Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L.
- 370 Downloads
Liriodendron tulipifera L., a member of Magnoliaceae in the order Magnoliales, has been used extensively as a reference species in studies on plant evolution. However, genomic resources for this tree species are limited. We constructed cDNA libraries from ten different types of tissues: premeiotic flower buds, postmeiotic flower buds, open flowers, developing fruit, terminal buds, leaves, cambium, xylem, roots, and seedlings. EST sequences were generated either by 454 GS FLX or Sanger methods. Assembly of almost 2.4 million sequencing reads from all libraries resulted in 137,923 unigenes (132,905 contigs and 4,599 singletons). About 50% of the unigenes had significant matches to publically available plant protein sequences, representing a wide variety of putative functions. Approximately 30,000 simple sequence repeats were identified. More than 97% of the cell wall formation genes in the Cell Wall Navigator and the MAIZEWALL databases are represented. The cinnamyl alcohol dehydrogenase (CAD) homologs identified in the L. tulipifera EST dataset showed different expression levels in the ten tissue types included in this study. In particular, the LtuCAD1 was found to partially recover the stiffness of the floral stems in the Arabidopsis thaliana CAD4 and CAD5 double mutant plants, of the LtuCAD1 in lignin biosynthesis. L. tulipifera genes have greater sequence similarity to homologs from other woody angiosperm species than to non-woody model plants. This large-scale genomic resour"HistryDatesce will be instrumental for gene discovery, cDNA microarray production, and marker-assisted breeding in L. tulipifera, and strengthen this species' role in comparative studies.
KeywordsEST database Xylogenesis Liriodendron Yellow-poplar Magnoliaceae
We thank Stephan Schuster and Lynn Tomsho for their assistance in 454 sequencing, Yi Hu for RNA isolations, Denis S. Diloreto for seedlings, Stephen Ficklin for the mining of SSRs, and Xinguo Li for providing the pure xylem unigenes for Populus, loblolly pine, and white spruce. This study was mainly supported by the National Science Foundation grant, Ancestral Angiosperm Genome project (Award # DBI-0638595, PI: dePamphilis). A National Institute of Food and Agriculture, USDA grant to HL (project number SC-1700324, technical contribution No. 5832 of the Clemson University Experiment Station) contributed the sequencing of a one half 454 plate.
- Bae K, Byun J (1987) Screening of leaves of higher plants for antibacterial action. Kor J Pharmacog 8:1Google Scholar
- Beck DE (1990) Liriodendron tulipifera L. yellow-poplar. In: Burns RM, Honkala BH (tech. coords.) Silvics of North America: 1. Conifers; 2. Hardwoods. Agriculture Handbook 654, USDA, Forest Service, Washington, DC, 2:877Google Scholar
- Carlson JE, Leebens-Mack JH, Wall PK, Zahn LM, Mueller LA, Landherr LL, Hu Y, Ilut DC, Arrington JM, Choirean S, Becker A, Field D, Tanksley SD, Ma H, dePamphilis CW (2006) EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot. Plant Mol Biol 62:351–369PubMedCrossRefGoogle Scholar
- Chanderbali AS, Yoo M-J, Zahn LM, Brockington SF, Wall PK, Gitzendanner MA, Albert VA, Leebens-Mack J, Altman NS, Ma H, dePamphilis DW, Soltis DE, Soltis PS (2010) Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. PNAS 107:22570–22575PubMedCrossRefGoogle 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. US Department of Agriculture, Forest Service, Forest Products Laboratory, MadisonGoogle Scholar
- Hunt D (1998) Magnolias and their allies. International Dendrology Society & Magnolia Society, pp 304Google Scholar
- Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee S-B, Peery R, McNeal JR, Kuehl JV, Boore JL (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. PNAS 104:19369–19374PubMedCrossRefGoogle Scholar
- Klugh KR, Cumming JC (2003) Variation in organic acid exudates among mycorrhizal species colonizing Liriodendron tulipifera L. (yellow poplar) in the presence of aluminum. Ecological Society of America Annual Meeting Abstracts 88:186Google Scholar
- Koo B-W, Min B-C, Park N, Eom C, Yeo H, Ryu K-O, Choi I-G (2008) Chemical and physical characterizations of Liriodendron tulipifera on growth periods. Proceedings of the 30th Symposium on Biotechnology for Fuels and Chemicals, 4–7 May, New Orleans, LA, USAGoogle Scholar
- Koo B-W, Park N, Yeo H, Lee S-Y, Kim H-Y, Kim H, Choi I-G (2009) Organosolv pretreatment of Liriodendron tulipifera with acid and alkali catalysts. Proceedings of the 31st Symposium on Biotechnology for Fuels and Chemicals, 3–6 May, San Francisco, CA, USAGoogle Scholar
- Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek M, Prince JP, Town CD, Havey MJ (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell 16:114–125PubMedCrossRefGoogle 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, MadisonGoogle Scholar
- Qiu YL, 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 analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. Intl J Plant Sci 166:815–842CrossRefGoogle Scholar
- Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols in the series Methods in Molecular Biology. Humana, Totowa, pp 365–386Google Scholar
- Sibout R, Eudes A, Pollet B, Goujon T, Mila I, Granier F, Séguin A, Lapierre C, Jouanin L (2003) Expression pattern of two paralogs encoding cinnamyl alcohol dehydrogenases in Arabidopsis: isolation and characterization of the corresponding mutants. Plant Physiol 132:848–860PubMedCrossRefGoogle Scholar
- Soltis PS, Soltis DE, Chase MW, Endress PK, Crane PR (2004) The diversification of flowering plants. In: Cracraft J, Donoghue MJ (eds) Assembling the tree of life. Oxford University Press, Oxford, pp 154–167Google Scholar
- Soltis DE, Soltis PS, Chase MW, Endress P (2005) Phylogeny, evolution, and classification of flowering plants. Sinauer Associates, SunderlandGoogle 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. For Prod J 54:96–101Google Scholar