Abstract
ABSTRACTBackgroundSugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing.ResultsHere we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2–6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 “subgenomes” after their divergence ∼3.8–4.6 million years ago and reveals single-nucleotide variants that may underlie their differences.ConclusionsThis assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.
Highlights
Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets of chromosomes from 2 Saccharum species
We report a representative gene space assembly of the genome sequence of SP80-3280 (GenBank accession number QPEU01000000), the cultivar used in Brazilian breeding programs with the largest collection of transcriptomic data available [20]
For a large fraction of the gene space, an average of 6 sugarcane haplotypes, putatively homo(eo)logs, were identified. This is the first release of an assembly of such a giant hybrid polyploid genome with part of the putatively homo(eo)logs resolved and their potential regulatory regions
Summary
Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets of chromosomes from 2 Saccharum species. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2–6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. Conclusions: This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production. Sugarcane bioenergy production by 2045 could displace up to 13.7% of crude oil consumption and 5.6% of the world’s CO2 emissions relative to 2014 This can be achieved without using forest preservation areas or land necessary for food production systems. The myriad of products that can derive from sugarcane biomass [8] further enhance opportunities for sugarcane in a portfolio of technologies needed to transition to a low-carbon “bioeconomy.”
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