Accelerating Pine Genomics Mississippi Genome Exploration Laboratory

APG Only
MGEL's BAC libraries are stored in -80C freezers
The pine BAC library is archived in -80C freezers at both MGEL and CUGI.

A major goal of the APG project was the construction of a bacterial artificial chromosome library for the loblolly pine genotype "7-56."  The library is now complete.  It is composed of 1,797,504 individually archived clones and affords roughly 8.1X coverage of the enormous (21.7 Gb) pine genome.  A manuscript on the BAC library is near completion (see Publications). 

The official distributor of the pine BAC library and its associated products is Clemson University Genomics Institute (CUGI), although those wishing to collaborate on projects involving the library should contact Dr. Daniel G. Peterson at the Mississippi Genome Exploration Laboratory.  The library, individual clones, and macroarrays are available for purchase from CUGI on a "cost-recovery" basis. 

Details on the loblolly pine "7-56" BAC library are presented below.  For reviews on BACs and their uses, see Peterson et al. (2000) and Zhang.

  The Pinus taeda L. 7-56 BAC Library
Library Name: PT_7Ba
Library Type: B: BAC
Status: Complete
Organism: Pinus taeda
Common Name: loblolly pine
Subspecies: none
Cultivar/Genotype: 7-56
Genome Size (Mb): 21,658
Number of Clones: 1,797,504
Number of 384-Well Plates: 4681
Mean Insert Size (Kb): 100
Genome Equivalents (Coverage): 8.1
Number of 5x5 Macroarrays:* 65
Constructed At: Mississippi Genome Exploration Laboratory
Constructed By: Zenaida V. Magbanua
Distributor: Clemson University Genomics Institute
  Distributor's Library Information: Loblolly Pine 7-56 BAC Library
Funding Agency/Source: National Science Foundation
  Funding Agency Program: Plant Genome Research Program
Award Number: DBI-0421717
Protocol: Peterson et al. (2000)
Host Strain: DH10B
Vector(s): pIndigoBAC5
Fragmentation Method: Partial HindIII digestion
Selectable Marker(s): Chloramphenicol
Distributed In: 384-well microtiter plates

* Each 5x5 macroarray contains 27,648 double-spotted BAC clones

Library Naming Conventions

DNA libraries produced at MGEL are named using the conventions utilized by the Clemson University Genomics Institute and the Arizona Genomics Institute.  Each library name consists of six identification fields.  Below is an example of a file name broken into its six fields and a legend explaining the meaning and limits of each field.

Library Name

Field 1 - First letter of the genus of the organism from which the library was derived.  In the example, the P stands for Pinus.

Field 2 - First letter of the species name of the organism from which the library was derived.  In the example, the T stands for taeda.

Field 3 - First letter of the subspecies from which the library was derived.  If a subspecies name is not known or not applicable, an underscore, _,  is used to show that the subspecies field is empty.  In the example above, the _ indicates that the P. taeda subspecies is unknown.

Field 4 - First letter or number of the cultivar/genotype from which the library was derived.  As with the Field 3, an underscore can be used to indicate the lack of a known cultivar or genotype. In the example, the 7 stands for 7-56, the individual tree (i.e., genotype) from which the BAC library was constructed.

Field 5 - A one letter abbreviation for the means by which the library was constructed.  At MGEL, we currently have libraries with the following Field 5 designations:

Field 6 - A one lowercase letter "wildcard" that can be used to differentiate similar libraries constructed from the same organism, e.g., a Pinus taeda BAC library produced using a partial HindIII digestion might be assigned the wildcard "a" while a Pinus taeda BAC library produced using a partial BstyI digestion might be assigned the wildcard "b."

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*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.