Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop
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, Sávio de Siqueira; Nishiyama Junior, Milton Yutaka; ten-Caten, Felipe; Ragagnin, Geovani Tolfo; Andrade, Pablo de Morais; Souza, Robson Francisco de; Nicastro, Gianlucca Gonçalves; 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.
Gigascience, v. 8, n. 12, p. 1-18, nov. 2019
Artículo
en Inglés
| SES-SP, SESSP-IBPROD, SES-SP | ID: bud-2873
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.
Biblioteca responsable:
BR78.1
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