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

Liang, Haiying; Carlson, John E.; Leebens‐Mack, James H.; Wall, P. Kerr; Mueller, Lukas A.; Buzgo, Matyas; Landherr, Lena; Hu, Yi; DiLoreto, Denis S; Ilut, Daniel C.; Field, Dawn; Tanksley, Steven D.; Mā, Hong; dePamphilis, Claude W.

doi:10.1007/s11295-007-0120-2

Cited by 34 publications

(26 citation statements)

References 40 publications

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“…Because of its phylogenetically important position, yellow-poplar has been used extensively as a benchmark species in studies on plant evolution (Parks and Wendel 1990;Endress and Igersheim 2000;Zahn et al 2005). Genomic resources are being developed quickly for yellow-poplar and recently include a 4.8× BAC library and a floral expressed sequence tag (EST) database that contains more than 6,000 unigenes (Liang et al 2007(Liang et al , 2008. Several new EST databases are being developed for different tissue types by the Ancestral Angiosperm Genome (2010; http://ancangio.uga.edu/).…”

Section: Introductionmentioning

confidence: 99%

Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron

Liang

Barakat

Schlarbaum

et al. 2010

Tree Genetics & Genomes

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FLORICAULA/LEAFY (FLO/LFY) plays an important role in the reproductive transition and controls flower spatial patterning by inducing the expression of the ABC floral organ identity genes. In this study, we sequenced two bacterial artificial chromosomes harboring a FLO/LFY and three other genes from yellow-poplar (Liriodendron tulipifera L.) and compared the gene order in this locus between several species. Besides the conserved terminal domains, key residues involved in interactions with DNA bases, backbone, and in dimerization were also conserved in the yellow-poplar FLO/LFY. Phylogenetic analysis of the FLO/LFY amino acid sequences placed yellow-poplar closer to eudicots than to monocotyledonous species. We found that gene content and order in this region of the yellow-poplar genome was more similar to corresponding regions in Vitis vinifera L., Carica papaya L., Populus trichocarpa Torr. & Gray, and Ricinus communis L., regardless of the evolutionary relationship. In addition, evidence for transposition, large insertions, and duplications were found, suggesting multiple and complex mechanisms of basal angiosperm genome evolution.

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Section: Introductionmentioning

confidence: 99%

Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron

Liang

Barakat

Schlarbaum

et al. 2010

Tree Genetics & Genomes

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“…Interestingly, there were only five (2.8%) tetramers and two (1.1%) pentamers. Dimer repeats were the most abundant SSRs that were also observed in L. tulipifera (Liang et al, 2008;Liang et al, 2011); in contrast, trimers mainly contributed to SSR-containing ESTs in rice, soybean, and Arabidopsis (Scott et al, 2000). Among the dimer repeats, GA/TC (56.9%) was the most frequent dinucleotide repeat and GC/GC was the least frequent in the Liriodendron hybrid EST dataset.…”

Section: Ssr Miningmentioning

confidence: 95%

“…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). …”

Section: Library Sequencing and Contig Assemblymentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Liu

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Liriodendron hybrids (Liriodendron chinense x L. tulipifera) are important landscaping and afforestation hardwood trees. To date, little genomic research on adventitious rooting has been reported in these hybrids, as well as in the genus Liriodendron. In the present study, we used adventitious roots to construct the first cDNA library for Liriodendron hybrids. A total of 5176 expressed sequence tags (ESTs) were generated and clustered into 2921 unigenes. Among these unigenes, 2547 had significant homology to the non-redundant protein database representing a wide variety of putative functions. Homologs of these genes regulated many aspects of adventitious rooting, including those for auxin signal transduction and root hair development. Results of quantitative real-time polymerase chain reaction showed that AUX1, IRE, and FB1 were highly expressed in adventitious roots and the expression of AUX1, ARF1, NAC1, RHD1, and IRE increased during the development of adventitious roots. Additionally, 181 simple sequence repeats were identified from 166 ESTs and more than 91.16% of these were dinucleotide and trinucleotide repeats. To the best of our knowledge, the present study reports the identification of the genes associated with adventitious rooting in the genus Liriodendron for the first time and provides a valuable resource for future genomic studies. Expression analysis of selected genes could allow us to identify regulatory genes that may be essential for adventitious rooting.

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“…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.…”

Section: Amplification Of Est-ssr Loci In Liriodendronmentioning

confidence: 99%

Genetic characterization of Liriodendron seed orchards with EST-SSR markers

Zhang¹,

Carlson²,

Tian³

et al. 2015

J Plant Sci Mol Breed

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Liriodendron tulipifera L., is a wide-spread, fast-growing pioneering tree species native to eastern North America. Commonly known as yellow-poplar, tulip tree, or tulip-poplar, the species is valued, both ecologically and economically. It is perhaps the most commonly used utility hardwood in the USA, and is planted widely for reforestation and, in varietal forms, as an ornamental. Although most seedlings used for reforestation today derive from collections in natural populations, two known seed orchards, established from plus-tree selections, i.e. superior phenotypes, in the 1960's and 1970's have been used for local and regional planting needs in Tennessee and South Carolina. However, very little is known about the population genetics of yellow-poplar nor the genetic composition of the existing seed orchards. In this study, 194 grafted yellow-poplar trees from a Clemson, SC orchard and a Knoxville, TN orchard were genetically characterized with 15 simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs). Of the 15 EST-SSR markers, 14 had a polymorphic information content (PIC) of at least 0.5. There was no significant difference between the Clemson and Knoxville orchards in average effective number of alleles (5.93 vs 3.95), observed and expected heterozygosity (Ho: 0.64 vs 0.58; He: 0.74 vs 0.70), Nei's expected heterozygosity (0.74 vs 0.58), or Shannon's Information index (1.84 vs 1.51). The larger Clemson orchard exhibited a significantly greater number of observed alleles than the Knoxville orchard (15.3 vs7.4). Overall, substantial genetic diversity is captured in the Clemson and Knoxville orchards.

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

Cited by 34 publications

References 40 publications

Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron

Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron

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

Genetic characterization of Liriodendron seed orchards with EST-SSR markers

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