Mississippi Genome Exploration Laboratory and Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America. zvm2@ msstate.edu
PLoS One. 2011 Jan 21;6(1):e16214. doi: 10.1371/journal.pone.0016214.
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).
火炬松（LP；Pinus taeda L.）是美国最重要的经济树种，也是东南部森林的基石物种。然而，由于针叶树基因组较大，LP 和其他针叶树的基因组学研究落后于开花植物的研究。作为加速针叶树基因组研究的一种手段，我们构建了 LP 基因型 7-56 的 BAC 文库。该 LP BAC 文库包含 1,824,768 个单独存档的克隆，是迄今为止构建的最大的单个 BAC 文库，平均插入片段大小为 96 kb，提供了 21.7 Gb LP 基因组的 7.6X 覆盖率。为了证明该文库在基因分离中的有效性，我们用来自 LP 染色体 10 上锚定的松树 EST 的过表达基因进行了宏阵列筛选。阳性 BAC 被测序，发现它包含预期的全长靶基因、几个基因样区域以及已知和新的重复序列。使用逆转座子 IFG-7（测序 BAC 中最丰富的重复序列）作为探针的宏阵列分析表明，IFG-7 大约存在 210,557 个拷贝，占 LP 核 DNA 的约 5.8%或 1.26 Gb；这段 DNA 数量是拟南芥基因组的八倍。除了本文所述的用于基因组特征描述和基因分离外，该 BAC 文库还应通过下一代测序策略/技术加速 LP 的全基因组测序，并通过分子育种和遗传工程促进树木的改良。该文库及其相关产品由克莱姆森大学基因组研究所（www.genome.clemson.edu）分发。
