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

Muyou Can,Dan Gao,Xing Zhao,Yuhong Bao,Hailing Zi,Li Wang,Magaweng Bai,Dengqunpei Tu,Wei Wei,Yunfei Liu,Guangpeng Qu,Shaofeng Chen

doi:10.1038/s41597-020-0518-3

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.

Highlights

Background & summaryThe Qinghai-Tibet Plateau, known as the “roof of the world”, is a vast alpine steppe with harsh natural conditions of high altitude, cold, intense ultraviolet radiation and drought
The genome assembly of K. littledalei provides an important framework for the additional study of adaption to environment of high altitude and cold weather and promote the protection of the environment in the Qinghai-Tibet Plateau
Leaf tissue of K. littledalei was used to construct a library for Hi-C analysis, and the NEBNext Ultra II DNA library Prep Kit from Illumina (NEB) was used to prepare the Hi-C library, which we sequenced using the Illumina HiSeq X Ten platform. 230,316,080 paired-end reads of 150 bp were obtained from the Illumina sequencing platform for the Hi-C library, which covered ~166.40X of the genome (Table s1)

Summary

OPEN Genome sequence of Kobresia

Muyou Can[1,2,4], Wei Wei[1,2,4], Hailing Zi3,4, Magaweng Bai[1,2], Yunfei Liu[1,2], Dan Gao[3], Dengqunpei Tu1,2, Yuhong Bao[1,2], Li Wang[1,2], Shaofeng Chen[1,2], Xing Zhao3,5 ✉ & Guangpeng Qu1,2,5 ✉. Kobresia plants are important forage resources in the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. 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. Additional investigation of the annotation identified 23,136 protein-coding genes. 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

Background & summary

Methods

Data Records

Findings

Additional information