koz"Вестник Северо-Казахстанского университета имени Манаша Козыбаева"Bulletin of Manash Kozybayev North Kazakhstan University2958-003X2958-0048М. Қозыбаев атындағы СҚУ10.54596/2958-0048-2025-3-26-33koz-2222Research ArticleБИОЛОГИЧЕСКИЕ НАУКИBIOLOGICAL SCIENCESЗначение эталонных геномов для сохранения видов - национальных символов Казахстана: на примере каспийского тюленя и тюльпана ГрейгаReference-grade genomes as a tool for conserving Kazakhstan’s national pride species: the cases of the Caspian seal and Greig’s tuliphttps://orcid.org/0009-0006-9454-0463MussurovaS.MussurovaS.

Петропавловск

Saule Mussurova, Scientific Coordinator at Center of Agrocompetence, 

Petropavlovsk

annual_stones.6o@icloud.comhttps://orcid.org/0000-0001-7574-0714ZuccoloA.ZuccoloA.

Петропавловск;

Пиза

Andrea Zuccolo, Professor, Petropavlovsk;

Pisa

azuccolo@ku.edu.kzhttps://orcid.org/0000-0001-6633-6226WingR. A.WingR.A.

Тувал, Саудовская Аравия;

Тусон

Rod Anthony Wing - professor at KAUST, Thuwal, Saudi Arabia;

Director of Arizona Genomics Institute, Tucson

rod.wing@kaust.edu.saНАО «Северо-Казахстанский университет имени Манаша Козыбаева»КазахстанManash Kozybayev North Kazakhstan University NPLCKazakhstanНАО «Северо-Казахстанский университет имени Манаша Козыбаева»; Скуола Супериоре Сант’АннаКазахстанManash Kozybayev North Kazakhstan University NPLC; Scuola Superiore Sant’AnnaKazakhstanKing Abdullah University of Science and Technology (KAUST); Университет АризоныСоединённые Штаты АмерикиKing Abdullah University of Science and Technology (KAUST); University of ArizonaUnited States20252410202503 (67)2633Copyright © Mussurova S., Zuccolo A., Wing R.A., 20252025Mussurova S., Zuccolo A., Wing R.A.Mussurova S., Zuccolo A., Wing R.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://vestnik.ku.edu.kz/jour/article/view/2222

В этой статье представлен потенциал технологий секвенирования третьего поколения (TGS) для поддержки усилий по сохранению биоразнообразия в Казахстане. Мы фокусируемся на двух знаковых видах - Pusa caspica (каспийский тюлень) и Tulipa greigii, которые оба находятся под угрозой сохранения и не имеют комплексных геномных ресурсов. В этом мини-обзоре подчеркивается преобразующая роль секвенирования третьего поколения (TGS) в сохранении биоразнообразия, используя Казахстан в качестве примера. Мы не ставим своей целью систематическое сравнение технологий секвенирования или исчерпывающую каталогизацию всех доступных геномных данных. Вместо этого мы обсуждаем, как высококачественные референтные геномы без пробелов, полученные с использованием платформ TGS, таких как PacBio HiFi и Oxford Nanopore, представляют собой эффективный инструмент для усилий по сохранению видов, предоставляя ценную информацию для оценки геномного здоровья популяции и для идентификации генов, связанных с адаптацией и устойчивостью к болезням. Наконец, мы предлагаем расширить этот подход, включив в него дополнительные виды национального значения, такие как сайгак, собаки тазы и тобет, а также розовый фламинго, в рамках национальной инициативы по геномному биоразнообразию.

 

This article presents the potential of third-generation sequencing (TGS) technologies to support biodiversity conservation efforts in Kazakhstan. We focus on two emblematic species - Pusa caspica (Caspian seal) and Tulipa greigii - that are both under conservation threat and lack comprehensive genomic resources. This mini-review highlights the transformative role of third-generation sequencing (TGS) in biodiversity conservation, using Kazakhstan as a case study. We do not aim to systematically compare sequencing technologies or exhaustively catalog all available genomic data. Rather, we discuss how high quality gapless reference genomes produced using TGS platforms such as PacBio HiFi and Oxford Nanopore represent an effective tool for species conservation efforts providing valuable information for the assessment of population genomic health, and for the identification of genes linked to adaptation and disease resistance. Finally, we suggest expanding this approach to include additional species of national importance, such as the saiga antelope, the Tazy and Tobet dogs, and the pink flamingo, as part of a national genomic biodiversity initiative.

геномика охраны природыкаспийский тюленьTulipa greigiiсеквенирование третьего поколенияэталонный геномбиоразнообразие Казахстанаconservation genomicsCaspian sealTulipa greigiithird-generation sequencingplatinumstandard reference genomeKazakhstan biodiversityReferencesAlmerekova, S. et al. (2024) ‘Comparative analysis of plastome sequences of seven tulipa L. (Liliaceae Juss.) species from section Kolpakowskianae RAAMSD. Ex Zonn and VELDK. ’, International Journal o f Molecular Sciences, 25(14), p. 7874. doi:10.3390/ijms25147874.Almerekova, S. et al. (2024) ‘Comparative analysis of plastome sequences of seven tulipa L. (Liliaceae Juss.) species from section Kolpakowskianae RAAMSD. Ex Zonn and VELDK. ’, International Journal o f Molecular Sciences, 25(14), p. 7874. doi:10.3390/ijms25147874.Almerekova, S., Yermagambetova, M., Ivashchenko, A., Abugalieva, S., & Turuspekov, Y. (2024). Assessment of Complete Plastid Genome Sequences of Tulipa alberti Regel and Tulipa greigii Regel Species from Kazakhstan. Genes, 15(11), 1447. https://doi.org/10.3390/genes151n447Almerekova, S., Yermagambetova, M., Ivashchenko, A., Abugalieva, S., & Turuspekov, Y. (2024). Assessment of Complete Plastid Genome Sequences of Tulipa alberti Regel and Tulipa greigii Regel Species from Kazakhstan. Genes, 15(11), 1447. https://doi.org/10.3390/genes151n447Caspian seal genome: Joint research between Caier and Kaust (2025) Главная - ЦАИЭИ. Available at:https://asianecology.kz/news_eng/tpost/nx2bigjpz1-caspian-seal-genome-joint-research-betwe (Accessed: 14 May 2025).Caspian seal genome: Joint research between Caier and Kaust (2025) Главная - ЦАИЭИ. Available at:https://asianecology.kz/news_eng/tpost/nx2bigjpz1-caspian-seal-genome-joint-research-betwe (Accessed: 14 May 2025).Cui, T. et al. (2023) ‘Chromosome-level genome assembly and population genomic analysis provide novel insights into the immunity and evolution of Sogatella furcifera’, Genomics, 115(6), p. 110729. doi:10.1016/j.ygeno.2023.110729.Cui, T. et al. (2023) ‘Chromosome-level genome assembly and population genomic analysis provide novel insights into the immunity and evolution of Sogatella furcifera’, Genomics, 115(6), p. 110729. doi:10.1016/j.ygeno.2023.110729.Dussex, N., van derValk, T., Morales, H.E., Wheat, C.W., Díez-del-Molmo, D. & Allentoft, M.E., 2021. Population genomics of the critically endangered kakapo. Cell Genomics, 1(1), p.100002. DOI: 10.1016/j.xgen.2021.100002Dussex, N., van derValk, T., Morales, H.E., Wheat, C.W., D^ez-del-Molmo, D. & Allentoft, M.E., 2021. Population genomics of the critically endangered kakapo. Cell Genomics, 1(1), p.100002. DOI: 10.1016/j.xgen.2021.100002Ferrette, B.L. et al. (2023) ‘Seascape genomics and phylogeography of the sailfish (istiophorus platypterus) ’, Genome Biology and Evolution, 15(4). doi:10.1093/gbe/evad042.Ferrette, B.L. et al. (2023) ‘Seascape genomics and phylogeography of the sailfish (istiophorus platypterus) ’, Genome Biology and Evolution, 15(4). doi:10.1093/gbe/evad042.Formenti, G. et al. (2022) ‘The era of reference genomes in conservation genomics’, Trends in Ecology & Evolution, 37(3), pp. 197-202. doi:10.1016/j.tree.2021.11.008.Formenti, G. et al. (2022) ‘The era of reference genomes in conservation genomics’, Trends in Ecology & Evolution, 37(3), pp. 197-202. doi:10.1016/j.tree.2021.11.008.Gadzhiev, A. et al. (2024) ‘Pinnipeds and avian influenza: A global timeline and review of research on the impact of highly pathogenic avian influenza on pinniped populations with particular reference to the endangered Caspian seal (Pusa CASPICA)’, Frontiers in Cellular and Infection Microbiology, 14. doi:10.3389/fcimb.2024.1325977.Gadzhiev, A. et al. (2024) ‘Pinnipeds and avian influenza: A global timeline and review of research on the impact of highly pathogenic avian influenza on pinniped populations with particular reference to the endangered Caspian seal (Pusa CASPICA)’, Frontiers in Cellular and Infection Microbiology, 14. doi:10.3389/fcimb.2024.1325977.Gomes-dos-Santos, Andre, Elsa Froufe, Viatcheslav V. Rozhnov, Ivan Bolotov, Ilya G. Meschersky, Sergey I. Meschersky, Maria A. Solovyeva, Fedor V. Klimov, L. Filipe C. Castro, and Manuel Lopes-Lima. 2025. “The Complete Genome Sequence of the Caspian Seal Pusa Caspica (Gmelin, 1788).” Biodiversity Genomes, March. https://doi.org/10.56179/001c.133591.Gomes-dos-Santos, Andre, Elsa Froufe, Viatcheslav V. Rozhnov, Ivan Bolotov, Ilya G. Meschersky, Sergey I. Meschersky, Maria A. Solovyeva, Fedor V. Klimov, L. Filipe C. Castro, and Manuel Lopes-Lima. 2025. “The Complete Genome Sequence of the Caspian Seal Pusa Caspica (Gmelin, 1788).” Biodiversity Genomes, March. https://doi.org/10.56179/001c.133591.Hogg, C.J., Ottewell, K., Latch, P., Rossetto, M., Biggs, J., Gilbert, A., Richmond, S. & Belov, K., 2022. Threatened Species Initiative: Empowering conservation action using genomic resources. Proceedings o f the National Academy o f Sciences o f the United States o f America, 119(4), e2115643118. https://doi.org/10.1073/pnas.2115643118Hogg, C.J., Ottewell, K., Latch, P., Rossetto, M., Biggs, J., Gilbert, A., Richmond, S. & Belov, K., 2022. Threatened Species Initiative: Empowering conservation action using genomic resources. Proceedings o f the National Academy o f Sciences o f the United States o f America, 119(4), e2115643118. https://doi.org/10.1073/pnas.2115643118Huddart, J.E.A., Crawford, A.J., Luna-Tapia, A.L., Restrepo, S., & Di Palma, F. (2022). EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development. Proceedings o f the National Academy o f Sciences o f the United States o f America, 119(4), e2115641119.Huddart, J.E.A., Crawford, A.J., Luna-Tapia, A.L., Restrepo, S., & Di Palma, F. (2022). EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development. Proceedings o f the National Academy o f Sciences o f the United States o f America, 119(4), e2115641119.Karamendin, K. et al. (2024) ‘Viral metagenomic survey of Caspian seals’, Frontiers in Veterinary Science, 11. doi:10.3389/fvets.2024.1461135.Karamendin, K. et al. (2024) ‘Viral metagenomic survey of Caspian seals’, Frontiers in Veterinary Science, 11. doi:10.3389/fvets.2024.1461135.Kolora, S.R.R., Randhawa, H., Deisseroth, A., Mukherjee, S., Phuong, M.A., Paten, B. & Lewin, H.A., 2021. Origins and evolution of extreme life span in Pacific Ocean rockfishes. Science, 374(6571), pp.842¬ 847. DOI: 10.1126/science.abg5332Kolora, S.R.R., Randhawa, H., Deisseroth, A., Mukherjee, S., Phuong, M.A., Paten, B. & Lewin, H.A., 2021. Origins and evolution of extreme life span in Pacific Ocean rockfishes. Science, 374(6571), pp.842¬ 847. DOI: 10.1126/science.abg5332Lewin, H.A. et al. (2022) ‘The Earth Biogenome Project 2020: Starting the Clock’, Proceedings o f the National Academy o f Sciences, 119(4). doi:10.1073/pnas.2115635118.Lewin, H.A. et al. (2022) ‘The Earth Biogenome Project 2020: Starting the Clock’, Proceedings o f the National Academy o f Sciences, 119(4). doi:10.1073/pnas.2115635118.Marx, V. (2023) ‘Method of the year: Long-read sequencing’, Nature Methods, 20(1), pp. 6-11. doi:10.1038/s41592-022-01730-w.Marx, V. (2023) ‘Method of the year: Long-read sequencing’, Nature Methods, 20(1), pp. 6-11. doi:10.1038/s41592-022-01730-w.Mu, W. et al. (2025) ‘The haplotype-resolved T2T genome for bauhinia x blakeana sheds light on the genetic basis of flower heterosis’, GigaScience, 14. doi:10.1093/gigascience/giaf044.Mu, W. et al. (2025) ‘The haplotype-resolved T2T genome for bauhinia x blakeana sheds light on the genetic basis of flower heterosis’, GigaScience, 14. doi:10.1093/gigascience/giaf044.Namroodi, S. et al. (2018) ‘Frequency of exposure of endangered Caspian seals to canine distemper virus, Leptospira interrogans, and Toxoplasma gondii’, PLOS ONE, 13(4). doi:10.1371/journal.pone.0196070.Namroodi, S. et al. (2018) ‘Frequency of exposure of endangered Caspian seals to canine distemper virus, Leptospira interrogans, and Toxoplasma gondii’, PLOS ONE, 13(4). doi:10.1371/journal.pone.0196070.Kathrine Torday Gulden (2023) Transnational collaboration to save the caspian seal - NIBIO, Nibio EN. Available at: https://www.nibio.no/en/news/transnational-collaboration-to-save-the-caspian-seal (Accessed: 14 May 2025).Kathrine Torday Gulden (2023) Transnational collaboration to save the caspian seal - NIBIO, Nibio EN. Available at: https://www.nibio.no/en/news/transnational-collaboration-to-save-the-caspian-seal (Accessed: 14 May 2025).Theissinger, K. et al. (2023) ‘How genomics can help biodiversity conservation’, Trends in Genetics, 39(7), pp. 545-559. doi:10.1016/j.tig.2023.01.005.Theissinger, K. et al. (2023) ‘How genomics can help biodiversity conservation’, Trends in Genetics, 39(7), pp. 545-559. doi:10.1016/j.tig.2023.01.005.Tussipkan, D., Shevtsov, V., Ramazanova, M., Rakhimzhanova, A., Shevtsov, A., & Manabayeva, S. (2024). Kazakhstan tulips: Comparative analysis of complete chloroplast genomes of four local and 1433253. https://doi.org/10.3389/fpls.2024.1433253Tussipkan, D., Shevtsov, V., Ramazanova, M., Rakhimzhanova, A., Shevtsov, A., & Manabayeva, S. (2024). Kazakhstan tulips: Comparative analysis of complete chloroplast genomes of four local and 1433253. https://doi.org/10.3389/fpls.2024.1433253Zuccolo, A. et al. (2023) ‘The Gyrfalcon (falco rusticolus) genome’, G3: Genes, Genomes, Genetics, 13(3). doi:10.1093/g3journal/jkad001.Zuccolo, A. et al. (2023) ‘The Gyrfalcon (falco rusticolus) genome’, G3: Genes, Genomes, Genetics, 13(3). doi:10.1093/g3journal/jkad001.‘Pusa Caspica: Goodman, S. & Dmitrieva, L.’ (2015) IUCN Red List o f Threatened Species [Preprint]. doi:10.2305/iucn.uk.2016-1.rlts.t41669a45230700.en.‘Pusa Caspica: Goodman, S. & Dmitrieva, L.’ (2015) IUCN Red List o f Threatened Species [Preprint]. doi:10.2305/iucn.uk.2016-1.rlts.t41669a45230700.en.

The authors declare that there are no conflicts of interest present.