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 Type:||B: BAC|
|Common Name:||loblolly pine|
|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|
|Protocol:||Peterson et al. (2000)|
|Fragmentation Method:||Partial HindIII digestion|
|Distributed In:||384-well microtiter plates|
* Each 5x5 macroarray contains 27,648 double-spotted BAC clones
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:
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."