Caracterização da região Bru1 no genoma da cultivar RB867515 (Saccharum spp.) utilizando sequenciamento de nova geração
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2014-09-25
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Universidade Federal de Goiás
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Sugarcane is known as one of the most important crops of the word for its sub products utilization.
Four countries, led by Brazil, supply the sugar international trade. Ethanol is other important
sugarcane sub product, recognized as an alternative product to sugar, and had great demand in
Brazilian trade, for its utilization as non-fossil fuel. The sugarcane genome is one of the most
complex among crops, with 10 Gb. Its complete genome is not available, but the recent innovations
in genomics tools open up new possibilities for the investigations about the sugarcane’s genome.
We did a genome assembly and annotation of a Brazilian sugarcane cultivar (RB867515) genome
region, correspondent to eight R570 homologous sequences already published. We use high
qualities paired-ends libraries produced by Illumina HiSeq 2000 sequencing platform. The reads
were aligned against eight R570 BACs (Bacterial Artificial Chromosome) sequences stored in
NCBI using Bowtie2. We used MaSuRCA to assemble the aligned reads de novo, and the
consensus sequences were obtained with SAMtools mpileup option. The transposable elements
were identified using RepeatMasker and the gene regions were annotated with Blastx against the
GenBank non-redundant protein database. After that, the consensus sequences were aligned with
the matching reference (R570) using ClustalW in Mega software, to look for the percentage of
mismatches and conserved sites between them. We obtained the number of scaffolds bigger than 1
kb ranging from 607 to 2,884, and the longest scaffold had near 21 kb. The consensus sequence
length ranged from 81 to 142 kb, and the recovery rate relative to the reference ranged from 82%
to 97%. The sequences amounted 1 Mb of RB867515 cultivar genome. We identified 5,145
repeated elements, which 4,662 were microsatellite and 460 were transposable elements, amounted
225 kb of repeated sequences. Among the mobile elements, the retrotransposons comprises 15% of
nucleotide composition, ranging from 8% to 29% among BACs. The 134 genes identified on the
eight BAC consensus sequences comprised a total of 243 kb, resulting in a density of one gene per
7.2 kb. The average number of genes per BAC was 16, with an average gene length of 1,841 bp.
The percentage of mismatches between the RB867515 and R570 BACs ranged from 0.27% to
1.32%. The sugarcane BACs correspond to homeologous genomic regions, with this alignment we
can suggest high divergence inside an homeologous group.
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SOUZA, I. P. Caracterização da região Bru1 no genoma da cultivar RB867515 (Saccharum spp.) utilizando sequenciamento de nova geração. 2014. 96 f. Dissertação (Mestrado em Genética e Melhoramento de Plantas) - Universidade Federal de Goiás, Goiânia, 2014.