Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop

Glaucia Mendes Souza, Marie Anne Van Sluys, Carolina Gimiliani Lembke, Hayan Lee, Gabriel Rodrigues Alves Margarido, Carlos Takeshi Hotta, Jonas Weissmann Gaiarsa, Augusto Lima Diniz, Mauro De Medeiros Oliveira, Sávio De Siqueira Ferreira, Milton Yutaka Nishiyama, Felipe Ten-Caten, Geovani Tolfo Ragagnin, Pablo De Morais Andrade, Robson Francisco De Souza, Gianlucca Gonçalves Nicastro, Ravi Pandya, Changsoo Kim, Hui Guo, Alan Mitchell DurhamMonalisa Sampaio Carneiro, Jisen Zhang, Xingtan Zhang, Qing Zhang, Ray Ming, Michael C. Schatz, Bob Davidson, Andrew H. Paterson, David Heckerman

Research output: Contribution to journalArticle

Abstract

Background: Sugarcane 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. Results: 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 2-6 (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. 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.

Original languageEnglish (US)
Article numbergiz129
JournalGigaScience
Volume8
Issue number12
DOIs
StatePublished - Dec 6 2019

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Keywords

  • allele
  • bioenergy
  • biomass
  • genome
  • polyploid

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

Cite this

Souza, G. M., Van Sluys, M. A., Lembke, C. G., Lee, H., Margarido, G. R. A., Hotta, C. T., Gaiarsa, J. W., Diniz, A. L., Oliveira, M. D. M., Ferreira, S. D. S., Nishiyama, M. Y., Ten-Caten, F., Ragagnin, G. T., Andrade, P. D. M., De Souza, R. F., Nicastro, G. G., Pandya, R., Kim, C., Guo, H., ... Heckerman, D. (2019). Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. GigaScience, 8(12), [giz129]. https://doi.org/10.1093/gigascience/giz129