Sequencing Loblolly Pine BACs - Mississippi Genome Exploration Laboratory - MGEL - Daniel G. Peterson - Genomics, Bioinformatics, Cytogenetics, Molecular Biology - Loblolly Pine, Pinus taeda, Gymnosperms, Cotton, Plant & Animal Pathogens/Pests, Cattle
Pinus taeda (loblolly pine)
Pinus taeda (loblolly pine) - Mississippi has more tree farms than any other state.

SEQUENCING PINE BACS

In 2008, MGEL's Daniel G. Peterson served as principal investigator and primary author on a Community Sequencing Program (CSP) proposal submitted to the Department of Energy's Joint Genome Institute (JGI).  Co-PIs on the proposal were Jeffrey F.D. Dean (U. of Georgia), C. Dana Nelson (US Forest Service), Ronald R. Sederoff (NC State), and Daniel S. Rokhsar (JGI).  The goal of the proposal was 10X sequencing of 100 clones from the loblolly pine '7-56' BAC library generated through NSF DBI-0421717.  Specifically, the investigators requested sequencing of 25 randomly-selected BACs, 25 BACs containing low-copy DNA (as determined by macroarray analysis), and 50 BACs containing genes involved in carbon metabolism (i.e., targeted BACs).

In July 2008, the JGI  announced the results of its 2009 CSP competition.  The first project highlighted in the DOE-JGI press release was the Peterson-led proposal on loblolly pine (also see http://www.jgi.doe.gov/sequencing/why/pine.html).  The success of the proposal was due, in part, to the considerable support it received from members of the international conifer community.  Of note, the proposal garnered letters of support from scientists and administrators in the USDA Forest Service, industry (Range Fuels, Int'l Paper, ArborGen, SAPPI, CellFor, Weyerhaeuser), the principal U.S. pine breeding cooperatives, non-profit agencies (e.g., the Pine Genome Initiative, Institute of Forest Biotechnology, Nat'l Council for Air and Stream Improvement, and the Nat'l Center for Genomic Resources), and conifer scientists from 20 academic institutions in nine nations.  While the CSP does not provide funds for non-DOE investigators, CSP proposers benefit through close collaboration with the DOE, leadership on key publications emerging from initial sequence analysis, establishment of important national and international collaborations, and publicity for their programs/institutions.  In Dr. Peterson's case, the CSP will directly leverage work done under NSF award DBI-0421717 (on which he is PI) and hence increase the scientific impact of the NSF grant.

Targeted genes

genes listed below have been proposed as targets for selecting BACs.  Asterisks are used to identify genes that appear to be up-regulated in developing xylem.

GENE NAME GENE PRODUCT
FUNCTION
CONTACT
PtAct1 Actin
cytoskeleton structure
Joe Nairn
PtAct2 Actin cytoskeleton structure Joe Nairn
  PtAct3 Actin cytoskeleton structure Joe Nairn  
  PtAct4 Actin cytoskeleton structure Joe Nairn  
  PtAct5 Actin cytoskeleton structure Joe Nairn  
           
  PtTubA1 Alpha-tubulin cytoskeleton structure Joe Nairn  
  PtTubA2 Alpha-tubulin cytoskeleton structure Joe Nairn  
  PtTubB1 Beta-tubulin cytoskeleton structure Joe Nairn  
  PtTubB3 Beta-tubulin cytoskeleton structure Joe Nairn  
  PtTubB4 Beta-tubulin cytoskeleton structure Joe Nairn  
  PtTubB5 Beta-tubulin cytoskeleton structure Joe Nairn  
  PtTubB6 Beta-tubulin cytoskeleton structure Joe Nairn  
           
  PtKat1 katanin-like microtubule severing Joe Nairn  
           
  PtCesA1* cellulose synthase cellulose metabolism Joe Nairn  
  PtCesA2* cellulose synthase cellulose metabolism Joe Nairn  
  PtCesA3* cellulose synthase cellulose metabolism Joe Nairn  
  PtKor1* Korrigan endoglucanase cellulose metabolism Joe Nairn  
  PtSuSy1* sucrose synthase cellulose metabolism Joe Nairn  
  PtUGP1* UDP glucose pyrophosphorylase cellulose metabolism Joe Nairn  
           
  PtCslA1* glucomannan synthase hemicellulose metabolism Joe Nairn  
  PtCslA2* glucomannan synthase hemicellulose metabolism Joe Nairn  
  PtGMP1* UGP mannose pyrophosphorylase hemicellulose metabolism Joe Nairn  
  PtGMP2* UGP mannose pyrophosphorylase hemicellulose metabolism Joe Nairn  
  PtGT47c* glycosyl transferase family 47 - xylan hemicellulose metabolism Joe Nairn  
  PtGT47d glycosyl transferase family 47 - pectin hemicellulose metabolism Joe Nairn  
  PtGT43 xylan? hemicellulose metabolism Joe Nairn  
           
  PtGH19(1)* glycoside hydrolase family 19 other cell wall Joe Nairn  
  PtGH19(5)* glycoside hydrolase family 19 other cell wall Joe Nairn  
  PtCobra* glycosylphosphatidylinositol other cell wall Joe Nairn  
  PtFLA1 fasciclin-like AGP other cell wall Joe Nairn  
  PtFLA4 fasciclin-like AGP other cell wall Joe Nairn  
  PtFLA5 fasciclin-like AGP other cell wall Joe Nairn  
  PtFLA6 fasciclin-like AGP other cell wall Joe Nairn  
  PtFLA7 fasciclin-like AGP other cell wall Joe Nairn  
  PtGDSL GDSL motif lipase/hydrolase other cell wall Joe Nairn  
  PtLRK leucine repeat kinase (transmembrane) other cell wall Joe Nairn  
           
  PtHDZ1 HD Zip III transcription factor Joe Nairn  
  PtHDZ2 HD Zip III transcription factor Joe Nairn  
  PtAP2 AP2 family transcription factor Joe Nairn  
  PtBZR1 brassinosteroid transcription factor Joe Nairn  
  PtBZR2 brassinosteroid transcription factor Joe Nairn  
  PtNAC21 NAC domain transcription factor Joe Nairn  
           
  PtVEP1 vein patterning vascular development Joe Nairn  
           
  PtCAD1 cinnamyl alcohol dehydrogenase lignin metabolism Joe Nairn  
  PtCOMT1 caffeic acid O-methyltransferase lignin metabolism Joe Nairn  
  PtPAL1 phenylalanine ammonia lyase lignin metabolism Joe Nairn  
  PtLac2 laccase lignin metabolism Joe Nairn  
  PtLac8 laccase lignin metabolism Joe Nairn