Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis |
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| Authors: | Haiying Liang Eric G. Fang Jeffrey P. Tomkins Meizhong Luo David Kudrna Hye Ran Kim K. Arumuganathan Shaying Zhao James Leebens-Mack Scott E. Schlarbaum Jo Ann Banks Claude W. dePamphilis Dina F. Mandoli Rod A. Wing John E. Carlson |
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| Affiliation: | (1) School of Forest Resources, Pennsylvania State University, University Park, PA 16802, USA;(2) Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA;(3) Department of Genetics and Biochemistry, Genomics Institute, Clemson University, Clemson, SC 29634, USA;(4) Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721, USA;(5) Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA;(6) Present address: Department of Genetics and Biochemistry, Clemson University, 100 Jordan Hall, Clemson, SC 29634, USA;(7) The Institute for Genomic Research, Rockville, MD 20850, USA;(8) Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA;(9) Department of Biology, Penn State University, University Park, PA 16802, USA;(10) Department of Forestry, Wildlife and Fisheries, Institute of Agriculture, The University of Tennessee at Knoxville, Knoxville, TN 37996-4563, USA;(11) Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47906, USA;(12) Department of Biology and Center for Developmental Biology, University of Washington, Box 355325, Seattle, WA 98195-5325, USA;(13) Present address: Department of Plant Biology, University of Georgia, Athens, GA 30602-7271, USA |
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| Abstract: | Liriodendron tulipifera L., a member of the Magnoliaceae, occupies an important phylogenetic position as a basal angiosperm that has retained numerous putatively ancestral morphological characters, and thus has often been used in studies of the evolution of flowering plants and of specific gene families. However, genomic resources for these early branching angiosperm lineages are very limited. In this study, we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from L. tulipifera. Flow cytometry estimates that this nuclear genome is approximately 1,802 Mbp per haploid genome (±16 SD). The BAC library contains 73,728 clones, a 4.8-fold genome coverage, with an average insert size of 117 kb, a chloroplast DNA content of 0.2%, and little to no bacterial sequences nor empty vector content clones. As a test of the utility of this BAC library, we screened the library with six single/low-copy genic probes. We obtained at least two positive clones for each gene and confirmed the clones by DNA sequencing. A total of 182 paired end sequences were obtained from 96 of the BAC clones. Using BLAST searches, we found that 25% of the BAC end sequences were similar to DNA sequences in GenBank. Of these, 68% shared sequence with transposable elements and 25% with genes from other taxa. This result closely reflected the content of random sequences obtained from a small insert genomic library for L. tulipifera, indicating that the BAC library construction process was not biased. The first genomic DNA sequences for Liriodendron genes are also reported. All the Liriodendron genomic sequences described in this paper have been deposited in the GenBank data library. The end sequences from shotgun genomic clones and BAC clones are under accession DU169330–DU169684. Partial sequences of Gigantea, Frigida, LEAFY, cinnamyl alcohol dehydrogenase, 4-coumarate:CoA ligase, and phenylalanine ammonia-lyase genes are under accession DQ223429–DQ223434. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. |
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| Keywords: | Yellow-poplar BAC library |
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