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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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.
KeywordsYellow-poplar BAC library
This study was supported by the National Science Foundation grant numbers 0207202 (dePamphilis and Carlson), 0211611 (Wing), and 0208502 (Mandoli) to The Green Plant BAC Library Project, and by the Schatz Center for Tree Molecular Genetics at Pennsylvania State University. We thank Jayson Talag, Sheila Plock, Kerr Wall, and Deb Grove for their assistance in developing and characterizing the BAC resource. We greatly acknowledge The Floral Genome Project for the prepublication access to cDNA probes and EST information on yellow-poplar, without which the library characterization might not have been possible. We are indebted to Abdelali Barakat for the many helpful discussions during the project and for the insightful comments on the manuscript.
CWD, DFM, JEC, JAB, JPT, and RAD participated in the design of the study and were co-PIs on the project. SES provided the biological samples from which the libraries were made. KA performed the cell flow cytometry genome-size determination. EGF and JPT constructed the BAC library. ML and DK constructed the plasmid shotgun library. DK, EGF, HL, HRK, ML, and SZ participated in library characterization. HL was the primary author of the manuscript. All authors have read and approved this report.
- Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo M-J, Frohlich MW, Perl-Treves R, Schlarbaum S, Bliss B, Tanksley S, Oppenheimer DG, Soltis PS, Ma H, dePamphilis CW, Leebens-Mack JH (2005) Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol 5:5PubMedCrossRefGoogle Scholar
- Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–219Google Scholar
- Bennett MD, Leitch IJ, Price HJ, Johnston JS (2003) Comparisons with Caenorhabditis (∼100 Mb) and Drosophila (∼175 Mb): using flow cytometry show genome size in Arabidopsis to be ∼157 Mb and thus ∼25% larger than the Arabidopsis genome initiative estimate of ∼125 Mb. Ann Bot 91:547–557PubMedCrossRefGoogle Scholar
- Frank MB (1997) Southern blot hybridizations. In: Frank MB (ed) Molecular biology protocols. Oklahoma City, OKGoogle Scholar
- Harlow WM, Harrar ES (1969) Textbook of dendrology. McGraw-Hill, New York, pp 512Google Scholar
- Hernandez R, Davalos JF, Sonti SS, Kim Y, Moody RC (1997) Strength and stiffness of reinforced yellow-poplar glued laminated beams. Res. Pap. FPL-RP-554, U.S. Department of Agriculture, Forest Service, Forest Products Laboratory, Madison, WIGoogle Scholar
- Hunt D (1998) Magnolias and their allies. International Dendrology Society & Magnolia Society, pp 304Google Scholar
- Little EL Jr (1979) Checklist of United States trees (native and naturalized). U.S. Department of Agriculture, Agriculture Handbook 541. Washington, DC, pp 375Google Scholar
- Maniatas T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, NYGoogle Scholar
- McCarthy EF (1933) Yellow-poplar characteristics, growth, and management. U.S. Department of Agriculture, Technical Bulletin 356. Washington, DC, pp 58Google Scholar
- Moody RC, Hernandez R, Davalos JF, Sonti SS (1993) Yellow poplar timber beam performance. Res. Pap. FPL-RP-520, Department of Agriculture, Forest Service, Forest Products Laboratory, Madison, WIGoogle Scholar
- Qiu Y-L, Dombrovska O, Lee J, Li L, Whitlock BA, Bernasconi-Quadroni F, Rest JS, Davis CC, Borsch T, Hilu KW, Renner SS, Soltis DE, Soltis PS, Zanis MJ, Cannone JJ, Gutell RR, Powell M, Savolainen V, Chatrou LW, Chase MW (2005) Phylogenetic analysis of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. Int J Plant Sci 166:815–842CrossRefGoogle Scholar
- Soltis DE, Soltis PS, Chase MW, Mort ME, Albach DC, Zanis M, Savolainen V, Hahn WH, Hoot SB, Fay MF, Axtell M, Swensen SM, Prince LM, Kress WJ, Nixon KC, Farris JS (2000) Angiosperm phylogeny inferred from a combined data set of 18S rDNA, rbcL and atpB sequences. Bot J Linn Soc 133:381–461CrossRefGoogle Scholar
- Tomkins JP, Peterson DG, Yang TJ, Main D, Wilkins TA, Paterson AH, Wing RA (2001) Development of genomic resources for cotton (Gosypium hirsutum): BAC library development, preliminary STC analysis, and identification of clones associated with fiber development. Mol Breed 8:255–261CrossRefGoogle Scholar
- Wei ZX, Wu ZY (1993) Pollen ultrastructure of Liriodendron and its systematic significance. Acta Bot Yunnanica 15:163–166Google Scholar
- Williams RS, Feist WC (2004) Durability of yellow-poplar and sweetgum and service life of finishes after long-term exposure. Forest Products J 54:96–101Google Scholar
- Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Brueggeman RS, Muehlbauer GJ, Wise RP, Wing RA (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor Appl Genet 101:1093–1099CrossRefGoogle Scholar