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

Abstract

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. Communicated by R. SederoffElectronic supplementary material The online version of this article (

Expressed sequence tag analysis of functional genes associated with adventitious rooting in Liriodendron hybrids

“…When compared to model species, the best BLASTX matches were with sequences from grape, poplar, rice, and Arabidopsis. Woody angiosperm species had more hits than non-woody species (Liang et al, 2011).…”

“…The read length of the ESTs ranged from 59 to 2349 bp, with an average length of 1001 bp, which was longer than floral bud ESTs of L. tulipifera, and petal and leaf ESTs of L. chinense (Liang et al, 2008;Liang et al, 2011;Yang et al, 2014) but was smaller than the secondary xylem ESTs of L. tulipifera (Jin et al, 2011). The GC content of 46.74% was comparable to that of other transcriptomes in Liriodendron (Liang et al, 2008;Yang et al, 2014), but was different from those of Arabidopis (42.7%) and rice (51.1%; Kuhl et al, 2004).…”

“…Recently, a large number of ESTs have been generated for many trees. Currently, there are three available EST databases (Albert et al, 2005;Liang et al, 2008;Jin et al, 2011;Liang et al, 2011) and one BAC library (Liang et al, 2007) for L. tulipifera and one EST database for L. chinense (Yang et al, 2014). Most of the cDNA libraries have been constructed from flowers, xylems, and leaves.…”

Genetic characterization of Liriodendron seed orchards with EST-SSR markers

“…These markers included seven Expressed Sequenced Tags (EST)-SSR markers (LT002, LT015, LT021, LT086, LT096, LT131, LT157) previously characterized by electrophoresis on 8% polyacrylamide gels [42] and thirteen new markers (LTCU19, LTCU40, LTCU51, LTCU53, LTCU125, LTCU139, LTCU142, LTCU143, doi: 10.7243/2050-2389-4-1 LTCU145, LTCU150, LTCU151, LTCU152, LTCU154) mined from a comprehensive EST dataset [22]. PCR amplification for each marker was performed with genomic DNA of Liriodendron trees from the Clemson and Knoxville seed orchards and the US National Arboretum.…”

“…This is expected because EST-SSRs have generally demonstrated a high frequency of cross-species transferability despite less polymorphism compared to genomic SSRs [9,12,44]. Among the 194 L. tulipifera trees included in the study, the number of alleles per locus ranged from 3 to 26 (mean=13.0) ( Table 2 Many genomic resources, such as expressed sequence tag (EST) databases [15,22,23] and genomic DNA libraries [24], have been developed for L. tulipifera. Through these resources, several thousand putative SSR markers have been identified by in silico mining.…”