructed using the NJ method showed similarity with the haplotype network obtained using the Neighbor-Net method. The work on depositing nucleotide sequences (NS) of ITS nuclear genome markers of species of the genus Juniperus into the NCBI international database has been completed. In 2022, 6 ITS NSes of species seravschanica, J. semiglobosa, J. communis, and J. pseudosabina from different populations were deposited.
  3. Genotyping of the collected populations of juniper species was continued using 16 microsatellite DNA markers. In 2022, 15 populations of seravschanica were analyzed for 10 polymorphic markers, 4 populations of J. sabina and 2 populations of J. turkestanica – for 10 markers. The results of statistical processing of 10 polymorphic markers for 15 populations of J. seravschanica showed a relatively high level of genetic polymorphism in the studied populations. Work will continue.
  4. Whole-genome sequencing of the chloroplast genome of the juniper species turkestanica (= J. pseudosabina) using the Illumina: NovaSeq 6000 platform was continued. According to preliminary data, the complete chloroplast genome of J. turkestanica (= J. pseudosabina) consists of 83 protein-coding genes, 29 tRNA genes and 4 rRNA. The content of GC bases in the studied chloroplast DNA corresponded to 35.04%, the genome size was 127,826 bp. The annotated genome-wide chloroplast DNA sequences of J. sabina and J. seravschanica were deposited in the NCBI international database under the numbers OL467323 and OL684343, respectively.

Publications (2022):

Publications in peer-reviewed foreign journals with a non-zero impact factor

Almerekova S., Yermagambetova M., Abugalieva S., Turuspekov Y. The complete chloroplast genome sequencing data of Juniperus sabina L. (Cupressaceae Bartl.) from Kazakhstan // Data in Brief. – 2022. – Vol.45: 108644.

Articles in peer-reviewed journals recommended by CCSES of Ministry of Education and Science of the RK

Yermagambetova M.M., Abugalieva S.I., Turuspekov Y.K., Almerekova S.S. Synopsis of the genus Juniperus L. growing in Kazakhstan // Works on applied botany, genetics and breeding. — 2022. — 183(3): 161-170. (in Russian)

Abstracts of the international conferences

  1. Yermagambetova M.M., Almerekova S.S., Abugalieva S.I., Turuspekov Y.K. Synopsis of the genus Juniperus L. growing in Kazakhstan. International scientific-practical conference «Introduction, biodiversity conservation and green building in a changing climate and anthropogenic impact.» — Aktau, 2022. 131-132 pp. (in Kazakh)
  2. Yermagambetova M.M., Almerekova S.S., Abugalieva S.I., Turginov O.T., Sultangaziyev O.E., Turuspekov Y.K. Distribution of Juniperus seravschanica Kom. in the mountainous regions of Kazakhstan, Kyrgyzstan and Uzbekistan. Proceedings of the international conference «Formation and development of experimental biology in Tajikistan», 2022, Dushanbe, Tajikistan, pp.266-267. (in Russian)
  3. Yermagambetova M., Almerekova S., Abugalieva S., Turuspekov Y. Genetic structure of Juniperus seravshanica Kom. from Kazakhstan using polymorphic microsatellite markers // International Conference on Veterinary, Agriculture and Life Sciences (ICVALS). – Antalya, 2022 – P.2. (oral presentation)