Obtenção e caracterização preliminar de um draft assembly do genoma de cana-de-açúcar (Saccharum spp.)
Nenhuma Miniatura disponível
Data
2019-05-31
Autores
Título da Revista
ISSN da Revista
Título de Volume
Editor
Universidade Federal de Goiás
Resumo
Sugarcane is known as one of the most important crops worldwide, and Brazil is its major
producer. Its genome is extremely complex: high chromosome number, highly abundant in
repetitive DNA, variable levels of polyploidy, aneuploidy, heterozygosity, and interspecific origin.
As a consequence, sugarcane has one of the largest genomes among grasses, comprising about 10
Gb. The first step towards achieving a reference genomic sequence for the crop is to produce a
suitable draft assembly. The objective of this study was to build and preliminary characterize a
draft genome assembly for the Brazilian sugarcane cultivar RB867515 (Saccharum spp.). Genomic
reads were obtained using Illumina and PacBio technologies on genomic DNA extracted from
RB867515 lateral buds. After filtering, the assembly was generated using three different
approaches, and the best of them was characterized regarding repetitive DNA content, gene
prediction, assembly contiguity and completeness. The draft assembly for RB867515 comprised
660,749 scaffolds, with mean size of 1,856 bp, N50 of 9,682 bp, adding up to 1.1 Gb. This size,
that represents ~23% of the estimated genome size (1C) for sugarcane (5.32 Gb), is compatible
with a monoploid version of the genome. The repetitive DNA content was estimated in 49.7%,
with 37.1% of retrotransposons, 9.2% of DNA transposons, 1.5% of satellite DNA and 0.6% of
simple repeats. Among retrotransposons, LTR elements were the most abundant (35.2%). A total
of 82,945 putative genes were predicted, with mean size of 1,473 bp, ranging from 200 bp to 33
kb. We found that ~19,0% of sorghum chromosomes were represented in the draft assembly. For S.
spontaneum chromosomes this rate was 60,1%. This is the first draft genome assembly described
for the Brazilian sugarcane cultivar RB867515, the most cultivated in Brazil. We conclude that the
draft assembly generated is a useful genomic resource for the culture. Adding a larger set of long
reads is going to benefit the assembly, raising its total size, contiguity and completeness.
Descrição
Palavras-chave
RB867515 , Genômica , Poliploide , PacBio , Illumina , RB867515 , Sugarcane genomics , Polyploidy , PacBio , Illumina
Citação
SOUZA, I. P. Obtenção e caracterização preliminar de um draft assembly do genoma de cana-de-açúcar (Saccharum spp.). 2019. 88 f. Tese (Doutorado em Genética e Melhoramento de Plantas) - Universidade Federal de Goiás, Goiânia, 2019.