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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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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Author(s):
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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]
Total Authors: 29
Affiliation:
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[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
Total Affiliations: 16
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: 12/51062-3 - Development of an algorithm for the assembly of the sugarcane polyploid genome
Grantee:Glaucia Mendes Souza
Support type: Program for Research on Bioenergy (BIOEN) - Research Partnership for Technological Innovation (PITE)
FAPESP's process: 11/50761-2 - Models and methods of e-Science for life and agricultural sciences
Grantee:Roberto Marcondes Cesar Junior
Support type: 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 type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 13/07467-1 - CeTICS - Center of Toxins, Immune-Response and Cell Signaling
Grantee:Hugo Aguirre Armelin
Support type: 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 type: Program for Research on Bioenergy (BIOEN) - Thematic Grants
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 type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 14/50921-8 - Signaling and regulatory network studies associated to the energy cane
Grantee:Glaucia Mendes Souza
Support type: 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 type: 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 type: Program for Research on Bioenergy (BIOEN) - 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 type: 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 type: Scholarships in Brazil - Post-Doctorate