Mathieu Rouard
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View article: Genetic databases in the era of ‘DSI’ benefit-sharing
Genetic databases in the era of ‘DSI’ benefit-sharing Open
Genetic databases drive research by enabling open access. Recently, parties to the Convention on Biological Diversity agreed on new rules for sharing benefits from the use of digital sequence information (DSI) which upholds open access, an…
View article: Shaping the future of bananas: advancing genetic trait regulation and breeding in the postgenomics era
Shaping the future of bananas: advancing genetic trait regulation and breeding in the postgenomics era Open
Bananas (Musa spp.) are among the top-produced food crops, serving as a primary source of food for millions of people. Cultivated bananas originated primarily from the wild diploid species Musa acuminata (A genome) and Musa balbisiana (B g…
View article: Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors
Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors Open
Hybridization between wild Musa species and subspecies from Southeast Asia is at the origin of cultivated bananas. The genomes of these cultivars are complex mosaics involving nine genetic groups, including two previously unknown contribut…
View article: BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community
BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community Open
Population growth and the impacts of climate change are placing increasing pressure on global agriculture and breeding programmes. Recent advancements in phenotyping techniques, genotyping technologies, and predictive modelling are acceler…
View article: Painting the diversity of a world's favorite fruit: A next generation catalog of cultivated bananas
Painting the diversity of a world's favorite fruit: A next generation catalog of cultivated bananas Open
Societal Impact Statement Bananas are nutritious fruits of major importance worldwide. Characterizing their diversity is essential to ensure their conservation and use. A catalog showcasing cultivated bananas genomic diversity was compiled…
View article: Painting the diversity of a world’s favourite fruit: A next generation catalogue of cultivated bananas
Painting the diversity of a world’s favourite fruit: A next generation catalogue of cultivated bananas Open
Societal impact statement Bananas are nutritious fruits of major importance in the tropics and subtropics. Characterizing their diversity is essential to ensure their conservation and use. A catalogue showcasing cultivated bananas genomic …
View article: Collecting and managing <i>in situ</i> banana genetic resources information (<i>Musa</i> spp.) using online resources and citizen science
Collecting and managing <i>in situ</i> banana genetic resources information (<i>Musa</i> spp.) using online resources and citizen science Open
The Musa Germplasm Information System (MGIS) stands as a pivotal database for managing global banana genetic resources information. In our latest effort, we have expanded MGIS to incorporate in situ observations. We thus incorporated more …
View article: Visualizing and Inferring Chromosome Segregation in the Pedigree of an Improved Banana Cultivar (Gold Finger) with Genome Ancestry Mosaic Painting
Visualizing and Inferring Chromosome Segregation in the Pedigree of an Improved Banana Cultivar (Gold Finger) with Genome Ancestry Mosaic Painting Open
Banana breeding faces numerous challenges, such as sterility and low seed viability. Enhancing our understanding of banana genetics, notably through next-generation sequencing, can help mitigate these challenges. The genotyping datasets cu…
View article: Pangenomic exploration of<i>Theobroma cacao</i>: New Insights into Gene Content Diversity and Selection During Domestication
Pangenomic exploration of<i>Theobroma cacao</i>: New Insights into Gene Content Diversity and Selection During Domestication Open
The Cacao tree ( Theobroma cacao L.) is a major cash crop and an important source of income for millions of farmers across Africa, Asia and Latin America. However, cacao farmers and producing countries are facing multiple challenges includ…
View article: Molecular Diagnosis and Vegetative Compatibility Group Analysis of Fusarium Wilt of Banana in Nepal
Molecular Diagnosis and Vegetative Compatibility Group Analysis of Fusarium Wilt of Banana in Nepal Open
Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc), is the most important constraint of the banana industry globally. In Nepal, epidemics resembling FWB have been increasingly observed on the Malbhog cultivar …
View article: Genome assembly of <i>Musa beccarii</i> shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes
Genome assembly of <i>Musa beccarii</i> shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes Open
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 …
View article: Ten simple rules for developing visualization tools in genomics
Ten simple rules for developing visualization tools in genomics Open
Our following 10 simple rules are dedicated to biologists and bioinformaticians who, while already being at the crossroads of many fields, want to venture further into the land of Data Visualization (“datavis” or “dataviz” for short). They…
View article: Genome-Wide Classification and Phylogenetic Analyses of the GDSL-Type Esterase/Lipase (GELP) Family in Flowering Plants
Genome-Wide Classification and Phylogenetic Analyses of the GDSL-Type Esterase/Lipase (GELP) Family in Flowering Plants Open
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 …
View article: Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas
Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas Open
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 o…
View article: Draft Genome Sequence of Fusarium oxysporum f. sp. <i>cubense</i> Tropical Race 4 from Peru, Obtained by Nanopore and Illumina Hybrid Assembly
Draft Genome Sequence of Fusarium oxysporum f. sp. <i>cubense</i> Tropical Race 4 from Peru, Obtained by Nanopore and Illumina Hybrid Assembly Open
Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is the causal agent of Fusarium wilt, a major threat to the banana industry worldwide. Here, we report the genome of a Foc TR4 strain from Peru, sequenced using a combination of I…
View article: Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genomes
Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genomes Open
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 fo…
View article: Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships
Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships Open
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 bana…
View article: Datasets from harmonised metabolic phenotyping of root, tuber and banana crop
Datasets from harmonised metabolic phenotyping of root, tuber and banana crop Open
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…
View article: Wheat Panache - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes
Wheat Panache - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes Open
Bread wheat 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 between cultivars, hampering genomic approaches for crop improvement. With the g…
View article: Bread wheat genomes graph pangenome
Bread wheat genomes graph pangenome Open
A Giraffe and a GFA-formatted minigraph assembly of sixteen bread wheat cultivar genome assemblies. 15-wheat10+.bed.gz is the relinearised graph from gfatools gfa2bed 15-wheat10+.gfa.gz is the graph in GFA format as built by minigraph inde…
View article: Bread wheat genomes graph pangenome
Bread wheat genomes graph pangenome Open
A Giraffe and a GFA-formatted minigraph assembly of sixteen bread wheat cultivar genome assemblies. 15-wheat10+.bed.gz is the relinearised graph from gfatools gfa2bed 15-wheat10+.gfa.gz is the graph in GFA format as built by minigraph inde…
View article: A chromosome-level reference genome of <i>Ensete glaucum</i> gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae
A chromosome-level reference genome of <i>Ensete glaucum</i> gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae Open
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 e…
View article: GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics Open
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 f…
View article: The banana genome hub: a community database for genomics in the Musaceae
The banana genome hub: a community database for genomics in the Musaceae Open
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 …
View article: First Report of <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> Tropical Race 4 Causing Fusarium Wilt in Cavendish Bananas in Peru
First Report of <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> Tropical Race 4 Causing Fusarium Wilt in Cavendish Bananas in Peru Open
Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), the causal agent of Fusarium wilt of banana (FWB), is currently the major threat to the banana industry worldwide (Dita et al. 2018). Restricted to South Asia for more than 20 ye…
View article: A chromosome-level reference genome of <i>Ensete glaucum</i> gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae
A chromosome-level reference genome of <i>Ensete glaucum</i> gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae Open
Background Ensete glaucum (2 n = 2 x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana ( Musa ). A high-quality reference genome sequence of E. glaucum offers a vital genomic resource for fun…