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An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron

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Abstract

Liriodendron tulipifera L. was selected by the Floral Genome Project for identification of new genes related to floral diversity in basal angiosperms. A large, non-normalized cDNA library was constructed from premeiotic and meiotic floral buds and sequenced to generate a database of 9,531 high-quality expressed sequence tags. These sequences clustered into 6,520 unigenes, of which 5,251 were singletons, and 1,269 were in contigs. Homologs of genes regulating many aspects of flower development were identified, including those for organ identity and development, cell and tissue differentiation, and cell-cycle control. Almost 5% of the transcriptome consisted of homologs to known floral gene families. Homologs of most of the genes involved in cell-wall construction were also recovered. This provides a new opportunity for comparative studies in lignin biosynthesis, a trait of key importance in the evolution of land plants and in the utilization of fiber from economically important tree species, such as Liriodendron. Also of note is that 1,089 unigenes did not match any sequence in the public databases, including the complete genomes of Arabidopsis, rice, and Populus. Some of these novel genes might be unique in basal angiosperm species and, when better characterized, may be informative for understanding the origins of diverged gene families. Thus, the Liriodendron expressed sequence tag database and library will help bridge our understanding of the mechanisms of flower initiation and development that are shared among basal angiosperms, eudicots, and monocots, and provide new opportunities for comparative analysis of gene families across angiosperm species.

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Abbreviations

ABI:

Applied Biosystems

AP :

APETALA gene

bp:

base pairs

DEPC:

diethylpyrocarbonate

EF-1-α:

Elongation Factor 1-alpha gene

EST:

expressed sequence tag

GO:

Gene Ontology Consortium

K s :

rate of synonymous substitutions

MYB :

myeloblastosis-like gene

PCR:

polymerase chain reaction

RCA:

rolling-circle amplification

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Acknowledgements

We thank David Oppenheimer and his lab for guidance on the in situ hybridization experiments. We thank the tree-improvement field crew at the University of Tennessee at Knoxville for collecting, freezing, and shipping the tissue samples used for RNA extraction. We thank Sheila Plock for assistance with manipulations and curation of the cDNA library, and Marlin Druckenmiller in the Schatz Center for Tree Molecular Genetics at Penn State for assistance in high throughput sequencing. The Floral Genome Project was supported by a grant to C. dePamphilis and co-PIs from the NSF Plant Genome Research Program (DBI-0115684). Dr. Liang was supported by a post-doctoral fellowship from The Schatz Center for Tree Molecular Genetics.

Author information

Author notes

  1. Haiying Liang

    Present address: Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA

  2. James H. Leebens-Mack

    Present address: Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA

  3. Matyas Buzgo

    Present address: Department of Biology, University of Louisiana in Shreveport, Shreveport, LA, 71115, USA

Authors and Affiliations

  1. School of Forest Resources, the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA

    Haiying Liang, John E. Carlson & D. Scott DiLoreto

  2. Department of Biology, the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA

    James H. Leebens-Mack, P. Kerr Wall, Lena L. Landherr, Yi Hu, Hong Ma & Claude W. dePamphilis

  3. Department of Plant Breeding, Cornell University, Ithaca, NY, 14853, USA

    Lukas A. Mueller, Daniel C. Ilut & Steven D. Tanksley

  4. Department of Botany, University of Florida, Gainesville, FL, 32611l, USA

    Matyas Buzgo

  5. Oxford Centre for Ecology and Hydrology, Mansfield Road, Oxford, OX1 3SR, UK

    Dawn Field

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  1. Haiying Liang
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Corresponding author

Correspondence to John E. Carlson.

Additional information

Communicated by A.E. Jeffery Dean

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Table S1Table S2Table S3

The annotations for the strongest BLASTx alignments from GenBank to the 4468 Ltu01 unigenes for matches with similarity (e) values <1e-5) (DOC 5.57 Mb)

The annotations for the strongest BLASTn alignments from GenBank to the 963 Ltu01 unigenes for matches with similarity (e) values <1e-5) (DOC 5.57 Mb)

Additional cell wall synthesis genes identified in Ltu01 (DOC 5.57 Mb)

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Liang, H., Carlson, J.E., Leebens-Mack, J.H. et al. An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron . Tree Genetics & Genomes 4, 419–433 (2008). https://doi.org/10.1007/s11295-007-0120-2

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