High-quality wild barley genome assemblies and annotation with Nanopore long reads and Hi-C sequencing data

Rui Pan; Haifei Hu; Yuhui Xiao; Le Xu; Yanhao Xu; Kai Ouyang; Chengdao Li; Tianhua He; Wenying Zhang

doi:10.1038/s41597-023-02434-2

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High-quality wild barley genome assemblies and annotation with Nanopore long reads and Hi-C sequencing data

Journal article

Open access

Peer reviewed

High-quality wild barley genome assemblies and annotation with Nanopore long reads and Hi-C sequencing data

Rui Pan, Haifei Hu, Yuhui Xiao, Le Xu, Yanhao Xu, Kai Ouyang, Chengdao Li, Tianhua He and Wenying Zhang

Scientific data, Vol.10(1), 535

2023

DOI: https://doi.org/10.1038/s41597-023-02434-2

PMID: 37563167

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Abstract

Data Descriptor

Plant ecology

Plant evolution

Wild barley, from “Evolution Canyon (EC)” in Mount Carmel, Israel, are ideal models for cereal chromosome evolution studies. Here, the wild barley EC_S1 is from the south slope with higher daily temperatures and drought, while EC_N1 is from the north slope with a cooler climate and higher relative humidity, which results in a differentiated selection due to contrasting environments. We assembled a 5.03 Gb genome with contig N50 of 3.53 Mb for wild barley EC_S1 and a 5.05 Gb genome with contig N50 of 3.45 Mb for EC_N1 using 145 Gb and 160.0 Gb Illumina sequencing data, 295.6 Gb and 285.35 Gb Nanopore sequencing data and 555.1 Gb and 514.5 Gb Hi-C sequencing data, respectively. BUSCOs and CEGMA evaluation suggested highly complete assemblies. Using full-length transcriptome data, we predicted 39,179 and 38,373 high-confidence genes in EC_S1 and EC_N1, in which 93.6% and 95.2% were functionally annotated, respectively. We annotated repetitive elements and non-coding RNAs. These two wild barley genome assemblies will provide a rich gene pool for domesticated barley.

Details

Title: High-quality wild barley genome assemblies and annotation with Nanopore long reads and Hi-C sequencing data
Authors/Creators: Rui Pan - Yangtze University
Haifei Hu - Murdoch University
Yuhui Xiao - Grandomics (China)
Le Xu - Yangtze University
Yanhao Xu - Yangtze University
Kai Ouyang - Grandomics (China)
Chengdao Li - Murdoch University, Centre for Crop and Food Innovation
Tianhua He - Murdoch University, Centre for Crop and Food Innovation
Wenying Zhang - Yangtze University
Publication Details: Scientific data, Vol.10(1), 535
Publisher: Nature Publishing Group UK
Identifiers: 991005599067207891
Murdoch Affiliation: State Agricultural Biotechnology Centre; Western Crop Genetics Alliance
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.1543 Flow Cytometry
Web Of Science research areas: Biotechnology & Applied Microbiology
ESI research areas: Biology & Biochemistry