A new comprehensive annotation of leucine-rich repeat-containing receptors in rice
Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine-rich repeat (LRR)-containing receptor (LRR-CR) families: the LRR-receptor-like kinase (LRR-RLK), LRR-receptor-like protein (LRR-RLP) and nucleotide-binding LRR receptor (NLR). Using lrrprofiler, a pipeline that we developed to annotate and classify these proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies that we observed for LRR-CR gene models led us to perform an in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a cultivar that is closely related to Nipponbare, using an optimized strategy. Here, we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to 'functional' and 'structural' annotations, we propose that the community adopts this approach, which we call 'comprehensive' annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR genes in order to promote their use in breeding future resilient varieties.
Main Authors: | , , , , , , |
---|---|
Format: | article biblioteca |
Language: | eng |
Subjects: | F30 - Génétique et amélioration des plantes, H20 - Maladies des plantes, phytogénétique, Oryza sativa, résistance aux maladies, leucine, http://aims.fao.org/aos/agrovoc/c_49985, http://aims.fao.org/aos/agrovoc/c_5438, http://aims.fao.org/aos/agrovoc/c_2328, http://aims.fao.org/aos/agrovoc/c_4292, |
Online Access: | http://agritrop.cirad.fr/599664/ http://agritrop.cirad.fr/599664/1/tpj.15456.pdf |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cirad-fr-599664 |
---|---|
record_format |
koha |
spelling |
dig-cirad-fr-5996642024-05-02T12:55:36Z http://agritrop.cirad.fr/599664/ http://agritrop.cirad.fr/599664/ A new comprehensive annotation of leucine-rich repeat-containing receptors in rice. Gottin Celine, Diévart Anne, Summo Marilyne, Droc Gaëtan, Périn Christophe, Ranwez Vincent, Chantret Nathalie. 2021. Plant Journal, 108 (2) : 492-508.https://doi.org/10.1111/tpj.15456 <https://doi.org/10.1111/tpj.15456> A new comprehensive annotation of leucine-rich repeat-containing receptors in rice Gottin, Celine Diévart, Anne Summo, Marilyne Droc, Gaëtan Périn, Christophe Ranwez, Vincent Chantret, Nathalie eng 2021 Plant Journal F30 - Génétique et amélioration des plantes H20 - Maladies des plantes phytogénétique Oryza sativa résistance aux maladies leucine http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_4292 Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine-rich repeat (LRR)-containing receptor (LRR-CR) families: the LRR-receptor-like kinase (LRR-RLK), LRR-receptor-like protein (LRR-RLP) and nucleotide-binding LRR receptor (NLR). Using lrrprofiler, a pipeline that we developed to annotate and classify these proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies that we observed for LRR-CR gene models led us to perform an in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a cultivar that is closely related to Nipponbare, using an optimized strategy. Here, we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to 'functional' and 'structural' annotations, we propose that the community adopts this approach, which we call 'comprehensive' annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR genes in order to promote their use in breeding future resilient varieties. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/599664/1/tpj.15456.pdf text cc_by_nc info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc/4.0/ https://doi.org/10.1111/tpj.15456 10.1111/tpj.15456 info:eu-repo/semantics/altIdentifier/doi/10.1111/tpj.15456 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1111/tpj.15456 info:eu-repo/semantics/dataset/purl/https://doi.org/10.5281/zenodo.5110015 info:eu-repo/semantics/reference/purl/https://rice-genome-hub.southgreen.fr/content/geloc |
institution |
CIRAD FR |
collection |
DSpace |
country |
Francia |
countrycode |
FR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cirad-fr |
tag |
biblioteca |
region |
Europa del Oeste |
libraryname |
Biblioteca del CIRAD Francia |
language |
eng |
topic |
F30 - Génétique et amélioration des plantes H20 - Maladies des plantes phytogénétique Oryza sativa résistance aux maladies leucine http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_4292 F30 - Génétique et amélioration des plantes H20 - Maladies des plantes phytogénétique Oryza sativa résistance aux maladies leucine http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_4292 |
spellingShingle |
F30 - Génétique et amélioration des plantes H20 - Maladies des plantes phytogénétique Oryza sativa résistance aux maladies leucine http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_4292 F30 - Génétique et amélioration des plantes H20 - Maladies des plantes phytogénétique Oryza sativa résistance aux maladies leucine http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_4292 Gottin, Celine Diévart, Anne Summo, Marilyne Droc, Gaëtan Périn, Christophe Ranwez, Vincent Chantret, Nathalie A new comprehensive annotation of leucine-rich repeat-containing receptors in rice |
description |
Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine-rich repeat (LRR)-containing receptor (LRR-CR) families: the LRR-receptor-like kinase (LRR-RLK), LRR-receptor-like protein (LRR-RLP) and nucleotide-binding LRR receptor (NLR). Using lrrprofiler, a pipeline that we developed to annotate and classify these proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies that we observed for LRR-CR gene models led us to perform an in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a cultivar that is closely related to Nipponbare, using an optimized strategy. Here, we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to 'functional' and 'structural' annotations, we propose that the community adopts this approach, which we call 'comprehensive' annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR genes in order to promote their use in breeding future resilient varieties. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes H20 - Maladies des plantes phytogénétique Oryza sativa résistance aux maladies leucine http://aims.fao.org/aos/agrovoc/c_49985 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_4292 |
author |
Gottin, Celine Diévart, Anne Summo, Marilyne Droc, Gaëtan Périn, Christophe Ranwez, Vincent Chantret, Nathalie |
author_facet |
Gottin, Celine Diévart, Anne Summo, Marilyne Droc, Gaëtan Périn, Christophe Ranwez, Vincent Chantret, Nathalie |
author_sort |
Gottin, Celine |
title |
A new comprehensive annotation of leucine-rich repeat-containing receptors in rice |
title_short |
A new comprehensive annotation of leucine-rich repeat-containing receptors in rice |
title_full |
A new comprehensive annotation of leucine-rich repeat-containing receptors in rice |
title_fullStr |
A new comprehensive annotation of leucine-rich repeat-containing receptors in rice |
title_full_unstemmed |
A new comprehensive annotation of leucine-rich repeat-containing receptors in rice |
title_sort |
new comprehensive annotation of leucine-rich repeat-containing receptors in rice |
url |
http://agritrop.cirad.fr/599664/ http://agritrop.cirad.fr/599664/1/tpj.15456.pdf |
work_keys_str_mv |
AT gottinceline anewcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT dievartanne anewcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT summomarilyne anewcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT drocgaetan anewcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT perinchristophe anewcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT ranwezvincent anewcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT chantretnathalie anewcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT gottinceline newcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT dievartanne newcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT summomarilyne newcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT drocgaetan newcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT perinchristophe newcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT ranwezvincent newcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice AT chantretnathalie newcomprehensiveannotationofleucinerichrepeatcontainingreceptorsinrice |
_version_ |
1798165069512572928 |