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

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

• Document type: Journal article
• Source: GIGASCIENCE; v. 8, n. 12, p. 18-pg., 2019-12-01.

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 similar to 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. (AU)

• FAPESP's process: 14/50921-8 - Signaling and regulatory network studies associated to the energy cane
• Grantee: Glaucia Mendes Souza
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• FAPESP's process: 08/52074-0 - Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function
• Grantee: Marie-Anne Van Sluys
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• FAPESP's process: 15/22993-7 - Transcriptomics for the identification of commercially important genes in sugarcane
• Grantee: Gabriel Rodrigues Alves Margarido
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants
• FAPESP's process: 08/52146-0 - Sugarcane signaling and regulatory networks
• Grantee: Glaucia Mendes Souza
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• FAPESP's process: 12/51062-3 - Development of an algorithm for the assembly of the sugarcane polyploid genome
• Grantee: Glaucia Mendes Souza
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Research Partnership for Technological Innovation (PITE)
• FAPESP's process: 13/07467-1 - CeTICS - Center of Toxins, Immune-Response and Cell Signaling
• Grantee: Hugo Aguirre Armelin
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 17/02270-6 - Evaluation of contrasting progenies transcriptome for the accumulation of biomass and identification of regulation networks
• Grantee: Augusto Lima Diniz
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 11/50761-2 - Models and methods of e-Science for life and agricultural sciences
• Grantee: Roberto Marcondes Cesar Junior
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 13/23048-9 - Functional analysis of sugarcane promoters and their allelic variation
• Grantee: Sávio de Siqueira Ferreira
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 16/06917-1 - Transcriptomic analysis and co-expression network construction in model systems for identification of genes involved in secondary cell wall deposition and lignin metabolism in grasses
• Grantee: Sávio de Siqueira Ferreira
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 16/17545-8 - Genes, genomes & transposable elements contribution to plant-microbe interaction: a sugarcane study case
• Grantee: Marie-Anne Van Sluys
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants