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

Scientific Data
Muyou CanGuangpeng Qu

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.

References

Apr 25, 1997·Journal of Molecular Biology·C Burge, S Karlin
Dec 24, 1998·Nucleic Acids Research·G Benson
May 18, 2004·BMC Bioinformatics·Ian Korf
May 18, 2004·Bioinformatics·W H MajorosS L Salzberg
May 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·A H PatersonB A Chapman
Jun 18, 2005·Bioinformatics·Alkes L PricePavel A Pevzner
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Apr 26, 2008·Science·Haibao TangAndrew H Paterson
May 17, 2008·International Journal of Plant Genomics·Ana Conesa, Stefan Götz
Mar 11, 2009·Current Protocols in Bioinformatics·Maja Tarailo-Graovac, Nansheng Chen
Aug 20, 2010·BMC Bioinformatics·L Steven JohnsonElon Portugaly
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Nov 5, 2013·Nature Biotechnology·Joshua N BurtonJay Shendure
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
Nov 28, 2014·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Jan 24, 2015·The New Phytologist·Susana MagallónTania Hernández-Hernández
Jan 28, 2015·GigaScience·Naim MatasciGane Ka-Shu Wong
Jun 6, 2015·Mobile DNA·Weidong BaoOleksiy Kohany
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Sep 24, 2015·Genome Biology·Kadir Caner Akdemir, Lynda Chin
Nov 3, 2015·Nature Genetics·Ray MingQingyi Yu
Dec 2, 2015·Genome Biology·Nicolas ServantEmmanuel Barillot
Feb 3, 2016·F1000Research·Steven WingettSimon Andrews
Nov 1, 2016·Nature Methods·Chen-Shan ChinMichael C Schatz
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The UniProt Consortium
Oct 10, 2018·Nature Genetics·Jisen ZhangRay Ming
Dec 1, 2018·BMC Bioinformatics·Michael J RoachAnthony R Borneman
Jan 27, 2019·Nature Communications·Changsong ZouHeng Zhang

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Citations

Sep 30, 2021·The Plant Journal : for Cell and Molecular Biology·Luyao YuMilton Brian Traw

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Datasets Mentioned

BETA
SRP198441

Methods Mentioned

BETA
Hi-seq
Hi-C
Illumina
PCR
RNA-seq

Software Mentioned

Lachesis
PAML
HiC
Pro
HiCUP
EVM
McScan
OrthoFinder
SOAPdenovo
HMMER

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