Targeted identification of genomic regions using TAGdb

Abstract

Background: The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes.

Results: We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome.

Conclusions: The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.

Figure 1

TAGdb. Screenshot of TAGdb showing the alignment of short reads from Brassica rapa cv Chiifu with the AtWD40 query sequence.

Figure 2

Positions of the B. rapa tags and PCR primer sequences with respect to the AtWD40 genomic region. Tag pairs and primer pairs used for PCR are labelled as per Table 2.

Figure 3

Amplification of BrWD40. 1% TAE-agarose gel showing amplification products (+) and negative controls (-) for PCR products (a) and (b).

Figure 4

Comparison of the AtWD40 and BrWD40 genomic regions. (A) Dot plot comparison of the AtWD40 and BrWD40 genomic regions. (B) Alignment of the predicted amino acid sequences for AtWD40 and BrWD40.