2011 Annual Report
1)Assemble the partial genome of Cercis chinensis using data from a 454 DNA sequencer; and.
2)Identify molecular markers from this partial preliminary genome, ie, single-nucleotide polymorphisms (SNPs). DNA sequence reads from the Cercis chinensis genome (454 DNA sequencer) were obtained, and assembled using the Abyss assembler as well as a second sequence assembler, CAP3, independently. An Entrez search of the results on the NCBI website for the Cercis chinensis revealed no records for the genome, three hits on the Protein database records, and 15 hits on the Nucleotide database records. The database search also revealed no SNPS for Cercis chinensis. A BLAST analysis of the assembled contigs from CAP3 for the dissimilar database provides results with apparent identities. However, running a BLAST analysis with a database of very similar species does not provide any similarity. Using the program RepeatMasker revealed that the genome contains retro-elements of about 1603 elements, 1578 LTR elements and 335 DNA transposons. Future plans call for identifying SNPs by comparing different species of same genus. Additional bioinformatic tools and aligners such as Glimmer and Bowtie are useful for verifying and determining variations within the sequences. Bowtie alignments can help identify variations within the genomes and aid in the identification of SNPs, and leading to the discovery of markers. Glimmer will be used to identify coding and noncoding DNA regions, which will help identify certain target regions for marker identification.
Research activities conducted under this agreement were monitored by regular email communication, submission of reports by the cooperator, and by visits by the cooperator and grad students.