Evidence for extensive hybridisation and past introgression events in feather grasses using genome-wide SNP genotyping.

BACKGROUND: The proper identification of feather grasses in nature is often limited due to phenotypic variability and high morphological similarity between many species. Among plausible factors influencing this issue are hybridisation and introgression recently detected in the genus. Nonetheless, to date, only a bounded set of taxa have been investigated using integrative taxonomy combining morphological and molecular data. Here, we report the first large-scale study on five feather grass species across several hybrid zones in Russia and Central Asia. In total, 302 specimens were sampled in the field and classified based on the current descriptions of these taxa. They were then genotyped with high density genome-wide markers and measured based on a set of morphological characters to delimitate species and assess levels of hybridisation and introgression. Moreover, we tested species for past introgression and estimated divergence times between them. RESULTS: Our findings demonstrated that 250 specimens represent five distinct species: S. baicalensis, S. capillata, S. glareosa, S. grandis and S. krylovii. The remaining 52 individuals provided evidence for extensive hybridisation between S. capillata and S. baicalensis, S. capillata and S. krylovii, S. baicalensis and S. krylovii, as well as to a lesser extent between S. grandis and S. krylovii, S. grandis and S. baicalensis. We detected past reticulation events between S. baicalensis, S. krylovii, S. grandis and inferred that diversification within species S. capillata, S. baicalensis, S. krylovii and S. grandis started ca. 130-96 kya. In addition, the assessment of genetic population structure revealed signs of contemporary gene flow between populations across species from the section Leiostipa, despite significant geographical distances between some of them. Lastly, we concluded that only 5 out of 52 hybrid taxa were properly identified solely based on morphology. CONCLUSIONS: Our results support the hypothesis that hybridisation is an important mechanism driving evolution in Stipa. As an outcome, this phenomenon complicates identification of hybrid taxa in the field using morphological characters alone. Thus, integrative taxonomy seems to be the only reliable way to properly resolve the phylogenetic issue of Stipa. Moreover, we believe that feather grasses may be a suitable genus to study hybridisation and introgression events in nature.

Preliminary checklist of the genus Festuca L. (Loliinae, Pooideae, Poaceae) in the Altai Mountains with outlines for further studies.

Here we present an updated checklist of the genus Festuca in the Altai Mountains (AM). The study was carried out on the abundant herbarium material and considered the latest published phylogenetic analyses. Festuca was revised within the scope of the fine-leaved group (clade) with two sections, sect. Aulaxyper and sect. Festuca. Two species, namely F.richardsonii and F.lenensis, were previously misidentified and are not present in the AM. Festucabrevissima is a new record for the Russian part of the AM and for the flora of Mongolia. In total, our revision shows that 17 species of fine-leaved fescues are present in the area of AM. In this paper, we provide a key to species identification, as well as illustrations of plants, habits, leaves, spikelets, and glumes. Information on nomenclature types, synonymy, flowering period, chromosome numbers, habitats, and general distribution along with distribution maps of the particular species within the AM are included.

First insight into the phylogeny of fine-leaved Festuca in the Altai Mountain Country based on genome-wide genotyping.

Festuca is one of the largest genera within the Poaceae family. Molecular phylogenies demonstrate that Festuca s.l. comprises two groups: broad- and fine-leaved species. The latter is the species-richest and taxonomically complicated group due to being paraphyletic. Here, we provide the first insight into the phylogeny of 17 fine-leaved species of Altai fescues. Based on genome-wide genotyping, the examined taxa were divided into three markedly differentiated clusters. The first cluster comprises species from the F. rubra complex, the second cluster includes the F. brachyphylla complex, and the third cluster contains taxa from the groups F. ovina, F. valesiaca, and F. kryloviana. Importantly, we detected a complex genetic pattern within the groups of F. valesiaca and F. kryloviana. Moreover, our findings underline a discrepancy between morphological and molecular data for some species distributed within the Altai Mountain Country. We suggest that in order to validate the current findings on the fine-leaved fescues, additional comprehensive research including morphological, karyological, and molecular methods is required. Nonetheless, our work provides a baseline for further investigations on the genus and studies on the floral diversity of Asia.

Resurrection of Stipatremula and taxonomy of the high-alpine species from the Stipapurpurea complex (Poaceae, Pooideae).

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.

The first draft genome of feather grasses using SMRT sequencing and its implications in molecular studies of Stipa.

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.

Virtual Herbarium ALTB: collection of vascular plants of the Altai Mountain Country.

BACKGROUND: The herbarium of the South-Siberian Botanical Garden of Altai State University (ALTB) houses the largest collection of plants from the Altai Mountain Country (AMC), an area that extends across Russia, Kazakhstan, Mongolia and China. The collection of ALTB includes more than 450,00 specimens, making it the seventh largest in Russia and the fourth largest amongst Russian university herbaria. Altai State University (ASU), the home of ALTB, is one of the most important centres of academic education and research in Siberia and the Russian Far East. It is a sociocultural centre that provides a distinguished learning environment for undergraduate and graduate students in many scholarly and professional fields, meeting the needs of today's knowledge-based post-industrial society and contributing to regional development. It actively promotes international cooperation and strategic collaboration amongst countries of the AMC in the fields of science, education and culture. In particular, the activities of the South-Siberian Botanical Garden include: development of measures to protect rare and endangered plant species, research on the flora and vegetation of the AMC, preparation and publication of a multi-volume work "Flora Altaica", monographic study of individual plant groups, conducting laboratory classes, summer practicals and special courses. The main purpose of this article is to attract the attention of the scientific community to the botanical research of transboundary territory of the Altai Mountain Country (Russia, Kazakhstan, China and Mongolia) and to the future development of digital plant collections in partnership with Global Biodiversity Information Facility (GBIF). NEW INFORMATION: The Virtual Herbarium ALTB (Russian interface - altb.asu.ru) is the largest digital collection of plants from the transboundary territory of the Altai Mountain Country and the main source of primary material for the "Flora Altaica" project (http://altaiflora.asu.ru/en/). Since 2017, when Altai State University became a GBIF data publisher, data from the Virtual Herbarium ALTB has been exported to the dataset "Virtual Herbarium ALTB (South-Siberian Botanical Garden)" in GBIF. Currently, it includes images and data from 22,466 vascular plants, of which 67% have geographic coordinates (accessed on 30.03.2021). Most of the specimens have been collected since 1977, with the most intensive collecting years being 1995-2008. In 2019, the label-data table of the Virtual Herbarium ALTB was modified to bring it into conformity with the Darwin Core specification (http://altb.asu.ru/). This effectively solved the major impediment to sharing plant diversity data from the AMC and adjacent regions in a multilingual environment.

Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae).

Hybridisation in the wild between closely related species is a common mechanism of speciation in the plant kingdom and, in particular, in the grass family. Here we explore the potential for natural hybridisation in Stipa (one of the largest genera in Poaceae) between genetically distant species at their distribution edges in Mountains of Central Asia using integrative taxonomy. Our research highlights the applicability of classical morphological and genome reduction approaches in studies on wild plant species. The obtained results revealed a new nothospecies, Stipa × lazkovii, which exhibits intermediate characters to S. krylovii and S. bungeana. A high-density DArTseq assay disclosed that S. × lazkovii is an F1 hybrid, and established that the plastid and mitochondrial DNA was inherited from S. bungeana. In addition, molecular markers detected a hybridisation event between morphologically and genetically distant species S. bungeana and probably S. glareosa. Moreover, our findings demonstrated an uncertainty on the taxonomic status of S. bungeana that currently belongs to the section Leiostipa, but it is genetically closer to S. breviflora from the section Barbatae. Finally, we noticed a discrepancy between the current molecular data with the previous findings on S. capillata and S. sareptana.

Synopsis of the tribe Stipeae (Poaceae) in Nepal.

In Nepal the Stipeae consists of six genera: Achnatherum, Orthoraphium, Piptatherum, Ptilagrostis, Stipa, Trikeraia, and 15 species. Two new combinations, Ptilagrostis duthiei (Hook. f.) M.Nobis & P.D.Gudkova and Achnatherum staintonii (Bor) M.Nobis & P.D.Gudkova, are proposed, and new country records for Stipa klimesii, Ptilagrostis dichotoma, Ptilagrostis concinna and Achnatherum jacquemontii are reported. The records of Stipa roborowskyi, S. przewalskyi, S. capillata, S. consanguinea, S. mongholica, and S. sibirica, previously thought to occur in Nepal were based on misidentifications, and these have been excluded from the list of Nepalese Stipeae. We present keys for the identification of genera and species, and a checklist including information on nomenclatural types, regional and national distribution, and habitat. A lectotype is designated for Stipa brandisii Mez.