Tree Genetics & Genomes

, Volume 7, Issue 5, pp 941–954 | Cite as

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

  • Haiying LiangEmail author
  • Saravanaraj Ayyampalayam
  • Norman Wickett
  • Abdelali Barakat
  • Yi Xu
  • Lena Landherr
  • Paula E. Ralph
  • Yuannian Jiao
  • Tao Xu
  • Scott E. Schlarbaum
  • Hong Ma
  • James H. Leebens-Mack
  • Claude W. dePamphilisEmail author
Original Paper


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.


EST 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.

Supplementary material

11295_2011_386_MOESM1_ESM.doc (57 kb)
Online Resource 1 Cumulative codon usage in Liriodendron tulipifera transcriptome (DOC 57 kb)
11295_2011_386_MOESM2_ESM.doc (32 kb)
Online Resource 2 Dinucleotide frequencies (DOC 31 kb)
11295_2011_386_MOESM3_ESM.txt (1 kb)
Online Resource 3 (TXT 0 kb)
11295_2011_386_MOESM4_ESM.pdf (24.9 mb)
Online Resource 4 (PDF 25,536 kb)
11295_2011_386_MOESM5_ESM.txt (5.5 mb)
Online Resource 5 (TXT 5,654 kb)
11295_2011_386_MOESM6_ESM.txt (15 kb)
Online Resource 6 (TXT 15 kb)
11295_2011_386_MOESM7_ESM.txt (5 kb)
Online Resource 7 Conserved miRNAs identified in Liriodendron tulipifera cDNA unigenes (TXT 4 kb)
11295_2011_386_MOESM8_ESM.txt (57 kb)
Online Resource 8 Liriodendron genes potentially targeted by the identified miRNAs. The targets having hits in the Cell Wall Navigator and/or Maize Wall databases are highlighted (TXT 57 kb)
11295_2011_386_MOESM9_ESM.txt (389 kb)
Online Resource 9 Liriodendron tulipifera unigenes with significant hits in the Cell Wall Navigator database (TXT 389 kb)
11295_2011_386_MOESM10_ESM.txt (619 kb)
Online Resource 10 Liriodendron tulipifera unigenes with significant hits in the Maize Wall database (TXT 619 kb)


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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Haiying Liang
    • 1
    Email author
  • Saravanaraj Ayyampalayam
    • 2
  • Norman Wickett
    • 3
  • Abdelali Barakat
    • 1
  • Yi Xu
    • 1
  • Lena Landherr
    • 3
    • 4
  • Paula E. Ralph
    • 3
  • Yuannian Jiao
    • 3
  • Tao Xu
    • 1
  • Scott E. Schlarbaum
    • 5
  • Hong Ma
    • 3
    • 6
    • 7
  • James H. Leebens-Mack
    • 2
  • Claude W. dePamphilis
    • 3
    Email author
  1. 1.Department of Genetics and BiochemistryClemson UniversityClemsonUSA
  2. 2.Department of Plant Biology, Plant Sciences BuildingUniversity of GeorgiaAthensUSA
  3. 3.Department of Biology and Huck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkUSA
  4. 4.Department of HorticulturePennsylvania State UniversityUniversity ParkUSA
  5. 5.Department of Forestry, Wildlife & Fisheries, Institute of AgricultureThe University of TennesseeKnoxvilleUSA
  6. 6.State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary BiologySchool of Life Sciences, Fudan UniversityShanghaiChina
  7. 7.Institutes of Biomedical SciencesFudan UniversityShanghaiChina

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