S. Aflitos, Exploring genetic variation in the tomato (Solanum section lycopersicon) clade by whole-genome sequencing, Tomato Genome Sequencing Consortium, vol.100, pp.136-148, 2014.

S. Alseekh, Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato, Plant Cell, vol.27, pp.485-512, 2015.

K. Berlin, S. Koren, C. S. Chin, J. P. Drake, J. M. Landolin et al., Assembling large genomes with singlemolecule sequencing and locality-sensitive hashing, Nat. Biotechnol, vol.33, pp.623-630, 2015.

A. Bolger, The genome of the stress-tolerant wild tomato species Solanum pennellii, Nat. Genet, vol.46, pp.1034-1038, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01204066

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014.

M. E. Bolger, B. Arsova, and B. Usadel, Plant genome and transcriptome annotations: from misconceptions to simple solutions, Brief. Bioinform. pii, p.135, 2017.

C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos et al., BLAST+: architecture and applications, BMC Bioinformatics, vol.10, p.421, 2009.

E. Datema, R. J. Hulzink, L. Blommers, E. Valle-inclan, J. Van-orsouw et al., The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only, 2016.

A. M. Davis, Using MinION nanopore sequencing to generate a de novo eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga Galdieria sulphuraria strain SAG, 2016.

A. L. Delcher, S. L. Salzberg, and A. M. Phillippy, Using MUMmer to identify similar regions in large sequence sets, Curr. Protoc. Bioinformatics, vol.10, 2003.

S. Deschamps, J. Mudge, C. Cameron, T. Ramaraj, A. Anand et al., , 2016.

, Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens, Sci. Rep, vol.6, p.28625

S. R. Eddy, Accelerated Profile HMM Searches, PLOS Comput. Biol, vol.7, p.1002195, 2011.

D. M. Emms, K. , and S. , OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biol, vol.16, p.157, 2015.

Y. Eshed and D. Zamir, 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.

J. P. Fernandez-moreno, D. Levy-samoha, S. Malitsky, A. J. Monforte, D. Orzaez et al., Uncovering tomato quantitative trait loci and candidate genes for fruit cuticular lipid composition using the Solanum pennellii introgression line population, J. Exp. Bot, vol.68, pp.2703-2716, 2017.

T. C. Glenn, Field guide to next-generation DNA sequencers, Mol. Ecol. Resour, vol.11, pp.759-769, 2011.

A. Gurevich, V. Saveliev, N. Vyahhi, and G. Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics, vol.29, pp.1072-1075, 2013.

C. N. Hirsch, Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize, Plant Cell, vol.28, pp.2700-2714, 2016.

C. L. Ip, MinION Analysis and Reference Consortium (2015) MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000 Res, vol.4, p.1075

B. Istace, de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer, Gigascience, vol.6, pp.1-13, 2017.

M. Jain, H. E. Olsen, B. Paten, A. , and M. , The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community, Genome Biol, vol.17, p.239, 2016.

D. E. Jarvis, The genome of Chenopodium quinoa, Nature, vol.542, pp.307-312, 2017.

W. Jiao and K. Schneeberger, The impact of third generation genomic technologies on plant genome assembly, Curr. Opin. Plant Biol, vol.36, pp.64-70, 2017.

W. Jiao, Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data, Genome Res, vol.27, pp.778-786, 2017.

K. Judge, S. R. Harris, S. Reuter, J. Parkhill, and S. J. Peacock, Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes, J. Antimicrob. Chemother, vol.70, pp.2775-2778, 2015.

D. Koenig, Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato, Proc. Natl. Acad. Sci. USA, vol.110, pp.2655-2662, 2013.

S. Koren, B. P. Walenz, K. Berlin, J. R. Miller, N. H. Bergman et al., Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res, vol.27, pp.722-736, 2017.

A. Kranz, A. Vogel, U. Degner, I. Kiefler, M. Bott et al., High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads, J. Biotechnol, vol.258, pp.197-205, 2017.

H. Li, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, 2013.

H. Li, Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences, Bioinformatics, vol.32, pp.2103-2110, 2016.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Genome Project Data Processing Subgroup, vol.25, pp.2078-2079, 1000.

T. Lin, Genomic analyses provide insights into the history of tomato breeding, Nat. Genet, vol.46, pp.1220-1226, 2014.

Z. B. Lippman, Y. Semel, and D. Zamir, An integrated view of quantitative trait variation using tomato interspecific introgression lines, Curr. Opin. Genet. Dev, vol.17, pp.545-552, 2007.

J. Lisec, N. Schauer, J. Kopka, L. Willmitzer, and A. R. Fernie, Gas chromatography mass spectrometry-based metabolite profiling in plants, Nat. Protoc, vol.1, pp.387-396, 2006.

M. Lohse, A. Nagel, T. Herter, P. May, M. Schroda et al., Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data, Plant Cell Environ, vol.37, pp.1250-1258, 2014.

N. J. Loman, J. Quick, and J. T. Simpson, A complete bacterial genome assembled de novo using only nanopore sequencing data, Nat. Methods, vol.12, pp.733-735, 2015.

H. Lu, F. Giordano, and Z. Ning, Oxford Nanopore MinION Sequencing and Genome Assembly, Genomics Proteomics Bioinformatics, vol.14, pp.265-279, 2016.

E. Lyons and M. Freeling, How to usefully compare homologous plant genes and chromosomes as DNA sequences, Plant J, vol.53, pp.661-673, 2008.

G. Marçais and C. Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, vol.27, pp.764-770, 2011.

T. P. Michael, F. Jupe, F. Bemm, S. T. Motley, J. P. Sandoval et al., High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02626875

J. Molinier, M. E. Stamm, and B. Hohn, SNM-dependent recombinational repair of oxidatively induced DNA damage in Arabidopsis thaliana, EMBO Rep, vol.5, pp.994-999, 2004.

I. Ofner, J. Lashbrooke, T. Pleban, A. Aharoni, and D. Zamir, Solanum pennellii backcross inbred lines (BILs) link small genomic bins with tomato traits, Plant J, vol.87, pp.151-160, 2016.

K. Okonechnikov, A. Conesa, and F. García-alcalde, Qualimap 2: advanced multi-sample quality control for highthroughput sequencing data, Bioinformatics, vol.32, pp.292-294, 2016.

J. B. Pease, D. C. Haak, M. W. Hahn, and L. C. Moyle, Phylogenomics reveals three sources of adaptive variation during a rapid radiation, PLoS Biol, vol.14, p.1002379, 2016.

J. B. Pease, R. F. Guerrero, N. A. Sherman, M. W. Hahn, and L. C. Moyle, Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis, Mol. Ecol, vol.25, pp.2592-2608, 2016.

M. J. Peña, R. Zhong, G. K. Zhou, E. A. Richardson, M. A. O'neill et al., Arabidopsis irregular xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis, Plant Cell, vol.19, pp.549-563, 2007.

L. Quadrana, Natural occurring epialleles determine vitamin E accumulation in tomato fruits, Nat. Commun, vol.5, p.3027, 2014.

J. Quick, Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella, Genome Biol, vol.16, p.114, 2015.

A. Ranjan, J. M. Budke, S. D. Rowland, D. H. Chitwood, R. Kumar et al., eQTL regulating transcript levels associated with diverse biological processes in tomato, Plant Physiol, vol.172, pp.328-340, 2016.

S. Reyes-chin-wo, Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce, Nat. Commun, vol.8, p.14953, 2017.

C. M. Rick and S. D. Tanksley, Genetic variation in Solanum pennellii: Comparisons with two other sympatric tomato species, Plant Syst. Evol, vol.139, pp.11-45, 1981.

F. A. Simão, R. M. Waterhouse, P. Ioannidis, E. V. Kriventseva, and E. M. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, pp.3210-3212, 2015.

J. T. Simpson, R. E. Workman, P. C. Zuzarte, M. David, L. J. Dursi et al., Detecting DNA cytosine methylation using nanopore sequencing, Nat. Methods, vol.14, pp.407-410, 2017.

M. M. Sohani, P. M. Schenk, C. J. Schultz, and O. Schmidt, Phylogenetic and transcriptional analysis of a strictosidine synthase-like gene family in Arabidopsis thaliana reveals involvement in plant defence responses, Plant Biol (Stuttg.), vol.11, pp.105-117, 2009.

M. Stanke and S. Waack, Gene prediction with a hidden Markov model and a new intron submodel, Bioinformatics, vol.19, pp.215-225, 2003.

M. Stanke, M. Diekhans, R. Baertsch, and D. Haussler, Using native and syntenically mapped cDNA alignments to improve de novo gene finding, Bioinformatics, vol.24, pp.637-644, 2008.

D. Tieman, A chemical genetic roadmap to improved tomato flavor, Science, vol.355, pp.391-394, 2017.

, The tomato genome sequence provides insights into fleshy fruit evolution, Tomato Genome Consortium, vol.485, pp.635-641, 2012.

R. Vanburen, Single-molecule sequencing of the desiccationtolerant grass Oropetium thomaeum, Nature, vol.527, pp.508-511, 2015.

R. Vaser, I. Sovi?, N. Nagarajan, and M. Siki?, Fast and accurate de novo genome assembly from long uncorrected reads, 2017.

, Genome Res, vol.27, pp.737-746

B. J. Walker, T. Abeel, T. Shea, M. Priest, A. Abouelliel et al., Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement, PLoS One, vol.9, p.112963, 2014.

Y. Wang, H. Tang, J. D. Debarry, X. Tan, J. Li et al., MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity, Nucleic Acids Res, vol.40, p.49, 2012.

X. Wang, Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction, Nat. Genet, vol.49, pp.765-772, 2017.

J. Weirather, M. De-cesare, Y. Wang, P. Piazza, V. Sebastiano et al., Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis, vol.6, p.100, 1000.

C. Ye, C. M. Hill, S. Wu, J. Ruan, and Z. S. Ma, DBG2OLC: Efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies, Sci. Rep, vol.6, p.31900, 2016.

S. Zhong, Z. Fei, Y. R. Chen, Y. Zheng, M. Huang et al., Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening, Nat. Biotechnol, vol.31, pp.154-159, 2013.

, , 2017.

A. M. Zamir, B. Bolger, and . Usadel,

R. Schurr, F. Chetelat, J. Maumus, S. Aury, A. R. Koren et al.,

M. Schmidt, A. Vogel, A. K. Denton, and B. Istace, Alexandra Accession Using Nanopore Sequencing Solanum pennellii De Novo Assembly of a New