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.

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

“…However, it’s noteworthy that only 19 branches garnered support levels exceeding 50% ( Krawczyk et al., 2017 ). Similarly, Baiakhmetov constructed phylogenetic relationships for 14 Stipa species using nucleolar organizing regions (NORs), and their findings also indicated relatively low support in the resulting tree ( Baiakhmetov et al., 2021b ). It appears that there is a paradox in Stipa genus phylogenetic research.…”

“…Later, Baiakhmetov employed a genome-wide approach to obtain thousands of SNP genotypes for a phylogenetic analysis of a population comprising five Stipa species. The results indicated that fewer than half of the branches could be supported with a value of ≥0.8 ( Baiakhmetov et al., 2021b ). In our study, the high-confidence phylogenetic trees of Stipa were obtained from dozens and thousands of protein-coding genes, with almost 100% support for all branches ( Figure 2 ).…”

“…However, S. breviflora , a member of Sect. Barbatae Junge, typically does not cluster within this section but is placed in non-QTP branches ( Peng, 2015 ; Nobis et al., 2020 ; Baiakhmetov et al., 2021b ; Krawczyk et al., 2022 ). Similarly, other members of Sect.…”

“…Rapid progress in sequencing technologies has provided significantly increased access to extensive genetic information. In recent years, there has been a notable expansion in research methodologies, including the application of complete chloroplast genomes ( Krawczyk et al., 2018 ; Krawczyk et al., 2022 ), thousands of Single Nucleotide Polymorphisms (SNPs) genotyping using genome-wide ( Baiakhmetov et al., 2021b ), and the exploration of nucleolar organizing regions (NORs) in the genomic analysis of Stipa ( Baiakhmetov et al., 2021a ). These phylogenetic studies are providing more comprehensive insights than earlier research, resulting in new progress regarding the phylogenetic relationships of species within the Stipa genus ( Krawczyk et al., 2018 ; Baiakhmetov et al., 2021b ; Krawczyk et al., 2022 ).…”

“…Compared with genomic sequencing, transcriptome sequencing efficiently provides significant-high-quality data regarding protein-coding genes, making it particularly suitable for studying nonmodel organisms ( Wickett et al., 2014 ; Zimmer and Wen, 2015 ; Zeng et al., 2017 ; Baiakhmetov et al., 2021b ). Comparative transcriptomics has emerged as an effective method for evolutionary analyses in plants ( Cheng et al., 2018 ; One Thousand Plant Transcriptomes Initiative, 2019 ; Kapli et al., 2020 ) and has significantly promoted the identification of phylogenetic relationships among closely related species, as demonstrated in Cyathophora ( Wang et al., 2017 ), Trigonopedia ( Guo et al., 2018 ), and Daghestanica ( Xie et al., 2020 ).…”