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Wang ZF, Rouard M, Droc G, Heslop-Harrison P(JS, Ge XJ. Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes. Gigascience 2022; 12:giad005. [PMID: 36807539 PMCID: PMC9941839 DOI: 10.1093/gigascience/giad005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/24/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae. FINDINGS The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes. CONCLUSIONS The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.
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Affiliation(s)
- Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Gaetan Droc
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pat (J S) Heslop-Harrison
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Xue-Jun Ge
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Cenci A, Concepción-Hernández M, Guignon V, Angenon G, Rouard M. Genome-Wide Classification and Phylogenetic Analyses of the GDSL-Type Esterase/Lipase (GELP) Family in Flowering Plants. Int J Mol Sci 2022; 23:ijms232012114. [PMID: 36292971 PMCID: PMC9602515 DOI: 10.3390/ijms232012114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds of members per plant species. To facilitate functional transfer between them, we conducted a genome-wide classification of GELP in 46 plant species. First, we applied an iterative phylogenetic method using a selected set of representative angiosperm genomes (three monocots and five dicots) and identified 10 main clusters, subdivided into 44 orthogroups (OGs). An expert curation for gene structures, orthogroup composition, and functional annotation was made based on a literature review. Then, using the HMM profiles as seeds, we expanded the classification to 46 plant species. Our results revealed the variable evolutionary dynamics between OGs in which some expanded, mostly through tandem duplications, while others were maintained as single copies. Among these, dicot-specific clusters and specific amplifications in monocots and wheat were characterized. This approach, by combining manual curation and automatic identification, was effective in characterizing a large gene family, allowing the establishment of a classification framework for gene function transfer and a better understanding of the evolutionary history of GELP.
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Affiliation(s)
- Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
- Correspondence: (A.C.); (M.R.)
| | - Mairenys Concepción-Hernández
- Instituto de Biotecnología de las Plantas, Universidad Central “Marta Abreu” de Las Villas (UCLV), Carretera a Camajuaní km 5.5, Santa Clara C.P. 54830, Villa Clara, Cuba
- Research Group Plant Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Geert Angenon
- Research Group Plant Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
- Correspondence: (A.C.); (M.R.)
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Sardos J, Breton C, Perrier X, Van den Houwe I, Carpentier S, Paofa J, Rouard M, Roux N. Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas. Front Plant Sci 2022; 13:969220. [PMID: 36275535 PMCID: PMC9586208 DOI: 10.3389/fpls.2022.969220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 06/08/2023]
Abstract
Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.
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Affiliation(s)
- Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Catherine Breton
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Xavier Perrier
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Janet Paofa
- Papua New Guinea (PNG) National Agricultural Research Institute, Southern Regional Centre, Laloki, Port Moresby, Papua New Guinea
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
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4
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Droc G, Martin G, Guignon V, Summo M, Sempéré G, Durant E, Soriano A, Baurens FC, Cenci A, Breton C, Shah T, Aury JM, Ge XJ, Harrison PH, Yahiaoui N, D’Hont A, Rouard M. The banana genome hub: a community database for genomics in the Musaceae. Hortic Res 2022; 9:uhac221. [PMID: 36479579 PMCID: PMC9720444 DOI: 10.1093/hr/uhac221] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.
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Affiliation(s)
| | - Guillaume Martin
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Valentin Guignon
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Marilyne Summo
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Guilhem Sempéré
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France
- INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Eloi Durant
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Syngenta Seeds SAS, Saint-Sauveur, 31790, France
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, 34830, France
| | - Alexandre Soriano
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Alberto Cenci
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Catherine Breton
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Pat Heslop Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
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5
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Bayer PE, Petereit J, Durant É, Monat C, Rouard M, Hu H, Chapman B, Li C, Cheng S, Batley J, Edwards D. Wheat Panache: A pangenome graph database representing presence-absence variation across sixteen bread wheat genomes. Plant Genome 2022; 15:e20221. [PMID: 35644986 DOI: 10.1002/tpg2.20221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Bread wheat (Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence-absence variation (PAV) between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate because of the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess PAV between bread wheat genomes.
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Affiliation(s)
- Philipp E Bayer
- School of Biological Sciences, The Univ. of Western Australia, Perth, 6009, Australia
| | - Jakob Petereit
- School of Biological Sciences, The Univ. of Western Australia, Perth, 6009, Australia
| | - Éloi Durant
- DIADE, Univ. of Montpellier, CIRAD, IRD, Montpellier, 34830, France
- Syngenta Seeds S.A.S., 12 chemin de l'Hobit, Saint-Sauveur, 31790, France
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France
- French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, 34398, France
| | - Cécile Monat
- Syngenta Seeds S.A.S., 12 chemin de l'Hobit, Saint-Sauveur, 31790, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France
- French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, 34398, France
| | - Haifei Hu
- Western Crop Genetics Alliance, Murdoch Univ., 90 South Street, Murdoch, 6150, Australia
| | - Brett Chapman
- Western Crop Genetics Alliance, Murdoch Univ., 90 South Street, Murdoch, 6150, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, Murdoch Univ., 90 South Street, Murdoch, 6150, Australia
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jacqueline Batley
- School of Biological Sciences, The Univ. of Western Australia, Perth, 6009, Australia
| | - David Edwards
- School of Biological Sciences, The Univ. of Western Australia, Perth, 6009, Australia
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Summo M, Comte A, Martin G, Perelle P, Weitz EM, Droc G, Rouard M. GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics. Database (Oxford) 2022; 2022:6645005. [PMID: 35849014 PMCID: PMC9290862 DOI: 10.1093/database/baac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 11/12/2022]
Abstract
In silico chromosome painting is a technique by which contributions of distinct genetic groups are represented along chromosomes of hybrid individuals. This type of analysis is used to study the mechanisms by which these individuals were formed. Such techniques are well adapted to identify genetic groups contributing to these individuals as well as hybridization events. It can also be used to follow chromosomal recombinations that occurred naturally or were generated by selective breeding. Here, we present GeMo, a novel interactive web-based and user-oriented interface to visualize in a linear-based fashion results of in silico chromosome painting. To facilitate data input generation, a script to execute analytical commands is provided and an interactive data curation mode is supported to ensure consistency of the automated procedure. GeMo contains preloaded datasets from published studies on crop domestication but can be applied to other purposes, such as breeding programs Although only applied so far on plants, GeMo can handle data from animals as well. Database URL: https://gemo.southgreen.fr/
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Affiliation(s)
- Marilyne Summo
- CIRAD, UMR AGAP Institut , Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier, 34398, France
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
| | - Aurore Comte
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
- IRD, CIRAD, INRAE, Institut Agro, PHIM Plant Health Institute, Montpellier University , Montpellier 34398, France
| | - Guillaume Martin
- CIRAD, UMR AGAP Institut , Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier, 34398, France
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
| | - Pierrick Perelle
- CIRAD, UMR AGAP Institut , Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier, 34398, France
| | - Eric M Weitz
- Data Sciences Platform, Broad Institute of MIT and Harvard , 105 Broadway, Cambridge, MA 02142, USA
| | - Gaëtan Droc
- CIRAD, UMR AGAP Institut , Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier, 34398, France
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
| | - Mathieu Rouard
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
- Bioversity International, Parc Scientifique Agropolis II , 34397, Montpellier, France
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Acuña R, Rouard M, Leiva AM, Marques C, Olortegui JA, Ureta C, Cabrera-Pintado RM, Rojas JC, Lopez-Alvarez D, Cenci A, Cuellar WJ, Dita M. First Report of Fusarium oxysporum f. sp. cubense Tropical Race 4 Causing Fusarium Wilt in Cavendish Bananas in Peru. Plant Dis 2022; 106:PDIS09211951PDN. [PMID: 34918946 DOI: 10.1094/pdis-09-21-1951-pdn] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- R Acuña
- Servicio Nacional de Sanidad Agraria, Servicio Nacional de Sanidad Agraria del Peru, La Molina, Lima 12, Perú
| | - M Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France
| | - A M Leiva
- Alliance of Bioversity International and CIAT, Cali, 763537, Colombia
| | - C Marques
- Servicio Nacional de Sanidad Agraria, Servicio Nacional de Sanidad Agraria del Peru, La Molina, Lima 12, Perú
| | - J A Olortegui
- Servicio Nacional de Sanidad Agraria, Servicio Nacional de Sanidad Agraria del Peru, La Molina, Lima 12, Perú
| | - C Ureta
- Servicio Nacional de Sanidad Agraria, Servicio Nacional de Sanidad Agraria del Peru, La Molina, Lima 12, Perú
| | | | - J C Rojas
- Instituto Nacional de Innovación Agraria, Lima, 2791, Peru
| | | | - A Cenci
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France
| | - W J Cuellar
- Alliance of Bioversity International and CIAT, Cali, 763537, Colombia
| | - M Dita
- Alliance of Bioversity International and CIAT, Cali, 763537, Colombia
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Drapal M, Perez-Fons L, Price EJ, Amah D, Bhattacharjee R, Heider B, Rouard M, Swennen R, Lopez-Lavalle LAB, Fraser PD. Datasets from harmonised metabolic phenotyping of root, tuber and banana crop. Data Brief 2022; 42:108041. [PMID: 35341032 PMCID: PMC8943254 DOI: 10.1016/j.dib.2022.108041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Biochemical characterisation of germplasm collections and crop wild relatives (CWRs) facilitates the assessment of biological potential and the selection of breeding lines for crop improvement. Data from the biochemical characterisation of staple root, tuber and banana (RTB) crops, i.e. banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas) and yam (Dioscorea spp.), using a metabolomics approach is presented. The data support the previously published research article “Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops” (Price et al., 2020) [1]. Diversity panels for each crop, which included a variety of species, accessions, landraces and CWRs, were characterised. The biochemical profile for potato was based on five elite lines under abiotic stress. Metabolites were extracted from the tissue of foliage and storage organs (tuber, root and banana pulp) via solvent partition. Extracts were analysed via a combination of liquid chromatography – mass spectrometry (LC-MS), gas chromatography (GC)-MS, high pressure liquid chromatography with photodiode array detector (HPLC-PDA) and ultra performance liquid chromatography (UPLC)-PDA. Metabolites were identified by mass spectral matching to in-house libraries comprised from authentic standards and comparison to databases or previously published literature.
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Affiliation(s)
- Margit Drapal
- Royal Holloway University of London, Surrey, TW20 0EX, United Kingdom
| | - Laura Perez-Fons
- Royal Holloway University of London, Surrey, TW20 0EX, United Kingdom
| | - Elliott J. Price
- Royal Holloway University of London, Surrey, TW20 0EX, United Kingdom
| | - Delphine Amah
- International Institute of Tropical Agriculture, PMB 5320, Ibadan, Nigeria
| | | | - Bettina Heider
- International Potato Center, La Molina, CP 1558, Lima, Peru
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001 Leuven, Belgium
- Bioversity International, Willem De Croylaan 42, B-3001 Leuven, Belgium
- International Institute of Tropical Agriculture. C/0 The Nelson Mandela African Institution of Science and Technology, P.O. Box 44, Arusha, Tanzania
| | | | - Paul D. Fraser
- Royal Holloway University of London, Surrey, TW20 0EX, United Kingdom
- Corresponding author. @FraserRhul
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Wang Z, Rouard M, Biswas MK, Droc G, Cui D, Roux N, Baurens FC, Ge XJ, Schwarzacher T, Heslop-Harrison P(JS, Liu Q. A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae. Gigascience 2022; 11:6576245. [PMID: 35488861 PMCID: PMC9055855 DOI: 10.1093/gigascience/giac027] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. FINDINGS Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11. CONCLUSIONS The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution.
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Affiliation(s)
- Ziwei Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France,French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Alliance Bioversity and CIAT, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gaetan Droc
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Alliance Bioversity and CIAT, CIRAD, INRAE, IRD, F-34398 Montpellier, France,CIRAD, UMR AGAP Institut, F-34398 Montpellier, France,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Dongli Cui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Pat (J S) Heslop-Harrison
- Correspondence address. Qing Liu. Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. Pat Heslop-Harrison. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE 7RH, UK Qing Liu. Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China E-mail:
| | - Qing Liu
- Correspondence address. Pat Heslop-Harrison. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE 7RH, UK. E-mail:
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10
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Fu N, Ji M, Rouard M, Yan HF, Ge XJ. Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships. BMC Genomics 2022; 23:223. [PMID: 35313810 PMCID: PMC8939231 DOI: 10.1186/s12864-022-08454-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/08/2022] [Indexed: 01/16/2023] Open
Abstract
Background Musaceae is an economically important family consisting of 70-80 species. Elucidation of the interspecific relationships of this family is essential for a more efficient conservation and utilization of genetic resources for banana improvement. However, the scarcity of herbarium specimens and quality molecular markers have limited our understanding of the phylogenetic relationships in wild species of Musaceae. Aiming at improving the phylogenetic resolution of Musaceae, we analyzed a comprehensive set of 49 plastomes for 48 species/subspecies representing all three genera of this family. Results Musaceae plastomes have a relatively well-conserved genomic size and gene content, with a full length ranging from 166,782 bp to 172,514 bp. Variations in the IR borders were found to show phylogenetic signals to a certain extent in Musa. Codon usage bias analysis showed different preferences for the same codon between species and three genera and a common preference for A/T-ending codons. Among the two genes detected under positive selection (dN/dS > 1), ycf2 was indicated under an intensive positive selection. The divergent hotspot analysis allowed the identification of four regions (ndhF-trnL, ndhF, matK-rps16, and accD) as specific DNA barcodes for Musaceae species. Bayesian and maximum likelihood phylogenetic analyses using full plastome resulted in nearly identical tree topologies with highly supported relationships between species. The monospecies genus Musella is sister to Ensete, and the genus Musa was divided into two large clades, which corresponded well to the basic number of n = x = 11 and n = x =10/9/7, respectively. Four subclades were divided within the genus Musa. A dating analysis covering the whole Zingiberales indicated that the divergence of Musaceae family originated in the Palaeocene (59.19 Ma), and the genus Musa diverged into two clades in the Eocene (50.70 Ma) and then started to diversify from the late Oligocene (29.92 Ma) to the late Miocene. Two lineages (Rhodochlamys and Australimusa) radiated recently in the Pliocene /Pleistocene periods. Conclusions The plastome sequences performed well in resolving the phylogenetic relationships of Musaceae and generated new insights into its evolution. Plastome sequences provided valuable resources for population genetics and phylogenetics at lower taxon. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08454-3.
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Affiliation(s)
- Ning Fu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Meiyuan Ji
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 5, France
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
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11
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Rijzaani H, Bayer PE, Rouard M, Doležel J, Batley J, Edwards D. The pangenome of banana highlights differences between genera and genomes. Plant Genome 2022; 15:e20100. [PMID: 34227250 DOI: 10.1002/tpg2.20100] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 05/19/2023]
Abstract
Banana (Musaceae family) has a complex genetic history and includes a genus Musa with a variety of cultivated clones with edible fruits, Ensete species that are grown for their edible corm, and monospecific Musella whose generic status has been questioned. The most commonly exported banana cultivars belong to Cavendish, a subgroup of Musa triploid cultivars, which is under threat by fungal pathogens, though there are also related species M. balbisiana Colla (B genome), M. textilis Née (T genome), and M. schizocarpa N. W. Simmonds (S genome), along with hybrids of these genomes, which potentially host genes of agronomic interest. Here we present the first cross-genus pangenome of banana, which contains representatives of the Musa and Ensete genera. Clusters based on gene presence-absence variation (PAV) clearly separate Musa and Ensete, while Musa is split further based on species. These results present the first pangenome study across genus boundaries and identifies genes that differentiate between Musaceae species, information that may support breeding programs in these crops.
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Affiliation(s)
- Habib Rijzaani
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- Indonesian Agency for Agricultural Research and Development, Jakarta, Indonesia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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12
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Sempéré G, Larmande P, Rouard M. Managing High-Density Genotyping Data with Gigwa. Methods Mol Biol 2022; 2443:415-427. [PMID: 35037218 DOI: 10.1007/978-1-0716-2067-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Next generation sequencing technologies enabled high-density genotyping for large numbers of samples. Nowadays SNP calling pipelines produce up to millions of such markers, but which need to be filtered in various ways according to the type of analyses. One of the main challenges still lies in the management of an increasing volume of genotyping files that are difficult to handle for many applications. Here, we provide a practical guide for efficiently managing large genomic variation data using Gigwa, a user-friendly, scalable and versatile application that may be deployed either remotely on web servers or on a local machine.
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Affiliation(s)
- Guilhem Sempéré
- CIRAD, UMR INTERTRYP, Montpellier, France
- INTERTRYP, Univ Montpellier, CIRAD, IRD, Montpellier, France
- French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France
| | - Pierre Larmande
- French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France.
- DIADE, Univ Montpellier, IRD, Montpellier, France.
| | - Mathieu Rouard
- French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
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13
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Durant É, Sabot F, Conte M, Rouard M. Panache: a Web Browser-Based Viewer for Linearized Pangenomes. Bioinformatics 2021; 37:4556-4558. [PMID: 34601567 PMCID: PMC8652104 DOI: 10.1093/bioinformatics/btab688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/28/2021] [Accepted: 09/24/2021] [Indexed: 11/15/2022] Open
Abstract
Motivation Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations come with their own challenges, and linearity remains a suitable option for user-friendliness. Results We introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective. Availability and implementation Panache is available at github.com/SouthGreenPlatform/panache under the MIT License.
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Affiliation(s)
- Éloi Durant
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, 34830, France.,Syngenta Seeds SAS, Saint-Sauveur, 31790, France.,Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France.,French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, 34398, France
| | - François Sabot
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, 34830, France.,French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, 34398, France
| | | | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France
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14
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Dufayard JF, Bocs S, Guignon V, Larivière D, Louis A, Oubda N, Rouard M, Ruiz M, de Lamotte F. RapGreen, an interactive software and web package to explore and analyze phylogenetic trees. NAR Genom Bioinform 2021; 3:lqab088. [PMID: 34568824 PMCID: PMC8459725 DOI: 10.1093/nargab/lqab088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
RapGreen is a modular software package targeted at scientists handling large datasets for phylogenetic analysis. Its primary function is the graphical visualization and exploration of large trees. In addition, RapGreen offers a tree pattern search function to seek evolutionary scenarios among large collections of phylogenetic trees. Other functionalities include tree reconciliation with a given species tree: the detection of duplication or loss events during evolution and tree rooting. Last but not least, RapGreen features the ability to integrate heterogeneous data while visualizing and otherwise analyzing phylogenetic trees.
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Affiliation(s)
- Jean-François Dufayard
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Valentin Guignon
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Delphine Larivière
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Alexandra Louis
- IBENS, Institut de Biologie de l’ENS, Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Nicolas Oubda
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Mathieu Rouard
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Manuel Ruiz
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Frédéric de Lamotte
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
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15
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Guignon V, Toure A, Droc G, Dufayard JF, Conte M, Rouard M. Correction to 'GreenPhylDB v5: a comparative pangenomic database for plant genomes'. Nucleic Acids Res 2021; 49:7203. [PMID: 34161571 PMCID: PMC8266608 DOI: 10.1093/nar/gkab564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France.,French Institute of Bioinformatics (IFB)--South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Abdel Toure
- Syngenta Seeds SAS, 31790 Saint-Sauveur, France
| | - Gaëtan Droc
- French Institute of Bioinformatics (IFB)--South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France.,AGAP, Univ de Montpellier, CIRAD, INRAE, Montpellier SupAgro, F-34398 Montpellier, France.,CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Jean-François Dufayard
- French Institute of Bioinformatics (IFB)--South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France.,AGAP, Univ de Montpellier, CIRAD, INRAE, Montpellier SupAgro, F-34398 Montpellier, France.,CIRAD, UMR AGAP, F-34398 Montpellier, France
| | | | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France.,French Institute of Bioinformatics (IFB)--South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
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16
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Cenci A, Sardos J, Hueber Y, Martin G, Breton C, Roux N, Swennen R, Carpentier SC, Rouard M. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas. Ann Bot 2021; 127:7-20. [PMID: 32104882 DOI: 10.1093/aob/mcaa032/5760888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security. METHODS Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes. KEY RESULTS Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups. CONCLUSIONS The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploids originated, and where cultivated M. balbisiana are abundant. The result of this study clarifies the classification of ABB cultivars, possibly leading to the revision of the classification of this subgroup.
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Affiliation(s)
- Alberto Cenci
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Julie Sardos
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Yann Hueber
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Guillaume Martin
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | | | - Nicolas Roux
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Rony Swennen
- Alliance Bioversity International - CIAT, Leuven, Belgium
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, c/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | | | - Mathieu Rouard
- Alliance Bioversity International - CIAT, Montpellier, France
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17
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Cenci A, Sardos J, Hueber Y, Martin G, Breton C, Roux N, Swennen R, Carpentier SC, Rouard M. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas. Ann Bot 2021; 127:7-20. [PMID: 32104882 PMCID: PMC7750727 DOI: 10.1093/aob/mcaa032] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security. METHODS Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes. KEY RESULTS Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups. CONCLUSIONS The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploids originated, and where cultivated M. balbisiana are abundant. The result of this study clarifies the classification of ABB cultivars, possibly leading to the revision of the classification of this subgroup.
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Affiliation(s)
- Alberto Cenci
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Julie Sardos
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Yann Hueber
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Guillaume Martin
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | | | - Nicolas Roux
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Rony Swennen
- Alliance Bioversity International - CIAT, Leuven, Belgium
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, c/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | | | - Mathieu Rouard
- Alliance Bioversity International - CIAT, Montpellier, France
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18
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McCouch S, Navabi ZK, Abberton M, Anglin NL, Barbieri RL, Baum M, Bett K, Booker H, Brown GL, Bryan GJ, Cattivelli L, Charest D, Eversole K, Freitas M, Ghamkhar K, Grattapaglia D, Henry R, Valadares Inglis MC, Islam T, Kehel Z, Kersey PJ, King GJ, Kresovich S, Marden E, Mayes S, Ndjiondjop MN, Nguyen HT, Paiva SR, Papa R, Phillips PWB, Rasheed A, Richards C, Rouard M, Amstalden Sampaio MJ, Scholz U, Shaw PD, Sherman B, Staton SE, Stein N, Svensson J, Tester M, Montenegro Valls JF, Varshney R, Visscher S, von Wettberg E, Waugh R, Wenzl P, Rieseberg LH. Mobilizing Crop Biodiversity. Mol Plant 2020; 13:1341-1344. [PMID: 32835887 DOI: 10.1016/j.molp.2020.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
- Susan McCouch
- Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Zahra Katy Navabi
- DivSeek, Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada; Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, Nigeria
| | - Noelle L Anglin
- International Potato Center (CIP) 1895 Avenida La Molina, Lima Peru 12, Lima 15023, Peru
| | - Rosa Lia Barbieri
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK S7N 5A8, Canada
| | - Helen Booker
- Department of Plant Agriculture, University of Guelph, Rm 316, Crop Science Bldg, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - Gerald L Brown
- Genome Prairie, 111 Research Drive, Suite 101, Saskatoon, SK, S7N 3R2, Canada
| | - Glenn J Bryan
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Luigi Cattivelli
- CREA, Research Centre for Genomics and Bioinformatics, via San Protaso 302, Fiorenzuola d'Arda, 29017, Italy
| | - David Charest
- Genome British Columbia, 400-575 West 8th Avenue, Vancouver, BC, V5Z 0C4, Canada
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, Lee's Summit, MO, 64086, USA
| | - Marcelo Freitas
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Kioumars Ghamkhar
- Forage Science, Grasslands Research Centre, AgResearch, Palmerston North, 4410, New Zealand
| | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Maria Cleria Valadares Inglis
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Graham J King
- Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Stephen Kresovich
- Feed the Future Innovation Lab for Crop Improvement, 431 Weill Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Marden
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Sean Mayes
- Crops For the Future (UK) CIC 76-80 Baddow Road, Chelmsford, Essex, CM2 7PJ, UK
| | - Marie Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Mbe Research Station, Bouaké, 01 BP 2511 Bouaké, Côte d'Ivoire
| | - Henry T Nguyen
- University of Missouri, Division of Plant Sciences, 25 Agriculture Lab Bldg, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Samuel Rezende Paiva
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Roberto Papa
- Università Politecnica delle Marche, D3A-Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Via Brecce Bianche, 60131, Ancona, Italy
| | - Peter W B Phillips
- Johnson Shoyama Graduate School of Public Policy, University of Saskatchewan, 101 Diefenbaker Place, Saskatoon, S7N 5B8, Canada
| | - Awais Rasheed
- CIMMYT-China office, Beijing 100081, Beijing, P.R. China
| | - Christopher Richards
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason St, Fort Collins, CO, 80521, USA
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Maria Jose Amstalden Sampaio
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany
| | - Paul D Shaw
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Brad Sherman
- Law School, University of Queensland, St Lucia, QLD, 4072, Australia
| | - S Evan Staton
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; CiBreed - Center for Integrated Breeding Research, Department of Crop Sciences, Georg-August University Göttingen, Von Siebold Straße 8, D-37075 Göttingen, Germany
| | | | - Mark Tester
- King Abdullah University of Science & Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jose Francisco Montenegro Valls
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Rajeev Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru - 502 324, Telangana State, India
| | - Stephen Visscher
- Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Eric von Wettberg
- University of Vermont, 63 Carrigan Drive, Jeffords Hall, Burlington, VT, 05405, USA
| | - Robbie Waugh
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK; School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Peter Wenzl
- Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, 763537 Cali, Colombia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada.
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19
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Selby P, Abbeloos R, Backlund JE, Basterrechea Salido M, Bauchet G, Benites-Alfaro OE, Birkett C, Calaminos VC, Carceller P, Cornut G, Vasques Costa B, Edwards JD, Finkers R, Yanxin Gao S, Ghaffar M, Glaser P, Guignon V, Hok P, Kilian A, König P, Lagare JEB, Lange M, Laporte MA, Larmande P, LeBauer DS, Lyon DA, Marshall DS, Matthews D, Milne I, Mistry N, Morales N, Mueller LA, Neveu P, Papoutsoglou E, Pearce B, Perez-Masias I, Pommier C, Ramírez-González RH, Rathore A, Raquel AM, Raubach S, Rife T, Robbins K, Rouard M, Sarma C, Scholz U, Sempéré G, Shaw PD, Simon R, Soldevilla N, Stephen G, Sun Q, Tovar C, Uszynski G, Verouden M. BrAPI-an application programming interface for plant breeding applications. Bioinformatics 2020; 35:4147-4155. [PMID: 30903186 PMCID: PMC6792114 DOI: 10.1093/bioinformatics/btz190] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/23/2018] [Accepted: 03/20/2019] [Indexed: 12/04/2022] Open
Abstract
Motivation Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. Availability and implementation More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.
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Affiliation(s)
- Peter Selby
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | | | | | | | | | - Omar E Benites-Alfaro
- International Potato Center (CIP), Lima, Peru.,International Food Policy Research Institute (IFPRI), Washington DC, USA
| | | | - Viana C Calaminos
- International Rice Research Institute (IRRI), Los Baños, Laguna, The Philippines
| | - Pierre Carceller
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | | | | | - Richard Finkers
- Department of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Star Yanxin Gao
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Mehmood Ghaffar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Philip Glaser
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | | | - Puthick Hok
- Diversity Arrays Technology, Bruce, Australia
| | | | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | - David S LeBauer
- College of Agricultural and Life Sciences, The University of Arizona, Tucson, AZ, USA
| | | | - David S Marshall
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK.,SRUC, Edinburgh, UK
| | | | - Iain Milne
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | | | | | | | - Pascal Neveu
- MISTEA, INRA, Montpellier SupAgro, Universite de Montpellier, Montpellier, France
| | - Evangelia Papoutsoglou
- Department of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | - Cyril Pommier
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | | | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Angel Manica Raquel
- International Rice Research Institute (IRRI), Los Baños, Laguna, The Philippines
| | - Sebastian Raubach
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Trevor Rife
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Kelly Robbins
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | | | - Chaitanya Sarma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Guilhem Sempéré
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INTERTRYP, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | - Paul D Shaw
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | | | - Nahuel Soldevilla
- Integrated Breeding Program (IBP), CIMMYT, Texcoco, Mexico.,LeafNode Technology, Buenos Aires, Argentina
| | - Gordon Stephen
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Qi Sun
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Clarysabel Tovar
- Integrated Breeding Program (IBP), CIMMYT, Texcoco, Mexico.,LeafNode Technology, Buenos Aires, Argentina
| | | | - Maikel Verouden
- Wageningen University & Research, Biometris, Wageningen PB, The Netherlands
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20
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Price EJ, Drapal M, Perez‐Fons L, Amah D, Bhattacharjee R, Heider B, Rouard M, Swennen R, Becerra Lopez‐Lavalle LA, Fraser PD. Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops. Plant J 2020; 101:1258-1268. [PMID: 31845400 PMCID: PMC7383867 DOI: 10.1111/tpj.14649] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/09/2019] [Accepted: 11/28/2019] [Indexed: 05/06/2023]
Abstract
Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large-scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics-based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on-going genomic and phenotypic studies will enhance 'omics-wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.
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Affiliation(s)
- Elliott J. Price
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
- Present address:
Masaryk UniversityBrno‐Bohunice625 00Czech Republic
| | - Margit Drapal
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
| | - Laura Perez‐Fons
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
| | - Delphine Amah
- International Institute of Tropical AgriculturePMB 5320IbadanNigeria
| | | | | | - Mathieu Rouard
- Bioversity InternationalParc Scientifique Agropolis II34397MontpellierFrance
| | - Rony Swennen
- Laboratory of Tropical Crop ImprovementDivision of Crop BiotechnicsKU LeuvenB‐3001LeuvenBelgium
- Bioversity InternationalWillem De Croylaan 42B‐3001LeuvenBelgium
- International Institute of Tropical Agriculture. C/0 The Nelson Mandela African Institution of Science and TechnologyP.O. Box 44ArushaTanzania
| | | | - Paul D. Fraser
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
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21
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Sempéré G, Pétel A, Rouard M, Frouin J, Hueber Y, De Bellis F, Larmande P. Gigwa v2-Extended and improved genotype investigator. Gigascience 2019; 8:5488103. [PMID: 31077313 PMCID: PMC6511067 DOI: 10.1093/gigascience/giz051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Accepted: 04/08/2019] [Indexed: 11/19/2022] Open
Abstract
Background The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. Results Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). Conclusions This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community.
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Affiliation(s)
- Guilhem Sempéré
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR INTERTRYP, F-34398 Montpellier, France.,South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,INTERTRYP, Univ Montpellier, CIRAD, Institut de Recherche pour le Développpement (IRD), Montpellier, France
| | - Adrien Pétel
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,DIADE, Univ Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Mathieu Rouard
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Julien Frouin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Institut national d'études supérieures agronomiques de Montpellier (Montpellier SupAgro), Montpellier, France
| | - Yann Hueber
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Fabien De Bellis
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Institut national d'études supérieures agronomiques de Montpellier (Montpellier SupAgro), Montpellier, France
| | - Pierre Larmande
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,DIADE, Univ Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier, France
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22
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Dupouy M, Baurens FC, Derouault P, Hervouet C, Cardi C, Cruaud C, Istace B, Labadie K, Guiougou C, Toubi L, Salmon F, Mournet P, Rouard M, Yahiaoui N, Lemainque A, Martin G, D’Hont A. Two large reciprocal translocations characterized in the disease resistance-rich burmannica genetic group of Musa acuminata. Ann Bot 2019; 124:319-329. [PMID: 31241133 PMCID: PMC6758587 DOI: 10.1093/aob/mcz078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/09/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Banana cultivars are derived from hybridizations involving Musa acuminata subspecies. The latter diverged following geographical isolation in distinct South-east Asian continental regions and islands. Observation of chromosome pairing irregularities in meiosis of hybrids between these subspecies suggested the presence of large chromosomal structural variations. The aim of this study was to characterize such rearrangements. METHODS Marker (single nucleotide polymorphism) segregation in a self-progeny of the 'Calcutta 4' accession and mate-pair sequencing were used to search for chromosomal rearrangements in comparison with the M. acuminata ssp. malaccensis genome reference sequence. Signature segment junctions of the revealed chromosome structures were identified and searched in whole-genome sequencing data from 123 wild and cultivated Musa accessions. KEY RESULTS Two large reciprocal translocations were characterized in the seedy banana M. acuminata ssp. burmannicoides 'Calcutta 4' accession. One consisted of an exchange of a 240 kb distal region of chromosome 2 with a 7.2 Mb distal region of chromosome 8. The other involved an exchange of a 20.8 Mb distal region of chromosome 1 with a 11.6 Mb distal region of chromosome 9. Both translocations were found only in wild accessions belonging to the burmannicoides/burmannica/siamea subspecies. Only two of the 87 cultivars analysed displayed the 2/8 translocation, while none displayed the 1/9 translocation. CONCLUSION Two large reciprocal translocations were identified that probably originated in the burmannica genetic group. Accurate characterization of these translocations should enhance the use of this disease resistance-rich burmannica group in breeding programmes.
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Affiliation(s)
- Marion Dupouy
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Paco Derouault
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Céline Cardi
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Corinne Cruaud
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Benjamin Istace
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | | | | | | | - Pierre Mournet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Arnaud Lemainque
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- For correspondence. E-mail
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23
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Wang Z, Miao H, Liu J, Xu B, Yao X, Xu C, Zhao S, Fang X, Jia C, Wang J, Zhang J, Li J, Xu Y, Wang J, Ma W, Wu Z, Yu L, Yang Y, Liu C, Guo Y, Sun S, Baurens FC, Martin G, Salmon F, Garsmeur O, Yahiaoui N, Hervouet C, Rouard M, Laboureau N, Habas R, Ricci S, Peng M, Guo A, Xie J, Li Y, Ding Z, Yan Y, Tie W, D'Hont A, Hu W, Jin Z. Musa balbisiana genome reveals subgenome evolution and functional divergence. Nat Plants 2019; 5:810-821. [PMID: 31308504 PMCID: PMC6784884 DOI: 10.1038/s41477-019-0452-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
Banana cultivars (Musa ssp.) are diploid, triploid and tetraploid hybrids derived from Musa acuminata and Musa balbisiana. We presented a high-quality draft genome assembly of M. balbisiana with 430 Mb (87%) assembled into 11 chromosomes. We identified that the recent divergence of M. acuminata (A-genome) and M. balbisiana (B-genome) occurred after lineage-specific whole-genome duplication, and that the B-genome may be more sensitive to the fractionation process compared to the A-genome. Homoeologous exchanges occurred frequently between A- and B-subgenomes in allopolyploids. Genomic variation within progenitors resulted in functional divergence of subgenomes. Global homoeologue expression dominance occurred between subgenomes of the allotriploid. Gene families related to ethylene biosynthesis and starch metabolism exhibited significant expansion at the pathway level and wide homoeologue expression dominance in the B-subgenome of the allotriploid. The independent origin of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) homoeologue gene pairs and tandem duplication-driven expansion of ACO genes in the B-subgenome contributed to rapid and major ethylene production post-harvest in allotriploid banana fruits. The findings of this study provide greater context for understanding fruit biology, and aid the development of tools for breeding optimal banana cultivars.
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Affiliation(s)
- Zhuo Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Hongxia Miao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Juhua Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Biyu Xu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Chunyan Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | | | - Caihong Jia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jingyi Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianbin Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jingyang Li
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yi Xu
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiashui Wang
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weihong Ma
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Lili Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yulan Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Silong Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frederic Salmon
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Guadeloupe, France
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Nathalie Laboureau
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Remy Habas
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Sebastien Ricci
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Guadeloupe, France
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianghui Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Zhiqiang Jin
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China.
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24
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Baurens FC, Martin G, Hervouet C, Salmon F, Yohomé D, Ricci S, Rouard M, Habas R, Lemainque A, Yahiaoui N, D'Hont A. Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes. Mol Biol Evol 2019; 36:97-111. [PMID: 30403808 PMCID: PMC6340459 DOI: 10.1093/molbev/msy199] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Admixture and polyploidization are major recognized eukaryotic genome evolutionary processes. Their impacts on genome dynamics vary among systems and are still partially deciphered. Many banana cultivars are triploid (sometimes diploid) interspecific hybrids between Musa acuminata (A genome) and M. balbisiana (B genome). They have no or very low fertility, are vegetatively propagated and have been classified as “AB,” “AAB,” or “ABB” based on morphological characters. We used NGS sequence data to characterize the A versus B chromosome composition of nine diploid and triploid interspecific cultivars, to compare the chromosome structures of A and B genomes and analyze A/B chromosome segregations in a polyploid context. We showed that interspecific recombination occurred frequently between A and B chromosomes. We identified two large structural variations between A and B genomes, a reciprocal translocation and an inversion that locally affected recombination and led to segregation distortion and aneuploidy in a triploid progeny. Interspecific recombination and large structural variations explained the mosaic genomes observed in edible bananas. The unprecedented resolution in deciphering their genome structure allowed us to start revisiting the origins of banana cultivars and provided new information to gain insight into the impact of interspecificity on genome evolution. It will also facilitate much more effective assessment of breeding strategies.
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Affiliation(s)
- Franc-Christophe Baurens
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frédéric Salmon
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,CIRAD, UMR AGAP, F-97130 Capesterre Belle Eau, Guadeloupe, France
| | | | - Sébastien Ricci
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,CIRAD, UMR AGAP, F-97130 Capesterre Belle Eau, Guadeloupe, France.,CARBAP, Bonanjo, Douala, Cameroon
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, Cedex 5, France
| | - Remy Habas
- CIRAD, UMR BGPI, F-34398 Montpellier, France.,BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Arnaud Lemainque
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François-Jacob, Genoscope, Evry, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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25
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Cenci A, Hueber Y, Zorrilla-Fontanesi Y, van Wesemael J, Kissel E, Gislard M, Sardos J, Swennen R, Roux N, Carpentier SC, Rouard M. Effect of paleopolyploidy and allopolyploidy on gene expression in banana. BMC Genomics 2019; 20:244. [PMID: 30917780 PMCID: PMC6438041 DOI: 10.1186/s12864-019-5618-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
Background Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B genome, respectively). Unresolved hybridizations finally led to banana diversification into several autotriploid (AAA) and allotriploid cultivars (AAB and ABB). Using transcriptomic data, we investigated the impact of the genome structure on gene expression patterns in roots of 12 different triploid genotypes covering AAA, AAB and ABB subgenome constitutions. Results We demonstrate that (i) there are different genome structures, (ii) expression patterns go beyond the predicted genomic groups, and (iii) the proportion of the B genome influences the gene expression. The presence of the B genome is associated with a higher expression of genes involved in flavonoid biosynthesis, fatty acid metabolism, amino sugar and nucleotide sugar metabolism and oxidative phosphorylation. There are cultivar-specific chromosome regions with biased B:A gene expression ratios that demonstrate homoeologous exchanges (HE) between A and B sub-genomes. In two cultivars, aneuploidy was detected. We identified 3674 genes with a different expression level between allotriploid and autotriploid with ~ 57% having recently duplicated copies (paralogous). We propose a Paralog Inclusive Expression (PIE) analysis that appears to be suitable for genomes still in a downsizing and fractionation process following whole genome duplications. Our approach allows highlighting the genes with a maximum likelihood to affect the plant phenotype. Conclusions This study on banana is a good case to investigate the effects of alloploidy in crops. We conclude that allopolyploidy triggered changes in the genome structure of a crop and it clearly influences the gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5618-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France.
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Yasmin Zorrilla-Fontanesi
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Jelle van Wesemael
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Ewaut Kissel
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Marie Gislard
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, F-34396, Montpellier, France
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium.,Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium.,International Institute of Tropical Agriculture. c/o The Nelson Mandela African Institution for Science and Technology (NM-AIST), P.O. Box 447, Arusha, Tanzania
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Sebastien Christian Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium.,Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France.
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26
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Drapal M, de Carvalho EB, Rouard M, Amah D, Sardos J, Van den Houwe I, Brown A, Roux N, Swennen R, Fraser PD. Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and pre-flowering growth stages. Sci Rep 2019; 9:4657. [PMID: 30874619 PMCID: PMC6420674 DOI: 10.1038/s41598-019-41037-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/22/2019] [Indexed: 11/16/2022] Open
Abstract
Bananas (Musa spp.) are consumed worldwide as dessert and cooking types. Edible banana varieties are for the most part seedless and sterile and therefore vegetatively propagated. This confers difficulties for breeding approaches against pressing biotic and abiotic threats and for the nutritional enhancement of banana pulp. A panel of banana accessions, representative of the diversity of wild and cultivated bananas, was analysed to assess the range of chemotypes available globally. The focus of this assessment was banana leaves at two growth stages (juvenile and pre-flowering), to see when during the plant growth metabolic differences can be established. The metabolic data corresponded to genomic trends reported in previous studies and demonstrated a link between metabolites/pathways and the genomes of M. acuminata and M. balbisiana. Furthermore, the vigour and resistance traits of M. balbisiana was connected to the phenolic composition and showed differences with the number of B genes in the hybrid accessions. Differences in the juvenile and pre-flowering data led to low correlation between the growth stages for prediction purposes.
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Affiliation(s)
- Margit Drapal
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | | | - Mathieu Rouard
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Delphine Amah
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Julie Sardos
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | | | - Allan Brown
- International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Nicolas Roux
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Rony Swennen
- International Institute of Tropical Agriculture, Arusha, Tanzania.,Bioversity International, W. De Croylaan 42, 3001, Heverlee, Belgium.,Department of Biosystem, KU Leuven University, Oude Markt 13 - bus 5005, 3000, Leuven, Belgium
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK.
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27
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Halewood M, Lopez Noriega I, Ellis D, Roa C, Rouard M, Sackville Hamilton R. Using Genomic Sequence Information to Increase Conservation and Sustainable Use of Crop Diversity and Benefit-Sharing. Biopreserv Biobank 2018; 16:368-376. [PMID: 30325667 PMCID: PMC6204560 DOI: 10.1089/bio.2018.0043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This article describes how CGIAR centers and partners are using genomic sequence information to promote the conservation and sustainable use of crop genetic diversity, and to generate and share benefits derived from those uses. The article highlights combined institutional, and benefit-sharing-related challenges that need to be addressed to support expanded use of digital sequence information in agricultural research and development.
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Affiliation(s)
| | | | - Dave Ellis
- 2 International Potato Center , Lima, Peru
| | - Carolina Roa
- 3 Centro Internacional de Agricultura Tropical , Cali, Colombia
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28
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Cenci A, Chantret N, Rouard M. Glycosyltransferase Family 61 in Liliopsida (Monocot): The Story of a Gene Family Expansion. Front Plant Sci 2018; 9:1843. [PMID: 30619412 PMCID: PMC6297846 DOI: 10.3389/fpls.2018.01843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Plant cell walls play a fundamental role in several plant traits and also influence crop use as livestock nutrition or biofuel production. The Glycosyltransferase family 61 (GT61) is involved in the synthesis of cell wall xylans. In grasses (Poaceae), a copy number expansion was reported for the GT61 family, and raised the question of the evolutionary history of this gene family in a broader taxonomic context. A phylogenetic study was performed on GT61 members from 13 species representing the major angiosperm clades, in order to classify the genes, reconstruct the evolutionary history of this gene family and study its expansion in monocots. Four orthogroups (OG) were identified in angiosperms with two of them displaying a copy number expansion in monocots. These copy number expansions resulted from both tandem and segmental duplications during the genome evolution of monocot lineages. Positive selection footprints were detected on the ancestral branch leading to one of the orthogroups suggesting that the gene number expansion was accompanied by functional diversification, at least partially. We propose an OG-based classification framework for the GT61 genes at different taxonomic levels of the angiosperm useful for any further functional or translational biology study.
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Affiliation(s)
- Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | | | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
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29
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Rouard M, Droc G, Martin G, Sardos J, Hueber Y, Guignon V, Cenci A, Geigle B, Hibbins MS, Yahiaoui N, Baurens FC, Berry V, Hahn MW, D’Hont A, Roux N. Three New Genome Assemblies Support a Rapid Radiation in Musa acuminata (Wild Banana). Genome Biol Evol 2018; 10:3129-3140. [PMID: 30321324 PMCID: PMC6282646 DOI: 10.1093/gbe/evy227] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.
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Affiliation(s)
- Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Gaetan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | | | - Mark S Hibbins
- Department of Biology, Indiana University
- Department of Computer Science, Indiana University
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Vincent Berry
- LIRMM, Université de Montpellier, CNRS, Montpellier, France
| | - Matthew W Hahn
- Department of Biology, Indiana University
- Department of Computer Science, Indiana University
| | - Angelique D’Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
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30
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Ruas M, Guignon V, Sempere G, Sardos J, Hueber Y, Duvergey H, Andrieu A, Chase R, Jenny C, Hazekamp T, Irish B, Jelali K, Adeka J, Ayala-Silva T, Chao CP, Daniells J, Dowiya B, Effa Effa B, Gueco L, Herradura L, Ibobondji L, Kempenaers E, Kilangi J, Muhangi S, Ngo Xuan P, Paofa J, Pavis C, Thiemele D, Tossou C, Sandoval J, Sutanto A, Vangu Paka G, Yi G, Van den Houwe I, Roux N, Rouard M. MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. Database (Oxford) 2018; 2017:3866796. [PMID: 29220435 PMCID: PMC5502358 DOI: 10.1093/database/bax046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/12/2017] [Indexed: 12/22/2022]
Abstract
Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL:https://www.crop-diversity.org/mgis/
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Affiliation(s)
- Max Ruas
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - V Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - G Sempere
- South Green Bioinformatics Platform, Montpellier, France.,CIRAD, UMR AGAP 34398 Montpellier Cedex 5, France
| | - J Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Y Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - H Duvergey
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - A Andrieu
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - R Chase
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - C Jenny
- CIRAD, UMR AGAP 34398 Montpellier Cedex 5, France
| | - T Hazekamp
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - B Irish
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, Puerto Rico
| | - K Jelali
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - J Adeka
- University of Kisangani, Kisangani (UNIKIS), Democratic Republic of Congo
| | - T Ayala-Silva
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, Puerto Rico
| | - C P Chao
- Taiwan Banana Research Institute (TBRI), Chiuju, Pingtung, Taiwan, Republic of China
| | - J Daniells
- Department of Agriculture, Fisheries and Forestry, Queensland Government (DAFF South Johnstone), Brisbane, Australia
| | - B Dowiya
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Democratic Republic of Congo
| | - B Effa Effa
- Centre National de la Recherche Scientifique et Technologique (CENAREST), Libreville, Gabon
| | - L Gueco
- Institute of Plant Breeding (IPB), University of the Philippines (UPLB), Los Baños, Philippines
| | - L Herradura
- Bureau of Plant Industry (BPI) - Davao National Crop Research and Development Center, Davao City, Philippines
| | - L Ibobondji
- Centre Africain de Recherche sur Bananes et Plantains (CARBAP), Njombe, Cameroon
| | - E Kempenaers
- Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - J Kilangi
- Agricultural Research Institute (ARI) Maruku, Bukoba, Tanzania
| | - S Muhangi
- National Agricultural Research Organization (NARO), Mbarara, Uganda
| | - P Ngo Xuan
- Fruit and Vegetable Research Institute (FAVRI), Hanoi, Vietnam
| | - J Paofa
- National Agricultural Research Institute (NARI), Laloki Papua, New Guinea
| | - C Pavis
- CRB Plantes Tropicales, CIRAD INRA - Neufchâteau, Guadeloupe, France
| | - D Thiemele
- Centre National de Recherches Agronomiques (CNRA), Abidjan, Cote d'Ivoire
| | - C Tossou
- Institut National de Recherche Agronomique du Bénin (INRAB), Cotonou, Bénin
| | - J Sandoval
- Corporación Bananera Nacional S.A (CORBANA), San José, Costa Rica
| | - A Sutanto
- Indonesian Centre for Horticultural Research and Development (ICHORD), Bogor, Indonesia
| | - G Vangu Paka
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Democratic Republic of Congo
| | - G Yi
- Institute of Fruit Tree Research (IFTR), Guangdong Academy of Agricultural Sciences (GDAAS), Guangdong, China
| | - I Van den Houwe
- Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - N Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - M Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
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Martin G, Carreel F, Coriton O, Hervouet C, Cardi C, Derouault P, Roques D, Salmon F, Rouard M, Sardos J, Labadie K, Baurens FC, D'Hont A. Evolution of the Banana Genome (Musa acuminata) Is Impacted by Large Chromosomal Translocations. Mol Biol Evol 2017; 34:2140-2152. [PMID: 28575404 PMCID: PMC5850475 DOI: 10.1093/molbev/msx164] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Most banana cultivars are triploid seedless parthenocarpic clones derived from hybridization between Musa acuminata subspecies and sometimes M. balbisiana. M. acuminata subspecies were suggested to differ by a few large chromosomal rearrangements based on chromosome pairing configurations in intersubspecies hybrids. We searched for large chromosomal rearrangements in a seedy M. acuminata ssp. malaccensis banana accession through mate-pair sequencing, BAC-FISH, targeted PCR and marker (DArTseq) segregation in its progeny. We identified a heterozygous reciprocal translocation involving two distal 3 and 10 Mb segments from chromosomes 01 and 04, respectively, and showed that it generated high segregation distortion, reduced recombination and linkage between chromosomes 01 and 04 in its progeny. The two chromosome structures were found to be mutually exclusive in gametes and the rearranged structure was preferentially transmitted to the progeny. The rearranged chromosome structure was frequently found in triploid cultivars but present only in wild malaccensis ssp. accessions, thus suggesting that this rearrangement occurred in M. acuminata ssp. malaccensis. We propose a mechanism for the spread of this rearrangement in Musa diversity and suggest that this rearrangement could have played a role in the emergence of triploid cultivars.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut Genomique (IG), Genoscope, Evry, France
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Cenci A, Rouard M. Evolutionary Analyses of GRAS Transcription Factors in Angiosperms. Front Plant Sci 2017; 8:273. [PMID: 28303145 PMCID: PMC5332381 DOI: 10.3389/fpls.2017.00273] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/14/2017] [Indexed: 05/21/2023]
Abstract
GRAS transcription factors (TFs) play critical roles in plant growth and development such as gibberellin and mycorrhizal signaling. Proteins belonging to this gene family contain a typical GRAS domain in the C-terminal sequence, whereas the N-terminal region is highly variable. Although, GRAS genes have been characterized in a number of plant species, their classification is still not completely resolved. Based on a panel of eight representative species of angiosperms, we identified 29 orthologous groups or orthogroups (OGs) for the GRAS gene family, suggesting that at least 29 ancestor genes were present in the angiosperm lineage before the "Amborella" evolutionary split. Interestingly, some taxonomic groups were missing members of one or more OGs. The gene number expansion usually observed in transcription factors was not observed in GRAS while the genome triplication ancestral to the eudicots (γ hexaploidization event) was detectable in a limited number of GRAS orthogroups. We also found conserved OG-specific motifs in the variable N-terminal region. Finally, we could regroup OGs in 17 subfamilies for which names were homogenized based on a literature review and described 5 new subfamilies (DLT, RAD1, RAM1, SCLA, and SCLB). This study establishes a consistent framework for the classification of GRAS members in angiosperm species, and thereby a tool to correctly establish the orthologous relationships of GRAS genes in most of the food crops in order to facilitate any subsequent functional analyses in the GRAS gene family. The multi-fasta file containing all the sequences used in our study could be used as database to perform diagnostic BLASTp to classify GRAS genes from other non-model species.
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Affiliation(s)
- Alberto Cenci
- Bioversity InternationalMontpellier, France
- CGIAR Research Programme on Roots, Tubers and BananasMontpellier, France
- *Correspondence: Alberto Cenci
| | - Mathieu Rouard
- Bioversity InternationalMontpellier, France
- CGIAR Research Programme on Roots, Tubers and BananasMontpellier, France
- Mathieu Rouard
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Wu W, Yang YL, He WM, Rouard M, Li WM, Xu M, Roux N, Ge XJ. Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus. Sci Rep 2016; 6:31586. [PMID: 27531320 PMCID: PMC4987669 DOI: 10.1038/srep31586] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/26/2016] [Indexed: 12/15/2022] Open
Abstract
Crop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans, a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since the approximate divergence around 5.8 million years ago, the genomes of Musa itinerans and Musa acuminata have shown conserved collinearity. Gene family expansions and contractions enrichment analysis revealed that some pathways were associated with phenotypic or physiological innovations. These include a transition from wood to herbaceous in the ancestral Musaceae, intensification of cold and drought tolerances, and reduced diseases resistance genes for subtropical marginally distributed Musa species. Prevalent purifying selection and transposed duplications were found to facilitate the diversification of NBS-encoding gene families for two Musa species. The population genome history analysis of M. itinerans revealed that the fluctuated population sizes were caused by the Pleistocene climate oscillations, and that the formation of Qiongzhou Strait might facilitate the population downsizing on the isolated Hainan Island about 10.3 Kya. The qualified assembly of the M. itinerans genome provides deep insights into the lineage-specific diversification and also valuable resources for future banana breeding.
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Affiliation(s)
- Wei Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China
| | | | | | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Wei-Ming Li
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Meng Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China
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34
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Zorrilla-Fontanesi Y, Rouard M, Cenci A, Kissel E, Do H, Dubois E, Nidelet S, Roux N, Swennen R, Carpentier SC. Corrigendum: Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. Sci Rep 2016; 7:25683. [PMID: 27203802 PMCID: PMC4874233 DOI: 10.1038/srep25683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Sardos J, Rouard M, Hueber Y, Cenci A, Hyma KE, van den Houwe I, Hribova E, Courtois B, Roux N. A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop. PLoS One 2016; 11:e0154448. [PMID: 27144345 PMCID: PMC4856271 DOI: 10.1371/journal.pone.0154448] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 04/13/2016] [Indexed: 11/19/2022] Open
Abstract
Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.
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Affiliation(s)
- Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
- * E-mail:
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Katie E. Hyma
- Institute of Biotechnology, Genomic Diversity Facility, Cornell University, Ithaca, NY, 14853, United States of America
| | | | - Eva Hribova
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
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Martin G, Baurens FC, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Doležel J, Aury JM, Alberti A, Carreel F, D'Hont A. Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods. BMC Genomics 2016; 17:243. [PMID: 26984673 PMCID: PMC4793746 DOI: 10.1186/s12864-016-2579-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 03/08/2016] [Indexed: 12/04/2022] Open
Abstract
Background Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata). Results We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80 %), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5 % of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70 %. Unknown sites (N) were reduced from 17.3 to 10.0 %. Conclusion The release of the Musa acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in other species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2579-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guillaume Martin
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France
| | - Franc-Christophe Baurens
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France
| | - Gaëtan Droc
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Andrzej Kilian
- Diversity Arrays Technology, Yarralumla, Australian Capital Territory, 2600, Australia
| | - Alex Hastie
- BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France
| | - Françoise Carreel
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France
| | - Angélique D'Hont
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France.
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Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G. The coffee genome hub: a resource for coffee genomes. Nucleic Acids Res 2014; 43:D1028-35. [PMID: 25392413 PMCID: PMC4383925 DOI: 10.1093/nar/gku1108] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager.
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Affiliation(s)
- Alexis Dereeper
- UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Stéphanie Bocs
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Sébastien Ravel
- UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Christine Tranchant-Dubreuil
- UMR Diversité Adaptation et DEveloppement des plantes (DIADE), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Valérie Poncet
- UMR Diversité Adaptation et DEveloppement des plantes (DIADE), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Olivier Garsmeur
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France
| | - Philippe Lashermes
- UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Gaëtan Droc
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France
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Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 2014; 345:1181-4. [PMID: 25190796 DOI: 10.1126/science.1255274] [Citation(s) in RCA: 336] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
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Affiliation(s)
- France Denoeud
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Lorenzo Carretero-Paulet
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA
| | - Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Gaëtan Droc
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Romain Guyot
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Marco Pietrella
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Adriana Alberti
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - François Anthony
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Stéphanie Bocs
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Claudine Campa
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Alberto Cenci
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Marie-Christine Combes
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Dominique Crouzillat
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | | | - Fabien De Bellis
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Stéphane Dussert
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Olivier Garsmeur
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Thomas Gayraud
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Katharina Jahn
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. Center for Biotechnology, Universität Bielefeld, Universitätsstraße 27, D-33615 Bielefeld, Germany. AG Genominformatik, Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Véronique Jamilloux
- Institut National de la Recherche Agronomique (INRA), Unité de Recherches en Génomique-Info (UR INRA 1164), Centre de Recherche de Versailles, 78026 Versailles Cedex, France
| | - Thierry Joët
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Tianying Lan
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. Department of Biology, Chongqing University of Science and Technology, 4000042 Chongqing, China
| | - Julie Leclercq
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Maud Lepelley
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Thierry Leroy
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Lei-Ting Li
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pablo Librado
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | | | - Adriana Muñoz
- Department of Mathematics, University of Maryland, Mathematics Building 084, University of Maryland, College Park, MD 20742, USA. School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Benjamin Noel
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | | | - Valérie Poncet
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - David Pot
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Priyono
- Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia
| | - Michel Rigoreau
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | - Christine Tranchant-Dubreuil
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Robert VanBuren
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qiong Zhang
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alan C Andrade
- Laboratório de Genética Molecular, Núcleo de Biotecnologia (NTBio), Embrapa Recursos Genéticos e Biotecnologia, Final Av. W/5 Norte, Parque Estação Biológia, Brasília-DF 70770-917, Brazil
| | - Xavier Argout
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Benoît Bertrand
- CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Alexandre de Kochko
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Giorgio Graziosi
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia
| | - Jayarama
- Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India
| | - Ray Ming
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chifumi Nagai
- Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA
| | - Steve Rounsley
- BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Victor A Albert
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France.
| | - Philippe Lashermes
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France.
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Cenci A, Guignon V, Roux N, Rouard M. Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots. Plant Mol Biol 2014; 85:63-80. [PMID: 24570169 PMCID: PMC4151281 DOI: 10.1007/s11103-013-0169-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 12/24/2013] [Indexed: 05/02/2023]
Abstract
Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species.
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Affiliation(s)
- Albero Cenci
- Bioversity International, Commodity Systems and Genetic Resources Programme, Parc Scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397, Montpellier Cedex 5, France,
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40
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Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard JF, Lengelle J, Baurens FC, Cenci A, Pitollat B, D'Hont A, Ruiz M, Rouard M, Bocs S. The banana genome hub. Database (Oxford) 2013; 2013:bat035. [PMID: 23707967 PMCID: PMC3662865 DOI: 10.1093/database/bat035] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/
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Affiliation(s)
- Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier F-34398, France.
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41
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D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quétier F, Yahiaoui N, Wincker P. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 2012; 488:213-7. [PMID: 22801500 DOI: 10.1038/nature11241] [Citation(s) in RCA: 603] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/18/2012] [Indexed: 01/17/2023]
Abstract
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.
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Affiliation(s)
- Angélique D'Hont
- Centre de coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, F-34398 Montpellier, France. angelique.d’
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Hippolyte I, Jenny C, Gardes L, Bakry F, Rivallan R, Pomies V, Cubry P, Tomekpe K, Risterucci AM, Roux N, Rouard M, Arnaud E, Kolesnikova-Allen M, Perrier X. Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers. Ann Bot 2012; 109:937-51. [PMID: 22323428 PMCID: PMC3310492 DOI: 10.1093/aob/mcs010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/19/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships. METHODS Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed. KEY RESULTS AND CONCLUSIONS We determine the closest diploid progenitors of the triploid 'Cavendish' and 'Gros Michel' subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. 'Cavendish', 'Plantain' and 'Mutika-Lujugira'), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference.
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Affiliation(s)
- I Hippolyte
- CIRAD, UMR AGAP, Montferrier sur Lez, France.
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Guignon V, Droc G, Alaux M, Baurens FC, Garsmeur O, Poiron C, Carver T, Rouard M, Bocs S. Chado controller: advanced annotation management with a community annotation system. ACTA ACUST UNITED AC 2012; 28:1054-6. [PMID: 22285827 PMCID: PMC3315714 DOI: 10.1093/bioinformatics/bts046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. Availability: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form Contact:valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr Supplementary information:Supplementary data are available at Bioinformatics online.
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Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, Zmasek CM, Périn C, Conte MG. GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res 2011; 39:D1095-102. [PMID: 20864446 PMCID: PMC3013755 DOI: 10.1093/nar/gkq811] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/19/2010] [Accepted: 08/23/2010] [Indexed: 11/20/2022] Open
Abstract
GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. Version 2 now contains sixteen full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families. For each gene cluster or gene family, easy access to gene composition, protein domains, publications, external links and orthologous gene predictions is provided. Web interfaces have been further developed to improve the navigation through information related to gene families. New analysis tools are also available, such as a gene family ontology browser that facilitates exploration. GreenPhylDB is a component of the South Green Bioinformatics Platform (http://southgreen.cirad.fr/) and is accessible at http://greenphyl.cirad.fr. It enables comparative genomics in a broad taxonomy context to enhance the understanding of evolutionary processes and thus tends to speed up gene discovery.
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Affiliation(s)
- Mathieu Rouard
- Bioversity International - CfL programme Parc Scientifique Agropolis II, 34397 Montpellier, France.
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Baurens FC, Bocs S, Rouard M, Matsumoto T, Miller RNG, Rodier-Goud M, MBéguié-A-MBéguié D, Yahiaoui N. Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana). BMC Plant Biol 2010; 10:149. [PMID: 20637079 PMCID: PMC3017797 DOI: 10.1186/1471-2229-10-149] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 07/16/2010] [Indexed: 05/09/2023]
Abstract
BACKGROUND Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). RESULTS Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. CONCLUSIONS A large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.
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Affiliation(s)
| | - Stéphanie Bocs
- CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, F-34397 Montpellier Cedex 5, France
| | - Takashi Matsumoto
- Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences (NIAS)/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8602, Japan
| | - Robert NG Miller
- Postgraduate program in Genomic Science and Biotechnology, Universidade Católica de Brasília, SGAN 916, Módulo B, CEP 70.790-160, Brasília, DF, Brazil
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Asa Norte, Brasília, Brazil
| | | | | | - Nabila Yahiaoui
- CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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Bruskiewich R, Senger M, Davenport G, Ruiz M, Rouard M, Hazekamp T, Takeya M, Doi K, Satoh K, Costa M, Simon R, Balaji J, Akintunde A, Mauleon R, Wanchana S, Shah T, Anacleto M, Portugal A, Ulat VJ, Thongjuea S, Braak K, Ritter S, Dereeper A, Skofic M, Rojas E, Martins N, Pappas G, Alamban R, Almodiel R, Barboza LH, Detras J, Manansala K, Mendoza MJ, Morales J, Peralta B, Valerio R, Zhang Y, Gregorio S, Hermocilla J, Echavez M, Yap JM, Farmer A, Schiltz G, Lee J, Casstevens T, Jaiswal P, Meintjes A, Wilkinson M, Good B, Wagner J, Morris J, Marshall D, Collins A, Kikuchi S, Metz T, McLaren G, van Hintum T. The generation challenge programme platform: semantic standards and workbench for crop science. Int J Plant Genomics 2008; 2008:369601. [PMID: 18483570 PMCID: PMC2375972 DOI: 10.1155/2008/369601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2007] [Accepted: 12/14/2007] [Indexed: 05/26/2023]
Abstract
The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.
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Abstract
GreenPhylDB (http://greenphyl.cirad.fr) is a comprehensive platform designed to facilitate comparative functional genomics in Oryza sativa and Arabidopsis thaliana genomes. The main functions of GreenPhylDB are to assign O. sativa and A. thaliana sequences to gene families using a semi-automatic clustering procedure and to create ‘orthologous’ groups using a phylogenomic approach. To date, GreenPhylDB comprises the most complete list of plant gene families, which have been manually curated (6421 families). GreenPhylDB also contains all of the phylogenomic relationships computed for 4375 families. A total of 492 TAIR, 1903 InterPro and 981 KEGG families and subfamilies were manually curated using the clusters created with the TribeMCL software. GreenPhylDB integrates information from several other databases including UniProt, KEGG, InterPro, TAIR and TIGR. Several entry points can be used to display phylogenomic relationships for A. thaliana or O. sativa sequences, using TAIR, TIGR gene ID, family name, InterPro, gene alias, UniProt or protein/nucleic sequence. Finally, a powerful phylogenomics tool, GreenPhyl Ortholog Search Tool (GOST), was incorporated into GreenPhylDB to predict orthologous relationships between O. sativa/A. thaliana protein(s) and sequences from other plant species.
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Affiliation(s)
- M G Conte
- CIRAD, Department BIOS, UMR DAP-TA40/03, 34398 Montpellier, France
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Wanchana S, Thongjuea S, Ulat VJ, Anacleto M, Mauleon R, Conte M, Rouard M, Ruiz M, Krishnamurthy N, Sjolander K, van Hintum T, Bruskiewich RM. The Generation Challenge Programme comparative plant stress-responsive gene catalogue. Nucleic Acids Res 2007; 36:D943-6. [PMID: 17933772 PMCID: PMC2238985 DOI: 10.1093/nar/gkm798] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Generation Challenge Programme (GCP; www.generationcp.org) has developed an online resource documenting stress-responsive genes comparatively across plant species. This public resource is a compendium of protein families, phylogenetic trees, multiple sequence alignments (MSA) and associated experimental evidence. The central objective of this resource is to elucidate orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress, mainly abiotic stresses such as water deficit (‘drought’). The web-based graphical user interface (GUI) of the resource includes query and visualization tools that allow diverse searches and browsing of the underlying project database. The web interface can be accessed at http://dayhoff.generationcp.org.
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Affiliation(s)
- Samart Wanchana
- Crop Research Informatics Laboratory - International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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Lefranc MP, Pommié C, Kaas Q, Duprat E, Bosc N, Guiraudou D, Jean C, Ruiz M, Da Piédade I, Rouard M, Foulquier E, Thouvenin V, Lefranc G. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 2005; 29:185-203. [PMID: 15572068 DOI: 10.1016/j.dci.2004.07.003] [Citation(s) in RCA: 186] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Accepted: 07/16/2004] [Indexed: 05/24/2023]
Abstract
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr) provides a common access to expertly annotated data on the genome, proteome, genetics and structure of immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates. The NUMEROTATION concept of IMGT-ONTOLOGY has allowed to define a unique numbering for the variable domains (V-DOMAINs) and for the V-LIKE-DOMAINs. In this paper, this standardized characterization is extended to the constant domains (C-DOMAINs), and to the C-LIKE-DOMAINs, leading, for the first time, to their standardized description of mutations, allelic polymorphisms, two-dimensional (2D) representations and tridimensional (3D) structures. The IMGT unique numbering is, therefore, highly valuable for the comparative, structural or evolutionary studies of the immunoglobulin superfamily (IgSF) domains, V-DOMAINs and C-DOMAINs of IG and TR in vertebrates, and V-LIKE-DOMAINs and C-LIKE-DOMAINs of proteins other than IG and TR, in any species.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, the International ImMunoGeneTics Information System, LIGM, Laboratoire d'ImmunoGénétique Moléculaire, Université Montpellier II, UPR CNRS 1142, IGH, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France.
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