Genomic variation in tomato, from wild ancestors to contemporary breeding accessions, BMC Genomics, vol.16, p.257, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02638064
Genomic analyses provide insights into the history of tomato breeding, Nat. Genet, vol.46, pp.1220-1226, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02639866
The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor, Nat. Genet, vol.51, pp.1044-1051, 2019. ,
Natural variations and genome-wide association studies in crop plants, Annu. Rev. Plant Biol, vol.65, pp.531-551, 2014. ,
Molecular markers in a commercial breeding program, Crop Sci, vol.47, p.154, 2007. ,
Evolution of crop species: genetics of domestication and diversification, Nat. Rev. Genet, vol.14, pp.840-852, 2013. ,
Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus, Nat. Plants, vol.6, pp.34-45, 2020. ,
Structural variants in 3000 rice genomes, Genome Res, vol.29, pp.870-880, 2019. ,
The impact of transposable elements on the structure, evolution and function of the rice genome, N. Phytol, vol.226, pp.44-49, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02434127
The population genetics of structural variants in grapevine domestication, Nat. Plants, vol.5, pp.965-979, 2019. ,
Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement, Nat. Genet, vol.51, pp.1052-1059, 2019. ,
Next-generation sequencing technologies and their implications for crop genetics and breeding, Trends Biotechnol, vol.27, pp.522-530, 2009. ,
Finding the missing heritability of complex diseases, Nature, vol.461, pp.747-753, 2009. ,
An integrated map of structural variation in 2,504 human genomes, Nature, vol.526, pp.75-81, 2015. ,
How important are transposons for plant evolution?, Nat. Rev. Genet, vol.14, pp.49-61, 2013. ,
Integration site selection by retroviruses and transposable elements in eukaryotes, Nat. Rev. Genet, vol.18, pp.292-308, 2017. ,
Regulatory activities of transposable elements: from conflicts to benefits, Nat. Rev. Genet, vol.18, pp.71-86, 2017. ,
Identification of a functional transposon insertion in the maize domestication gene tb1, Nat. Genet, vol.43, pp.1160-1163, 2011. ,
The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme, Cell, vol.60, pp.115-122, 1990. ,
Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions, Mol. Genet. Genomics, vol.274, pp.131-140, 2005. ,
Bypassing negative epistasis on yield in tomato imposed by a domestication gene, Cell, vol.169, pp.1142-1155, 2017. ,
A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit, Science, vol.319, pp.1527-1530, 2008. ,
Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening, BMC Genomics, vol.17, p.624, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-02631886
, The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution, Nature, vol.485, pp.635-641, 2012.
A chemical genetic roadmap to improved tomato flavor, Science, vol.355, pp.391-394, 2017. ,
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing, Plant J, vol.80, pp.136-148, 2014. ,
The Arabidopsis thaliana mobilome and its impact at the species level, Elife, vol.5, p.15716, 2016. ,
Shoot branching and leaf dissection in tomato are regulated by homologous gene modules, Plant Cell, vol.23, pp.3595-3609, 2011. ,
Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato, Sci. Rep, vol.7, p.4402, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01606968
How selfish is DNA?, Nature, vol.285, pp.617-618, 1980. ,
Transposition favors the generation of large effect mutations that may facilitate rapid adaption, Nat. Commun, vol.10, p.3421, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02398702
Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect, Genetics, vol.199, pp.85-93, 2015. ,
Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation, vol.5, p.20777, 2016. ,
Transposable elements are important contributors to standing variation in gene expression in Capsella grandiflora, Mol. Biol. Evol, vol.36, pp.1734-1745, 2019. ,
Rewiring of the fruit metabolome in tomato breeding, Cell, vol.172, pp.249-261, 2018. ,
A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses, Genes Dev, vol.32, pp.1155-1160, 2018. ,
Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato, Theor. Appl. Genet, vol.126, pp.2643-2653, 2013. ,
Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq, BMC Plant Biol, vol.14, p.120, 2014. ,
Characterization of a new xyloglucan endotransglucosylase/hydrolase (XTH) from ripening tomato fruit and implications for the diverse modes of enzymic action, Plant J, vol.47, pp.282-295, 2006. ,
Regulation of ripening and opportunities for control in tomato and other fruits, Plant Biotechnol. J, vol.11, pp.269-278, 2013. ,
Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression, Plant Mol. Biol, vol.22, pp.589-602, 1993. ,
The origin of the cultivated tomato, Economic Bot, vol.2, pp.379-392, 1948. ,
Plant volatiles, Curr. Biol, vol.20, pp.392-397, 2010. ,
Identification of malodorous, a wild species allele affecting tomato aroma that was selected against during domestication, J. Agric. Food Chem, vol.50, 2002. ,
Allyl/propenyl phenol synthases from the creosote bush and engineering production of specialty/commodity chemicals, eugenol/ isoeugenol, in Escherichia coli, Arch. Biochem. Biophys, vol.541, pp.37-46, 2014. ,
An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL, Genetics, vol.141, pp.1147-1162, 1995. ,
The genome of the stress-tolerant wild tomato species Solanum pennellii, Nat. Genet, vol.46, pp.1034-1037, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01204066
Identification of loci affecting flavour volatile emissions in tomato fruits, J. Exp. Bot, vol.57, pp.887-896, 2006. ,
Genomic evidence for complex domestication history of the cultivated tomato in Latin America, Mol. Biol. Evol, vol.37, pp.1118-1132, 2020. ,
Retrotranspositional landscape of Asian rice revealed by 3000 genomes, Nat. Commun, vol.10, p.24, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02098307
Relaxed purifying selection in autopolyploids drives transposable element overaccumulation which provides variants for local adaptation, Nat. Commun, vol.10, p.5818, 2019. ,
DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity, Genome Res, vol.26, pp.1520-1531, 2016. ,
Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot, Mob. DNA, vol.1, pp.1-17, 2019. ,
Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae), Mol. Ecol. Resour, vol.19, pp.773-787, 2019. ,
Transposable element evolution in the allotetraploid Capsella bursa-pastoris, Am. J. Bot, vol.103, pp.1197-1202, 2016. ,
Major Impacts of widespread structural variation on gene expression and crop improvement in tomato, Cell, vol.182, pp.145-161, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02927024
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell, Nat. Commun, vol.9, p.541, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02626875
Efficient detection of transposable element insertion polymorphisms between genomes using short-read sequencing data, 2020. ,
RaGOO: fast and accurate reference-guided scaffolding of draft genomes, Genome Biol, vol.20, p.224, 2019. ,
A benchmark of transposon insertion detection tools using real data, Mob. DNA, vol.10, p.53, 2019. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014. ,
PLINK: a tool set for whole-genome association and population-based linkage analyses, Am. J. Hum. Genet, vol.81, pp.559-575, 2007. ,
Variance component model to account for sample structure in genome-wide association studies, Nat. Genet, vol.42, pp.348-354, 2010. ,
qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots, 2014. ,
Assembling genomes and minimetagenomes from highly chimeric reads, Res. Comput. Mol. Biol, vol.10, pp.158-170, 2013. ,
A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase, Am. J. Hum. Genet, vol.78, pp.629-644, 2006. ,
Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, vol.34, pp.3094-3100, 2018. ,