A Chromosome-scale Reference Genome of Trifoliate Orange (Poncirus trifoliata) Provides Insights into Disease Resistance, Cold Tolerance and Genome Evolution in Citrus.

Publication Overview
TitleA Chromosome-scale Reference Genome of Trifoliate Orange (Poncirus trifoliata) Provides Insights into Disease Resistance, Cold Tolerance and Genome Evolution in Citrus.
AuthorsPeng Z, Bredeson JV, Wu GA, Shu S, Rawat N, Du D, Parajuli S, Yu Q, You Q, Rokhsar DS, Gmitter FG, Deng Z
TypeJournal Article
Journal NameThe Plant journal : for cell and molecular biology
Year2020
CitationPeng Z, Bredeson JV, Wu GA, Shu S, Rawat N, Du D, Parajuli S, Yu Q, You Q, Rokhsar DS, Gmitter FG, Deng Z. A Chromosome-scale Reference Genome of Trifoliate Orange (Poncirus trifoliata) Provides Insights into Disease Resistance, Cold Tolerance and Genome Evolution in Citrus.. The Plant journal : for cell and molecular biology. 2020 Sep 27.

Abstract

Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high-quality, chromosome-scale genome assembly of P. trifoliata. The 264.9 Mb assembly contains nine chromosomal pseudomolecules with 25,538 protein-coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species-specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C-repeat/DREB binding factor (CBF)-dependent and CBF-independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/Citrus hybrids shows a narrow genetic base in the U.S. germplasm collection and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non-dwarfing type. The high-quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.

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Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1365-313X
eISSN1365-313X
Publication Date2020 Sep 27
Journal AbbreviationPlant J.
DOI10.1111/tpj.14993
Elocation10.1111/tpj.14993
CopyrightThis article is protected by copyright. All rights reserved.
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
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PMID: PubMedPMID:32985030