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

Author(s):Show less -

Souza, Glaucia Mendes ^[1] ; Van Sluys, Marie-Anne ^[2] ; Lembke, Carolina Gimiliani ^[1] ; Lee, Hayan ^{[3, 4]} ; Margarido, Gabriel Rodrigues Alves ^[5] ; Hotta, Carlos Takeshi ^[1] ; Gaiarsa, Jonas Weissmann ^[2] ; Diniz, Augusto Lima ^[1] ; Oliveira, Mauro de Medeiros ^[1] ; Ferreira, Savio de Siqueira ^{[1, 2]} ; Nishiyama, Milton Yutaka ^{[1, 6]} ; ten-Caten, Felipe ^[1] ; Ragagnin, Geovani Tolfo ^[2] ; Andrade, Pablo de Morais ^[1] ; de Souza, Robson Francisco ^[7] ; Nicastro, Gianlucca Goncalves ^[7] ; Pandya, Ravi ^[8] ; Kim, Changsoo ^{[9, 10]} ; Guo, Hui ^[9] ; Durham, Alan Mitchell ^[11] ; Carneiro, Monalisa Sampaio ^[12] ; Zhang, Jisen ^[13] ; Zhang, Xingtan ^[13] ; Zhang, Qing ^[13] ; Ming, Ray ^{[13, 14]} ; Schatz, Michael C. ^{[4, 15, 16]} ; Davidson, Bob ^[8] ; Paterson, Andrew H. ^[9] ; Heckerman, David ^[8]

Affiliation:Show less -

^[1] Univ Sao Paulo, Inst Quim, Dept Bioquim, Ave Prof Lineu Prestes 748, BR-05508000 Sao Paulo, SP - Brazil

^[2] Univ Sao Paulo, Inst Biociencias, Dept Bot, Rua Matao 277, BR-05508090 Sao Paulo, SP - Brazil

^[3] US DOE, Joint Genome Inst, 2800 Mitchell Dr, Walnut Creek, CA 94598 - USA

^[4] Cold Spring Harbor Lab, One Bungtown Rd, Koch Bldg 1119, Cold Spring Harbor, NY 11724 - USA

^[5] Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, Ave Padua Dias 11, BR-13418900 Piracicaba, SP - Brazil

^[6] Inst Butantan, Lab Especial Toxinol Aplicada, Ave Vital Brasil 1500, BR-5503900 Sao Paulo, SP - Brazil

^[7] Univ Sao Paulo, Inst Ciencias Biomed, Dept Microbiol, Ave Prof Lineu Prestes 1734, BR-05508900 Sao Paulo, SP - Brazil

^[8] Microsoft Res, One Microsoft Way, Redmond, WA 98052 - USA

^[9] Univ Georgia, Plant Genome Mapping Lab, 120 Green St, Athens, GA 30602 - USA

^[10] Chungnam Natl Univ, Dept Crop Sci, 99 Daehak Ro, Deajeon 34134 - South Korea

^[11] Univ Sao Paulo, Inst Matemat & Estat, Dept Ciencias Computacao, Rua Matao 1010, BR-05508090 Sao Paulo, SP - Brazil

^[12] Univ Fed Sao Carlos, Ctr Ciencias Agr, Dept Biotecnol & Prod Vegetal & Anim, Rodovia Washington Luis Km 235, BR-13565905 Araras, SP - Brazil

^[13] Fujian Agr & Forestry Univ, FAFU & UIUC SIB Joint Ctr Genom & Biotechnol, Shangxiadian Rd, Fuzhou 350002, Fujian - Peoples R China

^[14] Univ Illinois, Dept Plant Biol, 201 W Gregory Dr Urbana, Urbana, IL 61801 - USA

^[15] Johns Hopkins Univ, Dept Comp Sci, 3400 North Charles St, Baltimore, MD 21218 - USA

^[16] Johns Hopkins Univ, Dept Biol, 3400 North Charles St, Baltimore, MD 21218 - USA

• Document type: Journal article
• Source: GIGASCIENCE; v. 8, n. 12 DEC 2019.
• Web of Science Citations: 3

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: 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: 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: 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: 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: 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: 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-Doctorate
• 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: 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
• 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-Doctorate
• 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-Doctorate
• 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