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

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.

SUBMITTER: Baiakhmetov E

PROVIDER: S-EPMC8319324 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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

Baiakhmetov Evgenii E Guyomar Cervin C Shelest Ekaterina E Nobis Marcin M Gudkova Polina D PD

Scientific reports 20210728 1

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 pre ...[more]

PMID: 34321531

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Project description:BackgroundThe 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.ResultsOur 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.ConclusionsOur 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.

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

Publications

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

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