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ESTs from a wild Arachis species for gene discovery and marker development.

Proite K, Leal-Bertioli SC, Bertioli DJ, Moretzsohn MC, da Silva FR, Martins NF, Guimarães PM - BMC Plant Biol. (2007)

Bottom Line: Two hundred and six microsatellites were found and markers have been developed for 188 of these.The microsatellite profile was analyzed and compared to other transcribed and genomic sequence data.The ESTs were released in the [GenBank:EH041934 to EH048197].

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Biologia Celular, Universidade de Brasília, Campus I, Brasília, DF. Brazil. proite@cenargen.embrapa.br

ABSTRACT

Background: Due to its origin, peanut has a very narrow genetic background. Wild relatives can be a source of genetic variability for cultivated peanut. In this study, the transcriptome of the wild species Arachis stenosperma accession V10309 was analyzed.

Results: ESTs were produced from four cDNA libraries of RNAs extracted from leaves and roots of A. stenosperma. Randomly selected cDNA clones were sequenced to generate 8,785 ESTs, of which 6,264 (71.3%) had high quality, with 3,500 clusters: 963 contigs and 2537 singlets. Only 55.9% matched homologous sequences of known genes. ESTs were classified into 23 different categories according to putative protein functions. Numerous sequences related to disease resistance, drought tolerance and human health were identified. Two hundred and six microsatellites were found and markers have been developed for 188 of these. The microsatellite profile was analyzed and compared to other transcribed and genomic sequence data.

Conclusion: This is, to date, the first report on the analysis of transcriptome of a wild relative of peanut. The ESTs produced in this study are a valuable resource for gene discovery, the characterization of new wild alleles, and for marker development. The ESTs were released in the [GenBank:EH041934 to EH048197].

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Functional classifications and comparative analysis of the ESTs of A. stenosperma roots. The ESTs were classified on the basis of their biological functions by alignment to proteins of the Genbank. Bars with vertical stripes represent frequency of sequences with homology with genes involved in cellular processes and signaling, black bars, information storage and processing, bars with horizontal stripes, metabolism, white bars, poorly characterized ESTs and grey bar, non-conclusively classified ESTs (that showed homology with at least two categories, so they were grouped separately).CELLULAR PROCESSES AND SIGNALINGM Cell wall/membrane/envelope biogenesisO Posttranslational modification, protein turnover, chaperonesT Signal transduction mechanismsU Intracellular trafficking, secretion, and vesicular transportV Defense mechanismsZ CytoskeletonINFORMATION STORAGE AND PROCESSINGA RNA processing and modificationB Chromatin structure and dynamicsJ Translation, ribosomal structure and biogenesisK TranscriptionL Replication, recombination and repairMETABOLISMC Energy production and conversionD Cell cycle control, cell division, chromosome partitioningE Amino acid transport and metabolismF Nucleotide transport and metabolismG Carbohydrate transport and metabolismH Coenzyme transport and metabolismI Lipid transport and metabolismP Inorganic ion transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolismPOORLY CHARACTERIZEDR General function prediction onlyS Function unknown
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Figure 1: Functional classifications and comparative analysis of the ESTs of A. stenosperma roots. The ESTs were classified on the basis of their biological functions by alignment to proteins of the Genbank. Bars with vertical stripes represent frequency of sequences with homology with genes involved in cellular processes and signaling, black bars, information storage and processing, bars with horizontal stripes, metabolism, white bars, poorly characterized ESTs and grey bar, non-conclusively classified ESTs (that showed homology with at least two categories, so they were grouped separately).CELLULAR PROCESSES AND SIGNALINGM Cell wall/membrane/envelope biogenesisO Posttranslational modification, protein turnover, chaperonesT Signal transduction mechanismsU Intracellular trafficking, secretion, and vesicular transportV Defense mechanismsZ CytoskeletonINFORMATION STORAGE AND PROCESSINGA RNA processing and modificationB Chromatin structure and dynamicsJ Translation, ribosomal structure and biogenesisK TranscriptionL Replication, recombination and repairMETABOLISMC Energy production and conversionD Cell cycle control, cell division, chromosome partitioningE Amino acid transport and metabolismF Nucleotide transport and metabolismG Carbohydrate transport and metabolismH Coenzyme transport and metabolismI Lipid transport and metabolismP Inorganic ion transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolismPOORLY CHARACTERIZEDR General function prediction onlyS Function unknown

Mentions: The annotation of the A. hypogaea ESTs was based on sequence homology. Each EST set inherited the annotation form the best match found in BlastX alignment against protein databases at NCBI. On the basis of the KOG (Clusters of Eukaryotic Orthologous Groups of Proteins), the EST sequences in the cDNA libraries were further functionally classified by sorting into 23 putative functional groups (Figure 1).


ESTs from a wild Arachis species for gene discovery and marker development.

Proite K, Leal-Bertioli SC, Bertioli DJ, Moretzsohn MC, da Silva FR, Martins NF, Guimarães PM - BMC Plant Biol. (2007)

Functional classifications and comparative analysis of the ESTs of A. stenosperma roots. The ESTs were classified on the basis of their biological functions by alignment to proteins of the Genbank. Bars with vertical stripes represent frequency of sequences with homology with genes involved in cellular processes and signaling, black bars, information storage and processing, bars with horizontal stripes, metabolism, white bars, poorly characterized ESTs and grey bar, non-conclusively classified ESTs (that showed homology with at least two categories, so they were grouped separately).CELLULAR PROCESSES AND SIGNALINGM Cell wall/membrane/envelope biogenesisO Posttranslational modification, protein turnover, chaperonesT Signal transduction mechanismsU Intracellular trafficking, secretion, and vesicular transportV Defense mechanismsZ CytoskeletonINFORMATION STORAGE AND PROCESSINGA RNA processing and modificationB Chromatin structure and dynamicsJ Translation, ribosomal structure and biogenesisK TranscriptionL Replication, recombination and repairMETABOLISMC Energy production and conversionD Cell cycle control, cell division, chromosome partitioningE Amino acid transport and metabolismF Nucleotide transport and metabolismG Carbohydrate transport and metabolismH Coenzyme transport and metabolismI Lipid transport and metabolismP Inorganic ion transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolismPOORLY CHARACTERIZEDR General function prediction onlyS Function unknown
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1808460&req=5

Figure 1: Functional classifications and comparative analysis of the ESTs of A. stenosperma roots. The ESTs were classified on the basis of their biological functions by alignment to proteins of the Genbank. Bars with vertical stripes represent frequency of sequences with homology with genes involved in cellular processes and signaling, black bars, information storage and processing, bars with horizontal stripes, metabolism, white bars, poorly characterized ESTs and grey bar, non-conclusively classified ESTs (that showed homology with at least two categories, so they were grouped separately).CELLULAR PROCESSES AND SIGNALINGM Cell wall/membrane/envelope biogenesisO Posttranslational modification, protein turnover, chaperonesT Signal transduction mechanismsU Intracellular trafficking, secretion, and vesicular transportV Defense mechanismsZ CytoskeletonINFORMATION STORAGE AND PROCESSINGA RNA processing and modificationB Chromatin structure and dynamicsJ Translation, ribosomal structure and biogenesisK TranscriptionL Replication, recombination and repairMETABOLISMC Energy production and conversionD Cell cycle control, cell division, chromosome partitioningE Amino acid transport and metabolismF Nucleotide transport and metabolismG Carbohydrate transport and metabolismH Coenzyme transport and metabolismI Lipid transport and metabolismP Inorganic ion transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolismPOORLY CHARACTERIZEDR General function prediction onlyS Function unknown
Mentions: The annotation of the A. hypogaea ESTs was based on sequence homology. Each EST set inherited the annotation form the best match found in BlastX alignment against protein databases at NCBI. On the basis of the KOG (Clusters of Eukaryotic Orthologous Groups of Proteins), the EST sequences in the cDNA libraries were further functionally classified by sorting into 23 putative functional groups (Figure 1).

Bottom Line: Two hundred and six microsatellites were found and markers have been developed for 188 of these.The microsatellite profile was analyzed and compared to other transcribed and genomic sequence data.The ESTs were released in the [GenBank:EH041934 to EH048197].

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Biologia Celular, Universidade de Brasília, Campus I, Brasília, DF. Brazil. proite@cenargen.embrapa.br

ABSTRACT

Background: Due to its origin, peanut has a very narrow genetic background. Wild relatives can be a source of genetic variability for cultivated peanut. In this study, the transcriptome of the wild species Arachis stenosperma accession V10309 was analyzed.

Results: ESTs were produced from four cDNA libraries of RNAs extracted from leaves and roots of A. stenosperma. Randomly selected cDNA clones were sequenced to generate 8,785 ESTs, of which 6,264 (71.3%) had high quality, with 3,500 clusters: 963 contigs and 2537 singlets. Only 55.9% matched homologous sequences of known genes. ESTs were classified into 23 different categories according to putative protein functions. Numerous sequences related to disease resistance, drought tolerance and human health were identified. Two hundred and six microsatellites were found and markers have been developed for 188 of these. The microsatellite profile was analyzed and compared to other transcribed and genomic sequence data.

Conclusion: This is, to date, the first report on the analysis of transcriptome of a wild relative of peanut. The ESTs produced in this study are a valuable resource for gene discovery, the characterization of new wild alleles, and for marker development. The ESTs were released in the [GenBank:EH041934 to EH048197].

Show MeSH