Identification and expression profiling analysis of NBS–LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage View Full Text


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Article Info

DATE

2019-05-04

AUTHORS

Zeci Liu, Jianming Xie, Huiping Wang, Xionghui Zhong, Hailong Li, Jihua Yu, Jungen Kang

ABSTRACT

As one of the most important resistance (R) gene families in plants, the NBS–LRR genes, encoding proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains, play significant roles in resisting pathogens. The published genomic data for cabbage (Brassica oleracea L.) provide valuable data to identify and characterize the genomic organization of cabbage NBS–LRR genes. Ultimately, we identified 105 TIR (N-terminal Toll/interleukin-1 receptor)-NBS–LRR (TNL) genes and 33 CC (coiled-coil)-NBS–LRR (CNL) genes. Further research indicated that 50.7% of the 138 NBS–LRR genes exist in 27 clusters and there are large differences among the gene structures and protein characteristics. Conserved motif and phylogenetic analysis showed that the structures of TNLs and CNLs were similar, with some differences. These NBS–LRRs are evolved under negative selection and mostly arose from whole-genome duplication events during evolution. Tissue-expression profiling of NBS–LRR genes revealed that 37.1% of the TNL genes are highly or specifically expressed in roots, especially the genes on chromosome 7 (76.5%). Digital gene expression and reverse transcription PCR analyses revealed the expression patterns of the NBS–LRR genes upon challenge by Fusarium oxysporum f.sp. conglutinans: nine genes were upregulated, and five were downregulated. The major resistance gene Foc1 probably works together with the other four genes in the same cluster to resist F. oxysporum infection. More... »

PAGES

202

References to SciGraph publications

  • 2008-01-30. Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: Isolation, RFLP marker development, and physical mapping in BMC PLANT BIOLOGY
  • 2014-05-23. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes in NATURE COMMUNICATIONS
  • 2015-05-07. Identification and distribution of the NBS-LRR gene family in the Cassava genome in BMC GENOMICS
  • 2008-02-05. Genome-wide identification of NBS resistance genes in Populus trichocarpa in PLANT MOLECULAR BIOLOGY
  • 2007-10-23. Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis in BMC PLANT BIOLOGY
  • 2012-11-12. ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons in BIOLOGY DIRECT
  • 2016-01-26. A survey of best practices for RNA-seq data analysis in GENOME BIOLOGY
  • 2008-06-19. Recent duplications dominate NBS-encoding gene expansion in two woody species in MOLECULAR GENETICS AND GENOMICS
  • 2014-11-01. Loss and retention of resistance genes in five species of the Brassicaceae family in BMC PLANT BIOLOGY
  • 2018-02-21. Genome-scale examination of NBS-encoding genes in blueberry in SCIENTIFIC REPORTS
  • 2016-08-26. Erratum to: A survey of best practices for RNA-seq data analysis in GENOME BIOLOGY
  • 2000-12. A. thaliana genome in NATURE
  • 2009-09-28. TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders in BMC RESEARCH NOTES
  • 2011-08-28. The genome of the mesopolyploid crop species Brassica rapa in NATURE GENETICS
  • 2013-08-14. Development of InDel markers linked to Fusarium wilt resistance in cabbage in MOLECULAR BREEDING
  • 2006-11-16. Plant NBS-LRR proteins in pathogen sensing and host defense in NATURE IMMUNOLOGY
  • 2013-02-19. Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops in BMC GENOMICS
  • 2015-11-03. Cloning of novel rice blast resistance genes from two rapidly evolving NBS-LRR gene families in rice in PLANT MOLECULAR BIOLOGY
  • 2014-10-29. Map-based cloning of a candidate gene conferring Fusarium yellows resistance in Brassica oleracea in THEORETICAL AND APPLIED GENETICS
  • 2001-06. Plant pathogens and integrated defence responses to infection in NATURE
  • 2014-01-03. Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana in BMC GENOMICS
  • 2018-06-21. Identification of NBS-encoding genes linked to black rot resistance in cabbage (Brassica oleracea var. capitata) in MOLECULAR BIOLOGY REPORTS
  • 2016-07-28. Genome-Wide Identification and Characterization of Nucleotide-Binding Site (NBS) Resistance Genes in Pineapple in TROPICAL PLANT BIOLOGY
  • 2016-09-09. Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum in BMC GENETICS
  • 2018-02-19. Inactivation of the indole-diterpene biosynthetic gene cluster of Claviceps paspali by Agrobacterium-mediated gene replacement in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s13205-019-1714-8

    DOI

    http://dx.doi.org/10.1007/s13205-019-1714-8

    DIMENSIONS

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    PUBMED

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