Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L.

Tree Genetics and Genomes

Volumn 7, Issue 5, 2011, Pages 941-954

  Liang, Haiying ^a   Ayyampalayam, Saravanaraj ^b   Wickett, Norman ^c   Barakat, Abdelali ^a   Xu, Yi ^a   Landherr, Lena ^c,d   Ralph, Paula E ^c   Jiao, Yuannian ^c   Xu, Tao ^a   Schlarbaum, Scott E ^e   Ma, Hong ^c,f,g   Leebens Mack, James H ^b   dePamphilis, Claude W ^c  

^a CLEMSON UNIVERSITY   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

^e UNIVERSITY OF TENNESSEE   (United States)

^f FUDAN UNIVERSITY   (China)

^g FUDAN UNIVERSITY   (China)

Author keywords

EST database; Liriodendron; Magnoliaceae; Xylogenesis; Yellow poplar

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; LIRIODENDRON; LIRIODENDRON TULIPIFERA; MAGNOLIACEAE; MAGNOLIALES; MAGNOLIOPHYTA;

EID: 80052758396     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-011-0386-2     Document Type: Article

References (68)

1. Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC et al (2005) Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol 5: 5.
2. Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207-221.
3. Altschul SF, Gish W, Miller EW, Myiers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
4. Axtella MJ, Bartel DP (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17: 1658-1673.
5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
6. Bae K, Byun J (1987) Screening of leaves of higher plants for antibacterial action. Kor J Pharmacog 8: 1.
7. Barakat A, Bagniewska-Zadworna A, Choi A, Plakkat U, DiLoreto D, Yellanki P, Carlson J (2009) The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression. BMC Plant Biol 9: 26.
8. Berlin A, Maximenko V, Bura R, Kang KY, Gilkes N, Saddler J (2005) A rapid microassay to evaluate enzymatic hydrolysis of lignocellulosic substrates. Biotechnol Bioeng 93: 880-886.
9. 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: 877.
10. 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: 351-369.
11. Çelen I, Harper D, Labbé N (2008) A multivariate approach to the acetylated poplar wood samples by near infrared spectroscopy. Holzforschung 62: 189-196.
12. 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: 22570-22575.
13. Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 113-116.
14. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14: 1147-1159.
15. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 24: P3.
16. Desfeux C, Clough SJ, Bent AF (2000) Female reproductive tissues are the primary target of Agrobacterium-mediated transformation by the Arabidopsis floral-dip method. Plant Physiol 123: 895-904.
17. Dsouza M, Larsen N, Overbeek R (1997) Searching for patterns in genomic data. Trends Genet 13: 497-498.
18. Girke T, Lauricha J, Tran H, Keegstra K, Raikhel NV (2004) The cell wall navigator database: a systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol 136: 3003-3008.
19. Guillaumie S, San Clemente H, Deswarte C, Martinez Y, Lapierre C, Murigneux A, Barrière Y, Pichon M, Goffner D (2007) MAIZEWALL: database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize. Plant Physiol 143: 339-363.
20. 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, Madison.
21. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protoc 4: 44-57.
22. Hunt D (1998) Magnolias and their allies. International Dendrology Society & Magnolia Society, pp 304.
23. Hwang SS, Lee SJ, Kim HK, Ka JO, Kim KJ, Song HG (2008) Biodegradation and saccharification of wood chips of Pinus strobus and Liriodendron tulipifera by white rot fungi. J Microbiol Biotechnol 18: 1819-1826.
24. 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: 19369-19374.
25. Jackson S, Rounsley S, Purugganan M (2006) Comparative sequencing of plant genomes: choices to make. Plant Cell 18: 1100-1104.
26. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14: 787-799.
27. Karlin S, Campbell AM, Mrázek J (1998) Comparative DNA analysis across diverse genomes. Ann Rev Gen 32: 185-225.
28. Kim KD, Lee EJ (2005) Potential tree species for use in the restoration of unsanitary landfills. Environ Manage 36: 1-14.
29. 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: 186.
30. 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, USA.
31. 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, USA.
32. 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: 114-125.
33. Kumpatla S, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48: 985.
34. Lafayette PR, Eriksson KE, Dean JF (1999) Characterization and heterologous expression of laccase cDNAs from the lignifying xylem of yellow-poplar (Liriodendron tulipifera). Plant Mol Biol 40: 23-35.
35. Li X, Wu HX, Dillon SK, Southerton SG (2009) Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don. BMC Genomics 10: 41.
36. Li X, Wu HX, Southerton SG (2010) Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants. BMC Evol Biol 10: 190.
37. Liang H, Barakat A, Schlarbaum SE, Carlson JE (2011) Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron. Tree Genet Genomes 7: 373-384.
38. Liang H, Barakat A, Schlarbaum SE, Mandoli DS, Carlson JE (2010) Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots and eudicots. Genome 53: 533-544.
39. Liang H, Carlson JE, Leebens-Mack JH, Wall PK, Mueller LA, Buzgo M et al (2008) An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genet Genomes 4: 419-433.
40. Liang H, Fang EG, Tomkins JP, Luo M, Kudrna D, Kim HR et al (2007) Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis. Tree Genet Genomes 3: 215-225.
41. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucl Acids Res 30: 281-283.
42. McInerney J (1998) GCUA (General Codon Usage Analysis). Bioinformatics 14: 372-373.
43. Merkle SA, Hoey MT, Watson-Pauley BA, Schlarbaum SE (1993) Propagation of Liriodendron hybrids via somatic embryogenesis. Plant Cell Tissue Organ Cult 34: 191-198.
44. 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.
45. Moon MK, Oh HM, Kwon BM, Baek NI, KimSH KJS, Kim DK (2007) Farnesyl protein transferase and tumor cell growth inhibitory activities of lipiferolide isolated from Liriodendron tulipifera. Arch Pharm Res 30: 299-302.
46. Moore MJ, Bell CD, Soltis PS, Soltis DE (2007) Using plastid genome-scale data to resolve enigmatic. PNAS 104: 19363-19368.
47. Murray EE, Lotzer J, Eberle M (1989) Codon usage in plant genes. Nucl Acid Res 17: 477-498.
48. Parks CR, Wendel JF (1990) Molecular divergence between Asian and North American species of Liriodendron (Magnoliaceae) with implications for interpretation of fossil floras. Am J Bot 77: 1243-1256.
49. Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, Buigues B, Tikhonov A, Huson DH, Tomsho LP, Auch A et al (2006) Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311: 392-394.
50. 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: 815-842.
51. Ranocha P, Chabannes M, Chamayou S, Danoun S, Jauneau A, Boudet AM, Goffner D (2002) Laccase down-regulation causes alterations in phenolic metabolism and cell wall structure in poplar. Plant Physiol 129: 145-155.
52. Rengel D, Clemente HS, Servant F, Ladouce N, Paux E, Wincker P, Couloux A, Sivadon P, Grima-Pettenati J (2009) A new Eucalyptus genomic resource dedicated to wood formation: a comprehensive survey. BMC Plant Biol 9: 36.
53. Ronse de Craene L, Soltis DE, Soltis PS (2003) Evolution of floral structures in basal angiosperms. Intl J Plant Sci 164: S329-S363.
54. 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 365-386.
55. Sibout R, Eudesb A, Mouilleb G, Polletc B, Lapierrec C, Jouaninb L, Séguin A (2005) CINNAMYL ALCOHOL DEHYDROGENASE-C and -D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell 17: 2059-2076.
56. 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: 848-860.
57. 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 154-167.
58. Soltis DE, Soltis PS, Chase MW, Endress P (2005) Phylogeny, evolution, and classification of flowering plants. Sinauer Associates, Sunderland.
59. Soltis DE, Ma H, Frohlich MW, Soltis PS, Albert VA, Oppenheimer DG, Altman NS, dePamphilis CD, Leebens-Mack J (2007) The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends Plant Sci 12: 358-367.
60. Wall PK, Leebens-Mack J, Müller KF, Field D, Altman NS, de Pamphilis CW (2008) PlantTribes: a gene and gene family resource for comparative genomics in plants. Nucleic Acids Res 36: D970-D976.
61. Wei ZX, Wu ZY (1993) Pollen ultrastructure of Liriodendron and its systematic significance. Acta Bot Yunnanica 15: 163-166.
62. Williams RS, Feist WC (2004) Durability of yellow-poplar and sweetgum and service life of finishes after long-term exposure. For Prod J 54: 96-101.
63. Xiang Q, Lee LYY, Torget RW (2004) Kinetics of glucose decomposition during dilute-acid hydrolysis of lignocellulosic biomass. Appl Biochem Biotechnol 114: 1127-1138.
64. Xu M, Li H, Zhang B (2006) Fifteen polymorphic simple sequence repeat markers from expressed sequence tags of Liriodendron tulipifera. Mol Ecol Notes 6: 728-730.
65. Xu M, Sun Y, Li H (2010) EST-SSRs development and paternity analysis for Liriodendron spp. New For 40: 361-382.
66. Zahn LM, Kong H, Leebens-Mack JH, Kim S, Soltis PS, Landherr LL, Soltis D, dePamphilis CW, Ma H (2005) The evolution of the SEPALLATA subfamily of MADS-box genes: a pre-angiosperm origin with multiple duplications throughout angiosperm history. Genetics 169: 2209-2223.
67. Zahn LM, Leebens-Mack J, de Pamphilis CW, Ma H, Theissen G (2006) To B or not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. J Hered 96: 225-240.
68. Zhang K, Qian Q, Huang Z, Wang Y, Li M, Hong L, Zeng D, Gu M, Chu C, Cheng C (2006) GOLD HULL and INTERNODE2 encodes a primarily multifunctional cinnamyl-alcohol dehydrogenase in rice. Plant Physiol 140: 972-983.