Accelerating Pine Genomics has resulted in the production of considerable sequence data for the Pinus taeda genotype 7-56. Of note:
(1) A new collaboration with John E. Carlson (Penn State) has allowed us to sequence uncloned kinetic components and genomic DNA using the new 454/Roche Applied Sciences GS20 platform. The 454 sequencing, performed with the permission of the NSF and requiring only minor re-budgeting, has resulted in production of 105 Mb of pine genomic sequence, i.e., 18 times more sequence than proposed in the original funded version of DBI-0421717. This “bonus” sequence has provided many new opportunities and challenges. Submission of the 454 sequence data to GenBank has been delayed as NCBI management has not yet decided how they want to handle large 454 data sets. Consequently, we have made the 454 sequence and quality files available for download from our Sequence Download page. The 454 sequences will be deposited in GenBank as soon as NCBI develops a suitable submission strategy. To facilitate timely characterization of these sequences, we have developed (and are continuing to develop/refine) several automated sequence analysis pipelines (see Algorithm & Software Development).
(2) As part of DBI-0421717, we have generated Cot-filtered highly repetitive (HR), moderately repetitive (MR), and single/low-copy (SL) sequence libraries. In addition, we created a random sequence genomic library. We have isolated plasmids from these clones and have sent the DNA to be sequenced using ABI 3730xl DNA analyzers. As promised, we are sequencing 1152 HR, 384 MR, 6144 SL, and 768 random genomic clones. Sequencing should be completed by mid-June, and sequence files will be made available through this website as soon as they are received (see DNA Sequences to download sequence files).
The sequence data from both ABI 3730xl and 454 synthesis sequencing should facilitate many aspects of pine genomics including detailed characterization of pine repeat sequences (e.g., see GenomeWeb News article).
*This material is based upon work supported by the National Science Foundation under Grant No. DBI-0421717. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. MGEL © 2006. Web design by Daniel G. Peterson. Last updated 08-Jun-2006.
