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
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Marie-Anne Van Sluys
    Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
  • Carolina Gimiliani Lembke
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Hayan Lee
    Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
  • Gabriel Rodrigues Alves Margarido
    Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP 13418-900, Brazil
  • Carlos Takeshi Hotta
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Jonas Weissmann Gaiarsa
    Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
  • Augusto Lima Diniz
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Mauro de Medeiros Oliveira
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Sávio de Siqueira Ferreira
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Milton Yutaka Nishiyama
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Felipe ten-Caten
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Geovani Tolfo Ragagnin
    Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
  • Pablo de Morais Andrade
    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
  • Robson Francisco de Souza
    Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
  • Gianlucca Gonçalves Nicastro
    Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
  • Ravi Pandya
    Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
  • Changsoo Kim
    Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
  • Hui Guo
    Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
  • Alan Mitchell Durham
    Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão, 1010, São Paulo, SP 05508-090, Brazil
  • Monalisa Sampaio Carneiro
    Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Washington Luis km 235, Araras, SP 13.565-905, Brazil
  • Jisen Zhang
    FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
  • Xingtan Zhang
    FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
  • Qing Zhang
    FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
  • Ray Ming
    FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
  • Michael C Schatz
    Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
  • Bob Davidson
    Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
  • Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
  • David Heckerman
    Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America

抄録

<jats:title>ABSTRACT</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>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.</jats:p> </jats:sec>

収録刊行物

  • GigaScience

    GigaScience 8 (12), 2019-11-29

    Oxford University Press (OUP)

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