Molecular Phylogenetics and Micromorphology of Australasian Stipeae (Poaceae, Subfamily Pooideae), and the Interrelation of Whole-Genome Duplication and Evolutionary Radiations in This Grass Tribe

Insights to the taxonomy and phylogeny of the genus Ptilagrostis worldwide (Poaceae, Stipeae) with a key to species identification, checklist and outlines for further studies

Ptilagrostis (false needlegrass) is a genus of high-mountain grasses distributed in Central and North-East Asia, as well as in North America. The phylogenetic position of the genus Ptilagrostis within the Stipeae is well defined based on micromorphological patterns of lemma epidermis and moleculs. However, there is a lack of a comprehensive taxonomic revision of the genus in its entire distribution range. In this study, we performed comprehensive analyses using integrative taxonomic methods, aiming at both micromorphological and macromorphological analyses, and molecular analyses based on SNPs obtained from DArT genome-wide sequencing, in which we considered all taxa representing the genus in order to establish phylogenetic relationships between its members. We analysed all species possessing the characteristic 'Ptilagrostis pattern' of the lemma epidermis, with a particular reference to species possessing the terminal segment of the awn (seta) covered by short (up to 1 mm long) hairs that, until now, were treated as representatives of the genus Achnatherum. Following with the result of our molecular, morphological and anatomical analyses, the genus Ptilagrostis is represented by 15 species, one subspecies and five varieties organised in three well supported phylogenetic clades corresponding to the three sections: Ptilagrostis, Barkworthia and Chenella. In this paper, we provide an original key to identifying false needlegrass species, together with a checklist containing the intrageneric species-organisation. In addition, for each species, we present the data regarding nomenclatural types, morphological description, and information on the geographical distribution, habitat preferences and altitudinal ranges. We proposed two new varieties within the genus Ptilagrostis, P.glabrifoliavar.himalayensis and P.concinnavar.xizangensis, and the new section Chenella comprising three species with awns scabrous or covered by very short hairs up to 0.3 mm long. Additionally, we transfer Stipachingii to Ptilagrostischingii, Achnatherumchingiivar.laxum to P.chingiivar.laxum, and Ptilagrostisconcinnasubsp.schischkinii to P.junatoviivar.schischkinii. Lectotypification was made for three taxa, Stipamongholicavar.minutiflora, P.czekanowskii, and P.tibetica.

Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia

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.

Elucidation of the evolutionary history of Stipa in China using comparative transcriptomic analysis

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.

Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology

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.

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.