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Sinaga P, Klichowska E, Nowak A, Nobis M. Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia. PLoS One 2024; 19:e0298760. [PMID: 38412151 PMCID: PMC10898772 DOI: 10.1371/journal.pone.0298760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Stipa is a genus comprising ca. 150 species found in warm temperate regions of the Old World and around 30% of its representatives are of hybrid origin. In this study, using integrative taxonomy approach, we tested the hypothesis that hybridization and introgression are the explanations of the morphological intermediacy in species belonging to Stipa sect. Smirnovia, one of the species-rich sections in the mountains of Central Asia. Two novel nothospecies, S. magnifica × S. caucasica subsp. nikolai and S. lingua × S. caucasica subsp. nikolai, were identified based on a combination of morphological characters and SNPs markers. SNPs marker revealed that all S. lingua × S. caucasica samples were F1 hybrids, whereas most of S. magnifica × S. caucasica samples were backcross hybrids. Furthermore, the above mentioned hybrids exhibit transgressive morphological characters to each of their parental species. These findings have implications for understanding the process of hybridization in the genus Stipa, particularly in the sect. Smirnovia. As a taxonomic conclusion, we describe the two new nothospecies S. × muksuensis (from Tajikistan) and S. × ochyrae (from Kyrgyzstan) and present an identification key to species morphologically similar to the taxa mentioned above.
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Affiliation(s)
- Patar Sinaga
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden – Center for Biological Diversity Conservation in Powsin, Warszawa, Poland
- Botanical Garden of the Wrocław University, Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
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Sha N, Li Z, Sun Q, Han Y, Tian L, Wu Y, Li X, Shi Y, Zhang J, Peng J, Wang L, Dang Z, Liang C. Elucidation of the evolutionary history of Stipa in China using comparative transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1275018. [PMID: 38148860 PMCID: PMC10751131 DOI: 10.3389/fpls.2023.1275018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/08/2023] [Indexed: 12/28/2023]
Abstract
Phylogenetic analysis provides crucial insights into the evolutionary relationships and diversification patterns within specific taxonomic groups. In this study, we aimed to identify the phylogenetic relationships and explore the evolutionary history of Stipa using transcriptomic data. Samples of 12 Stipa species were collected from the Qinghai-Tibet Plateau and Mongolian Plateau, where they are widely distributed, and transcriptome sequencing was performed using their fresh spikelet tissues. Using bidirectional best BLAST analysis, we identified two sets of one-to-one orthologous genes shared between Brachypodium distachyon and the 12 Stipa species (9397 and 2300 sequences, respectively), as well as 62 single-copy orthologous genes. Concatenation methods were used to construct a robust phylogenetic tree for Stipa, and molecular dating was used to estimate divergence times. Our results indicated that Stipa originated during the Pliocene. In approximately 0.8 million years, it diverged into two major clades each consisting of native species from the Mongolian Plateau and the Qinghai-Tibet Plateau, respectively. The evolution of Stipa was closely associated with the development of northern grassland landscapes. Important external factors such as global cooling during the Pleistocene, changes in monsoonal circulation, and tectonic movements contributed to the diversification of Stipa. This study provided a highly supported phylogenetic framework for understanding the evolution of the Stipa genus in China and insights into its diversification patterns.
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Affiliation(s)
- Na Sha
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Zhiyong Li
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Qiang Sun
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Ying Han
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Li Tian
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Yantao Wu
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Xing Li
- Institute of Landscape and Environment, Inner Mongolia Academy of Forestry Science, Hohhot, Inner Mongolia, China
| | - Yabo Shi
- School of Resources and Environment, Baotou Teachers’ College, Baotou, Inner Mongolia, China
| | - Jinghui Zhang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Jiangtao Peng
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Lixin Wang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Zhenhua Dang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Cunzhu Liang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
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Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology. Sci Rep 2022; 12:9424. [PMID: 35676304 PMCID: PMC9177672 DOI: 10.1038/s41598-022-13528-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022] Open
Abstract
Iris ruthenica Ker Gawl. and I. uniflora Pall. ex Link, which are rare and endangered species in Korea, possess considerable horticultural and medicinal value among Korean irises. However, discrimination of the species is hindered by extensive morphological similarity. Thus, the aim of the present study was to identify discriminating features by comparing the species’ complete plastid genome (i.e., plastome) sequences and micromorphological features, including leaf margins, stomatal complex distribution (hypostomatic vs. amphistomatic leaves), anther stomata density, and tepal epidermal cell patterns. Plastome comparison revealed slightly divergent regions within intergenic spacer regions, and the most variable sequences, which were distributed in non-coding regions, could be used as molecular markers for the discrimination of I. ruthenica and I. uniflora. Phylogenetic analysis of the Iris species revealed that I. ruthenica and I. uniflora formed a well-supported clade. The comparison of plastomes and micromorphological features performed in this study provides useful information for elucidating taxonomic, phylogenetic, and evolutionary relationships in Iridaceae. Further studies, including those based on molecular cytogenetic approaches using species specific markers, will offer insights into species delimitation of the two closely related Iris species.
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Nobis M, Krzempek M, Nowak A, Gudkova PD, Klichowska E. Resurrection of Stipatremula and taxonomy of the high-alpine species from the Stipapurpurea complex (Poaceae, Pooideae). PHYTOKEYS 2022; 196:21-47. [PMID: 36762029 PMCID: PMC9849017 DOI: 10.3897/phytokeys.196.82598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/11/2022] [Indexed: 06/18/2023]
Abstract
Stipapurpurea is a high-alpine species that occurs in cryophilous steppes, semi-deserts and stony slopes, from the Tian Shan and Pamirian Plateau through Qinghai-Xizang Plateau to the Himalayas and is characterised by a great morphological variability. During the revision of specimens of the taxon, we observed that the pattern of this variability is linked to the geographical distribution of the specimens. Numerical analyses (PCA and UPGMA) revealed three groups of OTUs corresponding to three morphotypes within the S.purpurea complex. A set of macro- and micromorphological characters, supported by a map of general distributional ranges, are presented to distinguish each of the three taxa within the complex and we reassess the status of Lasiagrostistremula described by Ruprecht in 1869. As a result, Stipatremula, S.purpurea and S.arenosa were distinguished within the complex. The intermediate characters of S.arenosa may suggest its putative hybrid origin (S.tremula × S.purpurea), whereas the presence of extremely long florets may be an expression of the gigas effect. We propose two new combinations (S.tremula and S.arenosa), describe a new nothospecies (S.×ladakhensis) that originated from hybridisation between S.klimesii and S.purpurea s.l. and designate the lectotype for Ptilagrostissemenovii. An identification key and detailed morphological description of species from the S.purpurea complex are also presented.
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Affiliation(s)
- Marcin Nobis
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakowPoland
| | - Marta Krzempek
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakowPoland
| | - Arkadiusz Nowak
- Institute of Biology, University of Opole, 45–052 Opole, PolandUniversity of OpoleOpolePoland
- Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, 02–976 Warszawa, PolandCenter for Biological Diversity Conservation, Polish Academy of SciencesWarsawaPoland
| | - Polina D. Gudkova
- Research Laboratory ‘Herbarium’, National Research Tomsk State University, Lenin 36 Ave., 634050 Tomsk, RussiaTomsk State UniversityTomskRussia
- Institute of Biology, Altai State University, Lenin 61 Ave., 656049, Barnaul, RussiaAltai State UniversityBarnaulRussia
| | - Ewelina Klichowska
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakowPoland
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Baiakhmetov E, Guyomar C, Shelest E, Nobis M, Gudkova PD. The first draft genome of feather grasses using SMRT sequencing and its implications in molecular studies of Stipa. Sci Rep 2021; 11:15345. [PMID: 34321531 PMCID: PMC8319324 DOI: 10.1038/s41598-021-94068-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/24/2021] [Indexed: 11/22/2022] Open
Abstract
The Eurasian plant Stipa capillata is the most widespread species within feather grasses. Many taxa of the genus are dominants in steppe plant communities and can be used for their classification and in studies related to climate change. Moreover, some species are of economic importance mainly as fodder plants and can be used for soil remediation processes. Although large-scale molecular data has begun to appear, there is still no complete or draft genome for any Stipa species. Thus, here we present a single-molecule long-read sequencing dataset generated using the Pacific Biosciences Sequel System. A draft genome of about 1004 Mb was obtained with a contig N50 length of 351 kb. Importantly, here we report 81,224 annotated protein-coding genes, present 77,614 perfect and 58 unique imperfect SSRs, reveal the putative allopolyploid nature of S. capillata, investigate the evolutionary history of the genus, demonstrate structural heteroplasmy of the chloroplast genome and announce for the first time the mitochondrial genome in Stipa. The assembled nuclear, mitochondrial and chloroplast genomes provide a significant source of genetic data for further works on phylogeny, hybridisation and population studies within Stipa and the grass family Poaceae.
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Affiliation(s)
- Evgenii Baiakhmetov
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland. .,Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., Tomsk, 634050, Russia.
| | - Cervin Guyomar
- German Centre for Integrative Biodiversity Research (iDiv), Puschstrasse 4, 04103, Leipzig, Germany.,Institute for Genetics, Environment and Plant Protection (IGEPP), Agrocampus Ouest, INRAE, University of Rennes 1, 35650, Le Rheu, France
| | - Ekaterina Shelest
- German Centre for Integrative Biodiversity Research (iDiv), Puschstrasse 4, 04103, Leipzig, Germany.,Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland. .,Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., Tomsk, 634050, Russia.
| | - Polina D Gudkova
- Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., Tomsk, 634050, Russia.,Department of Biology, Altai State University, Lenin 61 Ave., Barnaul, Russia, 656049
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