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Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron

Authors
  • Wang, Mingcheng1
  • Zhang, Lei2
  • Tong, Shaofei3
  • Jiang, Dechun4
  • Fu, Zhixi5
  • 1 Institute for Advanced Study, Chengdu University, China , (China)
  • 2 Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, China , (China)
  • 3 MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, China , (China)
  • 4 CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, China , (China)
  • 5 College of Life Sciences, Sichuan Normal University, China , (China)
Type
Published Article
Journal
DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Publisher
Oxford University Press
Publication Date
Mar 10, 2022
Volume
29
Issue
2
Identifiers
DOI: 10.1093/dnares/dsac006
PMID: 35266513
PMCID: PMC8946665
Source
PubMed Central
Keywords
Disciplines
  • AcademicSubjects/MED00774
  • AcademicSubjects/SCI01140
License
Unknown

Abstract

Haloxylon ammodendron is a xerophytic perennial shrub or small tree that has a high ecological value in anti-desertification due to its high tolerance to drought and salt stress. Here, we report a high-quality, chromosome-level genome assembly of H. ammodendron by integrating PacBio’s high-fidelity sequencing and Hi-C technology. The assembled genome size was 685.4 Mb, of which 99.6% was assigned to nine pseudochromosomes with a contig N50 value of 23.6 Mb. Evolutionary analysis showed that both the recent substantial amplification of long terminal repeat retrotransposons and tandem gene duplication may have contributed to its genome size expansion and arid adaptation. An ample amount of low-GC genes was closely related to functions that may contribute to the desert adaptation of H. ammodendron . Gene family clustering together with gene expression analysis identified differentially expressed genes that may play important roles in the direct response of H. ammodendron to water-deficit stress. We also identified several genes possibly related to the degraded scaly leaves and well-developed root system of H. ammodendron . The reference-level genome assembly presented here will provide a valuable genomic resource for studying the genome evolution of xerophytic plants, as well as for further genetic breeding studies of H. ammodendron .

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