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Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm.

Riju A, Chandrasekar A, Arunachalam V - Bioinformation (2007)

Bottom Line: We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp.ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02).The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies.

View Article: PubMed Central - PubMed

ABSTRACT
The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies.

No MeSH data available.


Related in: MedlinePlus

Frequency of SNPs and indel polymorphisms in EST libraries of different tissues of oil palm
© Copyright Policy - open-access
Related In: Results  -  Collection


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Figure 1: Frequency of SNPs and indel polymorphisms in EST libraries of different tissues of oil palm

Mentions: We found a total of 1180 SNP sites and 137 indel polymorphisms in 576 ESTs analyzed with frequency 1.36 SNPs / 100 bp. Results of the tissue wise SNP and indel discovery are listed in table 1 (supplementary material) and figure 1. Lambda Zap II tissue represents only two ESTs (BM402088, BM402089) and it contained no SNP/Indel hence we have eliminated Lambda Zap II library for further analysis.


Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm.

Riju A, Chandrasekar A, Arunachalam V - Bioinformation (2007)

Frequency of SNPs and indel polymorphisms in EST libraries of different tissues of oil palm
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2255072&req=5

Figure 1: Frequency of SNPs and indel polymorphisms in EST libraries of different tissues of oil palm
Mentions: We found a total of 1180 SNP sites and 137 indel polymorphisms in 576 ESTs analyzed with frequency 1.36 SNPs / 100 bp. Results of the tissue wise SNP and indel discovery are listed in table 1 (supplementary material) and figure 1. Lambda Zap II tissue represents only two ESTs (BM402088, BM402089) and it contained no SNP/Indel hence we have eliminated Lambda Zap II library for further analysis.

Bottom Line: We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp.ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02).The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies.

View Article: PubMed Central - PubMed

ABSTRACT
The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies.

No MeSH data available.


Related in: MedlinePlus