ABSTRACT
Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.
Subject(s)
Magnoliopsida/classification , Magnoliopsida/genetics , Saccharum/classification , Saccharum/genetics , Arabidopsis/classification , Arabidopsis/genetics , Chromosomes, Plant/genetics , Consensus Sequence , Evolution, Molecular , Expressed Sequence Tags , Genome, Plant , Oryza/classification , Oryza/genetics , Transcription, GeneticABSTRACT
To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.
Subject(s)
Computational Biology/methods , DNA, Complementary/analysis , DNA, Complementary/physiology , DNA, Plant/analysis , DNA, Plant/physiology , Expressed Sequence Tags , Saccharum/genetics , Saccharum/physiology , Computational Biology/statistics & numerical data , DNA, Complementary/classification , DNA, Plant/classification , Gene Expression Regulation, Plant , Gene Library , Molecular Sequence Data , Organ Specificity/genetics , Peptides/classification , Peptides/genetics , Peptides/physiology , Plant Proteins/classification , Plant Proteins/genetics , Plant Proteins/physiology , Polymorphism, Genetic/genetics , Protein Structure, Tertiary/genetics , Saccharum/growth & development , Sequence Analysis, DNA/methods , Signal Transduction/geneticsABSTRACT
A partir dos dados do projeto de sequenciamento de Ests da Cana de Açúcar (Sucest/FAPESP) e utilizando BLAST (tblastn) como ferramenta, foi realizada uma busca de genes homólogos aos elementos envolvidos nos processos de foto-recepçäo e já descritos para outras plantas, principalmente Arabidopsis. Foram obtidas altas identidades para os fitocromos A, B e C assim como para os críptocromos 1, 2 e a fototropina. Diversos elementos identificados como reguladores primários ou secundários na transduçäo de sinal de foto-receptores também foram identificados com baixos valores de E-value.
Subject(s)
Expressed Sequence Tags , Photoreceptor Cells , Photosynthetic Reaction Center Complex Proteins , Phytochrome , Plant Proteins , Software , Signal TransductionABSTRACT
É proposta uma modificaçäo para o tradicional protocolo de purificaçäo de DNA de fago que utiliza gradiente de cloreto de césio. Este método evita etapas enzimáticas assim como a necessidade de uma titulaçäo prévia, um processo que consome tempo e é proposto na maioria dos métodos em uso. A qualidade do DNA obtido permite manipulaçöes adicionais, tais como digestöes, ligaçöes, marcaçöes, subclonagem, etc.
