Genome-Wide Identification, Characterization, and Comparative Analysis of NLR Resistance Genes in Coffea spp
The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes...
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Published in | Frontiers in plant science Vol. 13; p. 868581 |
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Main Authors | , , , , , |
Format | Journal Article |
Language | English |
Published |
Frontiers Media S.A
07.07.2022
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Subjects | |
Online Access | Get full text |
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Summary: | The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (
Coffea canephora
,
Coffea eugenioides
and their interspecific hybrid
Coffea arabica
). A total of 1311 non-redundant NLR loci were identified in
C. arabica
, 927 in
C. canephora
, and 1079 in
C. eugenioides
, of which 809, 562, and 695 are complete loci, respectively. The NLR-Annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. The
C. arabica
genome presented a smaller number of NLR loci when compared to the sum of the parental genomes (
C. canephora
, and
C. eugenioides
). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared between
C. arabica
and the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: Maria Raffaella Ercolano, University of Naples Federico II, Italy Reviewed by: Marta Grech-Baran, Institute of Biochemistry and Biophysics (PAN), Poland; Vania Michelotti, Council for Agricultural and Economics Research (CREA), Italy These authors have contributed equally to this work and share last authorship This article was submitted to Plant Pathogen Interactions, a section of the journal Frontiers in Plant Science |
ISSN: | 1664-462X 1664-462X |
DOI: | 10.3389/fpls.2022.868581 |