Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae

Abstract

Kobresia plants are important forage resources in the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. Therefore, it is beneficial to obtain Kobresia genome resources and study the adaptive characteristics of Kobresia plants in the Qinghai-Tibetan Plateau. We assembled the genome of Kobresia littledalei C. B. Clarke, which was about 373.85 Mb in size. 96.82% of the bases were attached to 29 pseudo-chromosomes, combining PacBio, Illumina and Hi-C sequencing data. Additional investigation of the annotation identified 23,136 protein-coding genes. 98.95% of these were functionally annotated. According to phylogenetic analysis, K. littledalei in Cyperaceae separated from Poaceae about 97.6 million years ago after separating from Ananas comosus in Bromeliaceae about 114.3mya. For K. littledalei, we identified a high-quality genome at the chromosome level. This is the first time a reference genome has been established for a species of Cyperaceae. This genome will help additional studies focusing on the processes of plant adaptation to environments with high altitude and cold weather.

Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication

“…The most recent common ancestor of rice and sorghum had 32 Dof genes We inventoried Dof genes in rice (Figure 1, Table 1) in relation to their homeologs in sorghum, which split from rice 50 MYA (Salse et al, 2008), and Kobresia, which split from rice 97 MYA (Can et al, 2020). Rice and sorghum each have 30 Dof genes, whereas Kobresia has 25 Dof genes (Table 1, Table S1 and S2).…”

“…(a) Timeline of events leading to modern Kobresia littledalei, rice, and Sorghum bicolor, which currently have 25, 30, and 30 Dof genes, respectively. The most recent common ancestor of Kobresia and the two crop species was approximately 97 MYA (Can et al, 2020). The Rho WGD event in grasses was 70 MYA (Paterson et al, 2004).…”

“…Such comparisons for deeper WGD events have been difficult previously owing to the absence of appropriate outgroups. This has been particularly true for rice, where the closest sequenced outgroup genomes were pineapple and banana, prior to the recent publication of the genome for K. littledalei (Can et al, 2020). Kobresia is a lineage that split 97 MYA from the ancestor of rice, and this split therefore took place only 27 million years prior to the major WGD event 70 MYA in the grasses.…”

“…The genome of the sedge Kobresia littledalei (Can et al, 2020), hereafter 'Kobresia', fills a critical gap in the evolution of the monocots in that it represents a lineage that split 97 MYA from the grasses, which is only 27 million years prior to the major grass WGD event 70 MYA. Before publication of this genome, the closest sequenced genomes were pineapple (Ananas comosus) and banana (Musa acuminata), which are older diverged monocot lineages with extensive genomic rearrangements that complicate homeolog pairing.…”

Boundary domain genes were recruited to suppress bract growth and promote branching in maize

“…The process described above was repeated, but using only the genes included in the subclade as an input to MAFFT. Finally, tsh1 orthologous sequences identified from the recently published Cyperus littledalei genome (79) were manually aligned to the final alignment using Mesquite v.3.61, and this alignment was used to create the tree using IQTree as described above.…”