Genome-Wide Identification, Characterization, and Comparative Analysis of <i>NLR</i> Resistance Genes in <i>Coffea spp.</i>

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Abstract

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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Alexandros Stamatakis (2014)

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

K Katoh (2002)

A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.

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The plant immune system.

Jonathan Jones, Jeffery Dangl (2006)

Many plant-associated microbes are pathogens that impair plant growth and reproduction. Plants respond to infection using a two-branched innate immune system. The first branch recognizes and responds to molecules common to many classes of microbes, including non-pathogens. The second responds to pathogen virulence factors, either directly or through their effects on host targets. These plant immune systems, and the pathogen molecules to which they respond, provide extraordinary insights into molecular recognition, cell biology and evolution across biological kingdoms. A detailed understanding of plant immune function will underpin crop improvement for food, fibre and biofuels production.

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Author and article information

Contributors

Mariana de Lima Santos: URI : http://loop.frontiersin.org/people/1489863/overview

Gabriel Sérgio Costa Alves: URI : http://loop.frontiersin.org/people/1020164/overview

Jose Carlos Huguet-Tapia: URI : http://loop.frontiersin.org/people/474801/overview

Márcio Fernando Ribeiro de Júnior Resende: URI : http://loop.frontiersin.org/people/541243/overview

Jeremy Todd Brawner: URI : http://loop.frontiersin.org/people/1847463/overview

Journal

Journal ID (nlm-ta): Front Plant Sci

Journal ID (iso-abbrev): Front Plant Sci

Journal ID (publisher-id): Front. Plant Sci.

Title: Frontiers in Plant Science

Publisher: Frontiers Media S.A.

ISSN (Electronic): 1664-462X

Publication date (Electronic): 07 July 2022

Publication date Collection: 2022

Volume: 13

Electronic Location Identifier: 868581

Affiliations

[1] ¹Laboratório de Fisiologia do Parasitismo, Faculdade de Ciências Agrárias, Departamento de Fitopatologia, Universidade Federal de Lavras , Lavras, Brazil

[2] ²Laboratório de Processos Biológicos e Produtos Biotecnológicos, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília , Brasília, Brazil

[3] ³Institute of Food and Agricultural Sciences, Department of Plant Pathology, University of Florida , Gainesville, FL, United States

[4] ⁴Institute of Food and Agricultural Sciences, Horticultural Sciences Department, University of Florida , Gainesville, FL, United States

Author notes

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

*Correspondence: Mariana de Lima Santos, santos-ml@ 123456outlook.com

Jeremy Todd Brawner, jeremybrawner@ 123456ufl.edu

^†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

Article

DOI: 10.3389/fpls.2022.868581

PMC ID: 9301388

PubMed ID: 35874027

SO-VID: 89036c38-c2ac-49dd-b65f-b39938a910f3

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

History

Date received : 02 February 2022

Date accepted : 09 June 2022

Page count

Figures: 5, Tables: 1, Equations: 0, References: 84, Pages: 16, Words: 12051

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Genome-Wide Identification, Characterization, and Comparative Analysis of NLR Resistance Genes in Coffea spp.

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