Structural variations in plant genomes, Brief Funct Genomics, vol.13, pp.296-307, 2014. ,
Structural variation in the human genome, Nat Rev Genet, vol.7, pp.85-97, 2006. ,
Structural variation in the human genome and its role in disease, Annu Rev Med, vol.61, pp.437-55, 2010. ,
Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome, Nat Genet, vol.38, pp.1038-1080, 2006. ,
Exploring the role of copy number variants in human adaptation, Trends Genet, vol.28, pp.245-57, 2012. ,
A genome-wide survey of R gene polymorphisms in Arabidopsis, Plant Cell, vol.18, pp.1803-1821, 2006. ,
Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis Thaliana, Genetics, vol.172, pp.1243-50, 2006. ,
Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean, Science, vol.338, pp.1206-1215, 2012. ,
Copy number variation affecting the photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum Aestivum), PLoS One, vol.7, p.33234, 2012. ,
Structural variants in the soybean genome localize to clusters of biotic stress-response genes, Plant Physiol, vol.159, pp.1295-308, 2012. ,
A Papaver Somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine, Science, vol.336, pp.1704-1712, 2012. ,
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes, Nat Biotechnol, vol.30, pp.105-116, 2012. ,
Aluminum tolerance in maize is associated with higher MATE1 gene copy number, Proc Natl Acad Sci U S A, vol.110, pp.5241-5247, 2013. ,
High presence/ absence gene variability in defense-related gene clusters of Cucumis Melo<br>, BMC Genomics, vol.14, p.782, 2013. ,
Whole genome de novo assemblies of three divergent strains of rice, Oryza Sativa, document novel gene space of aus and indica, Genome Biol, vol.15, p.506, 2014. ,
Following Tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two Homeologs, PLoS Biol, vol.8, p.1000409, 2010. ,
Numbers and distribution of chromosome knobs in United States maize, Genetics, vol.34, pp.524-560, 1949. ,
Chromosome constitution of races of maize; its significance in the interpretation of relationships between races and varieties in the Americas. Chromosome constitution of races of maize; its significance in the interpretation of relationships between races and varieties in the Americas, 1981. ,
Fluorescence in situ hybridization analysis reveals multiple loci of knob-associated DNA elements in one-knob and knobless maize lines, J Histochem Cytochem, vol.52, pp.1113-1119, 2004. ,
Organization and variability of the maize genome, Curr Opin Plant Biol, vol.9, pp.157-63, 2006. ,
Molecular and functional diversity of maize, Curr Opin Plant Biol, vol.9, pp.172-178, 2006. ,
Intraspecific violation of genetic colinearity and its implications in maize, Proc Natl Acad Sci U S A, vol.99, pp.9573-9581, 2002. ,
Evolution of DNA sequence nonhomologies among maize inbreds, Plant Cell, vol.17, pp.343-60, 2005. ,
Dynamic evolution of bz orthologous regions in the Andropogoneae and other grasses, Plant J, vol.72, pp.212-233, 2012. ,
Meiotic instability of the R-r complex arising from displaced intragenic exchange and intrachromosomal rearrangement, Genetics, vol.129, pp.271-83, 1991. ,
Unequal sister chromatid and homolog recombination at a tandem duplication of the A1 locus in maize, Genetics, vol.173, pp.2211-2237, 2006. ,
Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content, PLoS Genet, vol.5, p.1000734, 2009. ,
Allelic genome structural variations in maize detected by array comparative genome hybridization, Theor Appl Genet, vol.120, pp.355-67, 2010. ,
Maize HapMap2 identifies extant variation from a genome in flux, Nat Genet, vol.44, pp.803-810, 2012. ,
Insights into the Maize Pan-Genome and Pan-Transcriptome. The Plant Cell Online, 2014. ,
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize, The Plant Cell, 2016. ,
Genome-wide patterns of genetic variation among elite maize inbred lines, Nat Genet, vol.42, pp.1027-1057, 2010. ,
Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor, Genome Res, vol.20, pp.1689-99, 2010. ,
A European perspective on maize history, C R Biol, vol.334, pp.221-229, 2011. ,
Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts, PLoS Genet, vol.13, p.1006666, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01605143
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, Bioinformatics, vol.23, pp.1061-1068, 2007. ,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, pp.3210-3212, 2015. ,
MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings, Trends Genet, vol.24, pp.529-567, 2008. ,
Towards plant pangenomics, Plant Biotechnol J, vol.14, issue.4, pp.1099-105, 2015. ,
Genome assembly forensics: finding the elusive mis-assembly, Genome Biol, vol.9, p.55, 2008. ,
Exploring structural variants in environmentally sensitive gene families, Curr Opin Plant Biol, vol.30, pp.19-24, 2016. ,
Multiple reference genomes and transcriptomes for Arabidopsis Thaliana, Nature, vol.477, pp.419-442, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00909088
Transposable elements and the plant pan-genomes, Curr Opin Plant Biol, vol.10, pp.149-55, 2007. ,
Structural variation and genome complexity: is dispensable really dispensable?, Curr Opin Plant Biol, vol.18, pp.31-37, 2014. ,
The B73 maize genome: complexity, diversity, and dynamics, Science, vol.326, pp.1112-1117, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00751527
Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome, Genome Biol, vol.14, p.58, 2013. ,
Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber, Plant Cell, vol.27, pp.1595-604, 2015. ,
DNA recombination in somatic plant cells: mechanisms and evolutionary consequences, Chromosom Res, vol.22, pp.191-201, 2014. ,
Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution, Proc Natl Acad Sci, vol.103, pp.17638-17681, 2006. ,
Handbook of maize. Handbook of maize, pp.307-334, 2009. ,
Transposable Elements and the evolving structure of the maize genome, Experimental Biology, pp.2-36, 2011. ,
Improved maize reference genome with single-molecule technologies, Nature, vol.546, issue.7659, p.524, 2017. ,
Highresolution genetic mapping of maize pan-genome sequence anchors, Nat Commun, vol.6, p.6914, 2015. ,
Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene, Genetics, vol.172, pp.2449-63, 2006. ,
A cytometric exercise in plant DNA histograms, with 2C values for 70 species, Biol Cell, vol.78, pp.41-51, 1993. ,
Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-867, 2011. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads. Cutadapt removes adapter sequences from highthroughput sequencing reads, 2012. ,
Fast identification and removal of sequence contamination from genomic and metagenomic datasets, PLoS One, vol.6, 2011. ,
FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-63, 2011. ,
ABySS: a parallel assembler for short read sequence data, Genome Res, vol.19, pp.1117-1140, 2009. ,
Scaffolding preassembled contigs using SSPACE, Bioinformatics, vol.27, pp.578-587, 2011. ,
Toward almost closed genomes with GapFiller, Genome Biol, vol.13, p.56, 2012. ,
Versatile and open software for comparing large genomes ,
, Genome Biol, vol.5, p.12, 2004.
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads, Bioinformatics, vol.25, pp.2865-71, 2009. ,
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation, Nat Methods, vol.6, pp.677-81, 2009. ,
YAHA: fast and flexible long-read alignment with optimal breakpoint detection, Bioinformatics, vol.28, pp.2417-2441, 2012. ,
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision, Bioinformatics, vol.27, pp.595-603, 2011. ,
Repbase update, a database of repetitive elements in eukaryotic genomes, Mob DNA, vol.6, p.11, 2015. ,
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol, vol.14, p.36, 2013. ,
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat Biotechnol, vol.28, pp.511-516, 2010. ,
InterProScan 5: genome-scale protein function classification, Bioinformatics, vol.30, pp.1236-1276, 2014. ,
Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads, Genome Res, vol.21, pp.936-945, 2011. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2087, 2009. ,
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res, vol.22, pp.568-76, 2012. ,
A large maize (Zea Mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome, PLoS One, vol.6, p.28334, 2011. ,
Maximum likelihood from incomplete data via the EM algorithm, J R Stat Soc Ser B Methodol, vol.1977, pp.1-38, 1977. ,
Error rate control for classification rules in multi-class mixture models. 45e, J. Statistique, SFDS Proceedings, 2013. ,
FactoMineR: Aan R package for multivariate analysis, J Stat Softw, vol.25, pp.1-18, 2008. ,
Secondgeneration PLINK: rising to the challenge of larger and richer datasets, GigaScience, vol.4, p.7, 2015. ,