Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid.

Jhon Henry Trujillo-Montenegro,Héctor Fabio Espitia-Navarro,María Juliana Rodríguez Cubillos,Carlos Arturo Viveros Valens,John J Riascos,Fredy Antonio Salazar Villareal,Jorge Duitama,José De Vega,Manuel Quintero,Cristian Darío Loaiza,Andrés Fernando González Barrios

doi:10.3389/fpls.2021.694859

Abstract

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. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940. Three types of sequencing technologies were combined for this assembly: PacBio long reads, Illumina paired short reads, and Hi-C reads. We achieved a median contig length of 34.94 Mbp and a total genome assembly of 903.2 Mbp. We annotated a total of 63,724 protein coding genes and performed a reconstruction and comparative analysis of the sucrose metabolism pathway. Nucleotide evolution measurements between orthologs with close species suggest that divergence between Saccharum officinarum and Saccharum spontaneum occurred <2 million years ago. Synteny analysis between CC 01-1940 and the S. spontaneum genome confirms the presence of translocation events between the species and a random contribution throughout the entire genome in current sugarcane hybrids. 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. 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.

Highlights

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 generated a pseudo-chromosome assembly of sugarcane genome from CC 01-1940, a Colombian sugarcane hybrid generated by the breeding program of CENICAÑA
An initial flow cytometry experiment revealed that the CC 01-1940 variety contains approximately a total amount of DNA of 11.21 ± 0.374 Gbp and its monoploid genome has a size of 1.019 ± 0.031 Gbp based on 11X ploidy (Supplementary Table 1)

Summary

Introduction

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). It is estimated that sugarcane contributes ∼80% of world sugar content. In the case of Colombia, the sugar industry has contributed significantly to Unraveling the Genome of a Colombian Sugarcane Hybrid the economical development of the country and it is considered one of the most efficient sugar industries in the world. The species S. officinarum and S. spontaneum possess polyploid genomes, with different chromosomal constitutions (Zhang et al, 2018). Current hybrids are polyploid with a non-uniform distribution of chromosomes in the same group (aneuploidy), in addition to a highly variable chromosomal constitution (x = 10–13, 2n = 100–130). The genome size of commercial sugarcane hybrids is variable and is estimated to be close to 10 Gbp (Moore et al, 2013)

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Results

Conclusion