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Review
. 2018 May 14:9:616.
doi: 10.3389/fpls.2018.00616. eCollection 2018.

The Challenge of Analyzing the Sugarcane Genome

Prathima P Thirugnanasambandam  1   2 , Nam V Hoang  3 , Robert J Henry  1
Affiliations
Review

The Challenge of Analyzing the Sugarcane Genome

Prathima P Thirugnanasambandam et al. Front Plant Sci. .

Abstract

Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.

Keywords: comparative genomics; genome sequencing; genome translating; polyploid genome; progenitors species; sugarcane genome; sugarcane sequencing.

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Figures

FIGURE 1
FIGURE 1
Scheme of the sugarcane hybrid nuclear sub-genomes and the genetic contributions of each parental species, the chloroplast genome and the mitochondrial genomes. Adapted from (D’Hont et al., 1996, 1998; Piperidis et al., 2010; Hoang et al., 2015b; Aitken et al., 2016; Shearman et al., 2016; Garsmeur et al., 2017).
FIGURE 2
FIGURE 2
Sequencing strategies proposed for sugarcane genome. (A) BAC by BAC sequencing strategy. (B) Whole genome shotgun sequencing by short-read and long-read technologies and de novo assembly. To simplify, the assembly of one chromosome (out of 10) is shown here. Adapted from (Aitken et al., 2016; Garsmeur et al., 2017).
FIGURE 3
FIGURE 3
Evolutionary history of sugarcane (Saccharum hybrids) in comparison with progenitor species S. officinarum, S. spontaneum, S. robustum, S. sinense, S. edule and other related genera in PACMAD and BEP clades. The whole genome doubling events are denoted by yellow ovals. Figure adapted and redrawn from (D’Hont et al., 2008; Metcalfe et al., 2015).
See this image and copyright information in PMC

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