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.

* 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.

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:

• B = bacterial artificial chromosome or BAC.  BACs are modified E. coli F plasmids capable of carrying inserts up to ca. 400 kb.  They are a staple of physical mapping and genome sequencing research.
• S = single/low-copy, Cot-filtered.  An 'S' library is prepared from the slowest, mathematically-discernible kinetic component of a genome as defined via standard Cot analysis.
• M = moderately repetitive, Cot-filtered.  An 'M' library is prepared from the middle component of a three component genome as delineated by standard Cot analysis.
• H = highly repetitive, Cot-filtered; An 'H' library is prepared from the fastest reassociating component (excluding foldback DNA) of a three component genome as defined by standard Cot analysis.
• R = repetitive, Cot-filtered; An 'R' library is prepared from the fastest reassociating component (excluding foldback DNA) of a two component genome as determined by standard Cot analysis OR a library prepared from the combined H and M components of a three component genome.
• U = ultra-rapidly reassociating.  A 'U' library is prepared from the DNA that binds to a HAP column (in 0.12 M sodium phosphate buffer) at a Cot value of virtually zero.  Such ultra-rapidly reassociating (or foldback DNA as it is often called) is presumably due to intramolecular base pairing, although recent studies suggest that this explanation may be too simplistic.
• T = theoretical single-copy, Cot-filtered.  A 'T' library is prepared from any DNA that remains single-stranded at 0.1*theoretical Cot½ value for single-copy DNA as predicted from genome size (see Peterson 2005 for further explanation).
• G = genomic (random) DNA cloned into a standard "small insert" plasmid vector (e.g., PUC or pGEM vector).

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."