title: Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine.
abstract: Loblolly pine (LP; Pinus taeda L.) is the most economically important tree in the U.S. and a cornerstone species in southeastern forests. However, genomics research on LP and other conifers has lagged behind studies on flowering plants due, in part, to the large size of conifer genomes. As a means to accelerate conifer genome research, we constructed a BAC library for the LP genotype 7-56. The LP BAC library consists of 1,824,768 individually-archived clones making it the largest single BAC library constructed to date, has a mean insert size of 96 kb, and affords 7.6X coverage of the 21.7 Gb LP genome. To demonstrate the efficacy of the library in gene isolation, we screened macroarrays with overgos designed from a pine EST anchored on LP chromosome 10. A positive BAC was sequenced and found to contain the expected full-length target gene, several gene-like regions, and both known and novel repeats. Macroarray analysis using the retrotransposon IFG-7 (the most abundant repeat in the sequenced BAC) as a probe indicates that IFG-7 is found in roughly 210,557 copies and constitutes about 5.8% or 1.26 Gb of LP nuclear DNA; this DNA quantity is eight times the Arabidopsis genome. In addition to its use in genome characterization and gene isolation as demonstrated herein, the BAC library should hasten whole genome sequencing of LP via next-generation sequencing strategies/technologies and facilitate improvement of trees through molecular breeding and genetic engineering. The library and associated products are distributed by the Clemson University Genomics Institute (www.genome.clemson.edu).
authors.affiliation: Mississippi Genome Exploration Laboratory and Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America. zvm2@ msstate.edu
authors.forename: Zenaida V
authors.initials: ZV
authors.lastname: Magbanua
authors.forename: Seval
authors.initials: S
authors.lastname: Ozkan
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Bartlett
authors.forename: Philippe
authors.initials: P
authors.lastname: Chouvarine
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Saski
authors.forename: Aaron
authors.initials: A
authors.lastname: Liston
authors.forename: Richard C
authors.initials: RC
authors.lastname: Cronn
authors.forename: C Dana
authors.initials: CD
authors.lastname: Nelson
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Peterson
mesh_terms: D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D015723:Gene Library; D018745:Genome, Plant; D041603:Pinus taeda / Q000235:genetics*; D017422:Sequence Analysis, DNA