Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração
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Data
2015-01-22
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Universidade Federal de Goiás
Resumo
The sugarcane is one of the most important crop species to provide sugar and
renewable energy in the world. Due to the high amount of repetitive elements and the
various polyploidization events suffer during its evolution, the Saccharum spp. genome has
not yet been assembled and annotated, unlike other agronomic important species. So, the
knowledge about sugarcane transcriptome become even more useful for supporting
genomic analyzes studies. A draft assembly of sugarcane transcriptome was obtained from
Illumina sequencing paired-ends libraries of five different plant organs, sampled from
thirty elite clones. Analyzes of quality control and normalization was done in the RNA-seq
data. Trinity package was used for de novo assembly. The scaffolds obtained and identified
as complete ORFs were annotated according to Gene Ontology terms. The draft assembly
was characterized by the identification of microsatellites and SNPs molecular markers and
for assessing the contribution of different plant organs for transcriptome final assembly.
The draft sugarcane transcriptome comprised 178 Mb, over 131,831 scaffolds, representing
61,225 genes. The transcripts average size was 1,350 bp and N50 value was 1,667 bp. A
total of 1,250 transcripts identified as complete ORFs showed no similarity to sequences of
the nr NCBI database, are considered new Transcript Active Regions (nTARs). The
annotation performed using the KEGG database identified 234 transcripts coding for
enzymes members of sucrose and starch metabolism, an important metabolic pathway for
understanding the relationship between photosynthetic rate and sucrose accumulation in
the stalk. The five plant organs used contributed equally for the draft sugarcane
transcriptome. A total of 12,931 genomic regions were identified containing perfect
microsatellites, with a predominance of di and tri nucleotide. On average, one SNP every
18 bp was identified, with more than four million SNPs identified with satisfactory values
of haplotype and quality scores. The nucleotide diversity of thirty elite clones used in this
study was high. The identification of these molecular markers, particularly SNPs markers,
provides the possibility of using these polymorphisms in genomic and genetic studies of
sugarcane, including the possibility of application of genome wide selection like breeding
strategy. The sugarcane transcriptome draft assembly proposed in this study has data and
analysis quality sufficient to be used in attempt to encompass a reference transcriptome for
the species of Saccharum spp.
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Palavras-chave
Saccharum spp. , Transcritoma , Trinity , Saccharum spp. , Transcriptome , RNA-seq , Trinity , RNA-seq
Citação
MELO, A. T. O. Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração. 2015. 102 f. Tese (Doutorado em Genetica e Melhoramento de Plantas) - Universidade Federal de Goiás, Goiânia, 2015.