Sequence and Analysis

From RadishDB

Sequences

• Sequences:1st Batch:First 5,000 clones, EST contigs
• Sequences:All: 25,000 clones from each library, EST contigs

Linkage map

Preliminary linkage map for radish (Raphanus raphanistrum).

Markers

SSR

• New York population of Raphanus raphanistrum, tested and variable
• New York population of Raphanus raphanistrum, tested with little variation
• Spreadsheet for primer tested: Updated 23 March 2009 (EDT)

• Computationally identified markers from all seven libraries

SNP

• Computationally identified markers from all seven libraries

Analysis Notes

Novel coding sequence

• The un-annotated regions in eukaryote genomes are found to be expressed in several tiling array studies. In addition, it is generally more difficult to predict small protein genes and many have been identified through experiments but not computational predictions.
• As a proof of concept, we have identified >900 small open reading frames that are highly likely to be real genes in the intergenic regions of the Arabidopsis thaliana genome. The work is done mainly through the support of the Radish transcriptome sequencing grant and has been published in Genome Research.

EST assembly

The contigs you can download in the are generated by the JCVI plant TA pipline. Assembling were taking place from each library and in following ways:

1. Use seqclean to clean all the est sequences which include discarding sequences shorter that 100bp, seraching internal UniVec database and screening out any vector sequences, using DUST to get rid of low complexity sequences.
2. Use the TGICL pipeline to generate contigs with the following parameters:
   • Minimum percent identity for overlaps (PID):95
   • Miminum overlap length: 50
   • Maximum length of unmatched overhangs:20

Marker identification

• Comparison of SSR conservation between plant species
• Identification of radish SSR
• Identification of dCAPS