{"id":657888,"date":"2020-05-11T09:39:30","date_gmt":"2020-05-11T16:39:30","guid":{"rendered":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/?post_type=msr-research-item&#038;p=657888"},"modified":"2020-05-11T09:39:30","modified_gmt":"2020-05-11T16:39:30","slug":"assembly-of-the-373k-gene-space-of-the-polyploid-sugarcane-genome-reveals-reservoirs-of-functional-diversity-in-the-worlds-leading-biomass-crop","status":"publish","type":"msr-research-item","link":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/publication\/assembly-of-the-373k-gene-space-of-the-polyploid-sugarcane-genome-reveals-reservoirs-of-functional-diversity-in-the-worlds-leading-biomass-crop\/","title":{"rendered":"Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world&#8217;s leading biomass crop"},"content":{"rendered":"<div class=\"sec\">\n<div class=\"title\"><strong>Background<\/strong><\/div>\n<p class=\"chapter-para\">Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10\u201313 sets of chromosomes from 2\u00a0<em>Saccharum<\/em> species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing.<\/p>\n<\/div>\n<div class=\"sec\">\n<div class=\"title\"><strong>Results<\/strong><\/div>\n<p class=\"chapter-para\">Here 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\u20136 (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\u00a0<em>Saccharum spontaneum<\/em>. 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 \u201csubgenomes\u201d after their divergence \u223c3.8\u20134.6 million years ago and reveals single-nucleotide variants that may underlie their differences.<\/p>\n<\/div>\n<div class=\"sec\">\n<div class=\"title\"><strong>Conclusions<\/strong><\/div>\n<p class=\"chapter-para\">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.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Background Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10\u201313 sets of chromosomes from 2\u00a0Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. Results Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory 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