Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae - PubMed (original) (raw)

doi: 10.1038/s41597-020-0518-3.

Wei Wei # 1 2, Hailing Zi # 3, Magaweng Bai 1 2, Yunfei Liu 1 2, Dan Gao 3, Dengqunpei Tu 1 2, Yuhong Bao 1 2, Li Wang 1 2, Shaofeng Chen 1 2, Xing Zhao 4, Guangpeng Qu 5 6

Affiliations

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

Muyou Can et al. Sci Data. 2020.

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1

Fig. 1

A representative individual of Kobresia littledalei.

Fig. 2

Fig. 2

Heat map of chromatin contact matrices generated by aligning a Hi-C dataset to the Kobresia littledalei genome. The frequency of interactions was calculated using a window size of 500 K.

Fig. 3

Fig. 3

Features of the Kobresia littledalei genome.

Fig. 4

Fig. 4

The phylogenetic relationships and divergence times of commelinid plants, and contraction and expansion of gene families. (a) The phylogenetic relationships and divergence times of commelinid plants. Phylogenetic reconstructions using concatenation of 1,077 genes and the maximum likelihood (ML) method with A. thaliana as the distant outgroup. Divergence times were estimated using the ‘mcmctree’ program incorporated in the PAML package. (b) Contraction and expansion of gene families. Numbers in green represent expanded families on this clade, and numbers in red represent contracted families on this clade.

Fig. 5

Fig. 5

Whole genome duplication events in Kobresia littledalei and other Poaceae plants.

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