Doutorado em Genética e Melhoramento de Plantas (EA)
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Navegando Doutorado em Genética e Melhoramento de Plantas (EA) por Por Orientador "Coelho, Alexandre Siqueira Guedes"
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Item Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração(Universidade Federal de Goiás, 2015-01-22) Melo, Arthur Tavares de Oliveira; Coelho, Alexandre Siqueira Guedes; http://lattes.cnpq.br/0840926305216925; Coelho, Alexandre Siqueira Guedes; Pappas Júnior, Georgios Joannis; Borba, Tereza Cristina de Oliveira; Brondani , Cláudio; Novaes, EvandroThe 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.Item Obtenção e caracterização preliminar de um draft assembly do genoma de cana-de-açúcar (Saccharum spp.)(Universidade Federal de Goiás, 2019-05-31) Souza, Isabela Pavanelli de; Coelho, Alexandre Siqueira Guedes; http://lattes.cnpq.br/0840926305216925; Coelho, Alexandre Siqueira Guedes; Antunes, Adriana Maria; Vianello, Rosana Pereira; Vidigal, Pedro Marcus; Brondani, ClaudioSugarcane 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.