Abstract
Sugarcane exhibits a complex genome mainly due to its aneuploid nature and high ploidy level, and sequencing of its genome poses a great challenge. Closely related species with well-assembled and annotated genomes can be used to help assemble complex genomes. Here, a stable quantitative trait locus (QTL) related to sugar accumulation in sorghum was successfully transferred to the sugarcane genome. Gene sequences related to this QTL were identified in silico from sugarcane transcriptome data, and molecular markers based on these sequences were developed to select bacterial artificial chromosome (BAC) clones from the sugarcane variety SP80-3280. Sixty-eight BAC clones containing at least two gene sequences associated with the sorghum QTL were sequenced using Pacific Biosciences (PacBio) technology. Twenty BAC sequences were found to be related to the syntenic region, of which nine were sufficient to represent this region. The strategy we propose is called “targeted sequencing by gene synteny,” which is a simpler approach to understanding the genome structure of complex genomic regions associated with traits of interest.
Highlights
When no previously reported genome is available, genome reconstruction is based on a de novo assembly strategy
Sugarcane (Saccharum sp.) is the crop with the most complex genome structure because modern sugarcane varieties are derived from interspecific hybridization between Saccharum officinarum and Saccharum spontaneum
We propose the “targeted sequencing by gene synteny” strategy of sugarcane bacterial artificial chromosome (BAC) selection for the reconstruction of a complex sugarcane genome region linked to a quantitative trait locus (QTL) mapped for sugar accumulation (Brix) (Murray et al, 2008) at a specific position on sorghum chromosome 3 (SB-03), based on the high synteny between the sugarcane and sorghum genomes
Summary
When no previously reported genome is available, genome reconstruction is based on a de novo assembly strategy (based on sequence read overlap). This task becomes more complicated when an organism has a large genome with highly abundant repetitive elements. Polyploid species account for approximately one-third of all plants (Wood et al, 2009), many of which are crops with great economic importance, such as wheat, cotton, potato and sugarcane. The resulting hybrids are highly polyploid and aneuploid, with chromosome numbers ranging from 80 to 128 (D’Hont et al, 1998; Irvine, 1999; Grivet and Arruda, 2001) and an estimated whole-genome size of 10 Gb (D’Hont and Glaszmann, 2001). Previous studies have shown that ∼50% of the sugarcane genome is composed of repetitive sequences (Figueira et al, 2012; Kim et al, 2013; de Setta et al, 2014)
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