X. Argout, J. Salse, J. Aury, M. Guiltinan, G. Droc et al., The genome of Theobroma cacao, Nature Genetics, vol.11, issue.2, pp.101-109, 2011.
DOI : 10.1101/gr.1224503

URL : https://hal.archives-ouvertes.fr/hal-00855922

J. Motamayor, P. Lachenaud, E. Da-silva, J. Mota, R. Loor et al., Geographic and Genetic Population Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L), PLoS ONE, vol.53, issue.10, p.3311, 2008.
DOI : 10.1371/journal.pone.0003311.s005

X. Argout, O. Fouet, P. Wincker, K. Gramacho, T. Legavre et al., Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions, BMC Genomics, vol.9, issue.1, p.512, 2008.
DOI : 10.1186/1471-2164-9-512

J. Motamayor, K. Mockaitis, J. Schmutz, N. Haiminen, I. Dl et al., The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color, Genome Biology, vol.29, issue.6, p.53, 2013.
DOI : 10.1093/nar/29.9.e45

P. Chain, D. Grafham, R. Fulton, M. Fitzgerald, J. Hostetler et al., Genome Project Standards in a New Era of Sequencing, Science, vol.36, issue.suppl_1, pp.236-243, 2009.
DOI : 10.1093/nar/gkm884

C. Alkan, S. Sajjadian, and E. Eichler, Limitations of next-generation genome sequence assembly, Nature Methods, vol.431, issue.1, pp.61-66, 2011.
DOI : 10.1038/nmeth.1451

A. English, S. Richards, Y. Han, M. Wang, V. Vee et al., Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology, PLoS ONE, vol.15, issue.Suppl 1, p.47768, 2012.
DOI : 10.1371/journal.pone.0047768.t003

M. Boetzer, C. Henkel, H. Jansen, D. Butler, and W. Pirovano, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, vol.27, issue.4, pp.578-587, 2011.
DOI : 10.1093/bioinformatics/btq683

S. Kosugi, H. Hirakawa, and S. Tabata, GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments, Bioinformatics, vol.https, 2015.
DOI : 10.1093/bioinformatics/btv465

G. Martin, F. Baurens, G. Droc, M. Rouard, A. Cenci et al., Improvement of the banana ???Musa acuminata??? reference sequence using NGS data and semi-automated bioinformatics methods, BMC Genomics, vol.2013, issue.1, p.243, 2016.
DOI : 10.1093/database/bat035

X. Huang, Q. Feng, Q. Qian, Q. Zhao, L. Wang et al., High-throughput genotyping by whole-genome resequencing, Genome Research, vol.19, issue.6, pp.1068-76, 2009.
DOI : 10.1101/gr.089516.108

M. Mascher and N. Stein, Genetic anchoring of whole-genome shotgun assemblies, Frontiers in Genetics, vol.107, issue.e1000212, p.208, 2014.
DOI : 10.1073/pnas.1005931107

A. Glazer, E. Killingbeck, T. Mitros, D. Rokhsar, and C. Miller, Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing, G3: Genes|Genomes|Genetics, vol.5, issue.7, pp.1463-72, 2015.
DOI : 10.1534/g3.115.017905

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, issue.1, pp.10-12, 2011.
DOI : 10.14806/ej.17.1.200

L. Salmela and E. Rivals, LoRDEC: accurate and efficient long read error correction, Bioinformatics, vol.30, issue.24, 2014.
DOI : 10.1093/bioinformatics/btu538

URL : https://hal.archives-ouvertes.fr/lirmm-01100451

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-366, 2012.
DOI : 10.1093/bioinformatics/btp352

C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos et al., BLAST+: architecture and applications, BMC Bioinformatics, vol.10, issue.1, p.421, 2009.
DOI : 10.1186/1471-2105-10-421

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, GigaScience, vol.1, issue.1, p.18, 2012.
DOI : 10.1186/2047-217X-1-18

J. Glaubitz, T. Casstevens, F. Lu, J. Harriman, R. Elshire et al., TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline, PLoS ONE, vol.22, issue.5, p.90346, 2014.
DOI : 10.1371/journal.pone.0090346.s002

P. Danecek, A. Auton, G. Abecasis, C. Albers, E. Banks et al., The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, pp.2156-2164, 2011.
DOI : 10.1093/bioinformatics/btr330

J. Van-ooijen, Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species, Genetics Research, vol.79, issue.05, pp.343-352, 2011.
DOI : 10.1006/tpbi.2002.1577

E. Zdobnov and R. Apweiler, InterProScan - an integration platform for the signature-recognition methods in InterPro, Bioinformatics, vol.17, issue.9, pp.847-855, 2001.
DOI : 10.1093/bioinformatics/17.9.847

S. Hunter, R. Apweiler, T. Attwood, A. Bairoch, A. Bateman et al., InterPro: the integrative protein signature database, Nucleic Acids Research, vol.37, issue.Database, pp.211-216, 2009.
DOI : 10.1093/nar/gkn785

URL : https://hal.archives-ouvertes.fr/hal-00428250

M. Kanehisa, M. Furumichi, M. Tanabe, Y. Sato, and K. Morishima, KEGG: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Research, vol.45, issue.D1, 2016.
DOI : 10.1093/nar/gkw1092

M. Kanehisa, Y. Sato, and K. Morishima, BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences, Journal of Molecular Biology, vol.428, issue.4, pp.726-757, 2016.
DOI : 10.1016/j.jmb.2015.11.006

N. Kane, S. Sveinsson, H. Dempewolf, J. Yang, D. Zhang et al., Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA, American Journal of Botany, vol.99, issue.2, pp.320-329, 2012.
DOI : 10.3732/ajb.1100570

G. Liu, D. Cao, S. Li, A. Su, J. Geng et al., The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes Adaptive seeds tame genomic sequence comparison, PLoS One. Genome Research, vol.821, issue.3, pp.487-93, 2011.

C. Rezvoy, D. Charif, L. Gueguen, and G. Marais, MareyMap: an R-based tool with graphical interface for estimating recombination rates, Bioinformatics, vol.23, issue.16, pp.2188-2197, 2007.
DOI : 10.1093/bioinformatics/btm315

URL : https://hal.archives-ouvertes.fr/hal-00434645