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It is estimated that sugarcane contributes ~80% of world sugar content. Sugarcane ( Saccharum spp.) is used worldwide for the production of sugar, bioethanol, and energy ( OECD and FAO, 2019), making this crop a main component for the economy of tropical and subtropical countries ( Kandel et al., 2018). We expect the resources presented here to serve as a source of information to improve the selection processes of new varieties of the breeding programs of sugarcane. Analysis of RNA-Seq data from leaf and root tissue of contrasting sugarcane genotypes subjected to water stress treatments revealed 17,490 differentially expressed genes, from which 3,633 correspond to genes expressed exclusively in tolerant genotypes. spontaneum genome confirms the presence of translocation events between the species and a random contribution throughout the entire genome in current sugarcane hybrids. Synteny analysis between CC 01-1940 and the S. Nucleotide evolution measurements between orthologs with close species suggest that divergence between Saccharum officinarum and Saccharum spontaneum occurred <2 million years ago. We annotated a total of 63,724 protein coding genes and performed a reconstruction and comparative analysis of the sucrose metabolism pathway. We achieved a median contig length of 34.94 Mbp and a total genome assembly of 903.2 Mbp. Three types of sequencing technologies were combined for this assembly: PacBio long reads, Illumina paired short reads, and Hi-C reads. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. 5Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.4Earlham Institute, Norwich Research Park, Norwich, United Kingdom.3Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Faculty of Engineering, Universidad de los Andes, Bogotá, Colombia.2Research Group in Bioinformatics, Department of Computer Science, Faculty of Engineering, Universidad Del Valle, Cali, Colombia.1Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia.Jhon Henry Trujillo-Montenegro 1,2, María Juliana Rodríguez Cubillos 3, Cristian Darío Loaiza 1, Manuel Quintero 1, Héctor Fabio Espitia-Navarro 1, Fredy Antonio Salazar Villareal 1, Carlos Arturo Viveros Valens 1, Andrés Fernando González Barrios 3, José De Vega 4, Jorge Duitama 5 and John J.