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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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Related in: MedlinePlus

Microsatellite distribution in ESTs from A. stenosperma V10309 and Genome Survey Sequences from A. duranensis. SSRs were sorted according to motif type and number of repeats. Y axis is percentage of total sequences and X axis is the number of repeats for (A) Di-nucleotide microsatellites and (B) Tri-nucleotide microsatellites.
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Figure 2: Microsatellite distribution in ESTs from A. stenosperma V10309 and Genome Survey Sequences from A. duranensis. SSRs were sorted according to motif type and number of repeats. Y axis is percentage of total sequences and X axis is the number of repeats for (A) Di-nucleotide microsatellites and (B) Tri-nucleotide microsatellites.

Mentions: Out of the 3,500 contig and singleton sequences analysed, 206 (5.9%) had microsatellites. Most of these are di- or tri- nucleotide motifs, being 119 (3.4%) and 79 (2.3%) respectively. The vast majority of the microsatellites (191/206) are short, with 6–10 motif repetitions. Of the di-nucleotide motifs most are TC or AT (102/119). An analysis of A. hypogaea clustered transcripts from Genbank gave similar results, except with slightly higher percentages of microsatellite containing sequences (6.8%) and tri-nucleotide repeats (3.4%). In order to compare the microsatellite compositions of non-coding and transcribed genomic sequences in Arachis we also analyzed 1,530 clustered A. duranensis genome survey sequences (GSSs) from GenBank. A. duranensis is a wild species with an AA genome quite closely related to A. stenosperma. From these sequences, 118 (7.7%) contained microsatellites, and again the vast majority are di- or tri- nucleotide motifs, being 86 (5.6%) and 27 (1.8%) respectively. As with the EST data, most di-nucleotide microsatellites are TC or AT (70/86). However, there are also some distinct contrasts in the profiles of microsatellites in ESTs compared to genome survey sequences. Di-nucleotide microsatellites of all repeat lengths are more common in genome survey sequences than in ESTs, but tri-nucleotide microsatellites are somewhat more common in the ESTs than the genome survey sequences (Figure 2A and 2B).


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)

Microsatellite distribution in ESTs from A. stenosperma V10309 and Genome Survey Sequences from A. duranensis. SSRs were sorted according to motif type and number of repeats. Y axis is percentage of total sequences and X axis is the number of repeats for (A) Di-nucleotide microsatellites and (B) Tri-nucleotide microsatellites.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Microsatellite distribution in ESTs from A. stenosperma V10309 and Genome Survey Sequences from A. duranensis. SSRs were sorted according to motif type and number of repeats. Y axis is percentage of total sequences and X axis is the number of repeats for (A) Di-nucleotide microsatellites and (B) Tri-nucleotide microsatellites.
Mentions: Out of the 3,500 contig and singleton sequences analysed, 206 (5.9%) had microsatellites. Most of these are di- or tri- nucleotide motifs, being 119 (3.4%) and 79 (2.3%) respectively. The vast majority of the microsatellites (191/206) are short, with 6–10 motif repetitions. Of the di-nucleotide motifs most are TC or AT (102/119). An analysis of A. hypogaea clustered transcripts from Genbank gave similar results, except with slightly higher percentages of microsatellite containing sequences (6.8%) and tri-nucleotide repeats (3.4%). In order to compare the microsatellite compositions of non-coding and transcribed genomic sequences in Arachis we also analyzed 1,530 clustered A. duranensis genome survey sequences (GSSs) from GenBank. A. duranensis is a wild species with an AA genome quite closely related to A. stenosperma. From these sequences, 118 (7.7%) contained microsatellites, and again the vast majority are di- or tri- nucleotide motifs, being 86 (5.6%) and 27 (1.8%) respectively. As with the EST data, most di-nucleotide microsatellites are TC or AT (70/86). However, there are also some distinct contrasts in the profiles of microsatellites in ESTs compared to genome survey sequences. Di-nucleotide microsatellites of all repeat lengths are more common in genome survey sequences than in ESTs, but tri-nucleotide microsatellites are somewhat more common in the ESTs than the genome survey sequences (Figure 2A and 2B).

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
Related in: MedlinePlus