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Haiying Liang - One of the best experts on this subject based on the ideXlab platform.
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ltucad1 is a cinnamyl alcohol dehydrogenase ortholog involved in lignin biosynthesis in Liriodendron tulipifera l a basal angiosperm timber species
Plant Molecular Biology Reporter, 2013Co-Authors: Yi Xu, Shivegowda Thammannagowda, Tina P Thomas, Parastoo Azadi, Scott E Schlarbaum, Haiying LiangAbstract:Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis and catalyzes the final step in the synthesis of monolignols. Seven CAD homologs (LtuCAD1 to LtuCAD7) have been previously identified from a basal angiosperm species Liriodendron tulipifera L., which is an important timber tree species with significant ecological and economic values. The phylogenetic analysis indicates that LtuCAD1 is the only Liriodendron CAD grouped with the bona fide CADs, the primary CAD genes involved in lignification. In this study, the predicted protein sequence of LtuCAD1 was found to have conserved domains and the same key determinant site with the bona fide CADs in other plant species. Additionally, LtuCAD1 had the highest expression level in xylem as revealed by quantitative RT-PCR analysis. The expression of beta-glucuronidase (GUS) driven by the LtuCAD1 promoter was largely localized in vascular tissues in Arabidopsis. In stem cross sections, GUS staining was found exclusively in xylem and phloem. When expressed in the Arabidopsis cad4 cad5 double mutant, LtuCAD1 was able to restore the total lignin content and decrease the S/G lignin ratio. Our data indicate that LtuCAD1 is a CAD ortholog involved in lignin biosynthesis in Liriodendron.
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investigation of genome structure of a cinnamyl alcohol dehydrogenase locus in a basal angiosperm hardwood species Liriodendron tulipifera l reveals low synteny
Journal of Systematics and Evolution, 2011Co-Authors: X U Yi, Scott E Schlarbaum, Haiying LiangAbstract:Abstract Basal angiosperms contain a wide diversity of floral and growth forms and gave rise to the largest recent angiosperm lineages. As none of the basal angiosperm genomes has been sequenced, examining large bacterial artificial chromosome (BAC) inserts remains the main approach to providing a first glimpse of the structure and organization of their genomes. In this study, we sequenced a 126.9âkbp BAC contig harboring a cinnamyl alcohol dehydrogenase gene (LtuCAD1) in a basal angiosperm species, Liriodendron tulipifera L., an important timber tree species with significant ecological and economic values. A key enzyme in lignin biosynthesis, CAD catalyzes the final step in the synthesis of monolignols. We carried out phylogenetic analyses of seven fullâlength CAD family genes (LtuCAD1â7) obtained from a comprehensive Liriodendron expressed sequence tag dataset. The phylogenetic tree suggests that LtuCAD1 is the primary CAD gene involved in lignifications as it is the only Liriodendron CAD grouped with the bona fide CADs class. As well as the LtuCAD1, the BAC contig contained fragmented sequences for one integrase, eight hypothetical proteins, two gagâpol polyproteins, one RNase H family protein, and one chromatin binding protein. Comparative analysis with other angiosperm species suggests that the genomic segment in this BAC has undergone frequent arrangement. This study is our initial step in identifying and understanding lignin biosynthesis genes from basal angiosperm species. Such knowledge can help bridge the information gap between hardwood (angiosperm) and softwood (gymnosperm) species and benefit potential breeding and biotechnology application for enhanced production of biomass and digestibility in L. tulipifera.
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an est database for Liriodendron tulipifera l floral buds the first est resource for functional and comparative genomics in Liriodendron
Tree Genetics & Genomes, 2008Co-Authors: Haiying Liang, John E Carlson, Jim Leebensmack, Kerr P Wall, Lukas A Mueller, Matyas Buzgo, Lena LandherrAbstract:Liriodendron tulipifera L. was selected by the Floral Genome Project for identification of new genes related to floral diversity in basal angiosperms. A large, non-normalized cDNA library was constructed from premeiotic and meiotic floral buds and sequenced to generate a database of 9,531 high-quality expressed sequence tags. These sequences clustered into 6,520 unigenes, of which 5,251 were singletons, and 1,269 were in contigs. Homologs of genes regulating many aspects of flower development were identified, including those for organ identity and development, cell and tissue differentiation, and cell-cycle control. Almost 5% of the transcriptome consisted of homologs to known floral gene families. Homologs of most of the genes involved in cell-wall construction were also recovered. This provides a new opportunity for comparative studies in lignin biosynthesis, a trait of key importance in the evolution of land plants and in the utilization of fiber from economically important tree species, such as Liriodendron. Also of note is that 1,089 unigenes did not match any sequence in the public databases, including the complete genomes of Arabidopsis, rice, and Populus. Some of these novel genes might be unique in basal angiosperm species and, when better characterized, may be informative for understanding the origins of diverged gene families. Thus, the Liriodendron expressed sequence tag database and library will help bridge our understanding of the mechanisms of flower initiation and development that are shared among basal angiosperms, eudicots, and monocots, and provide new opportunities for comparative analysis of gene families across angiosperm species.
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development of a bac library for yellow poplar Liriodendron tulipifera and the identification of genes associated with flower development and lignin biosynthesis
Tree Genetics & Genomes, 2007Co-Authors: Haiying Liang, Jim Leebensmack, Eric Fang, Jeffrey P Tomkins, David A Kudrna, K Arumuganathan, Shaying Zhao, Scott E SchlarbaumAbstract:Liriodendron tulipifera L., a member of the Magnoliaceae, occupies an important phylogenetic position as a basal angiosperm that has retained numerous putatively ancestral morphological characters, and thus has often been used in studies of the evolution of flowering plants and of specific gene families. However, genomic resources for these early branching angiosperm lineages are very limited. In this study, we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from L. tulipifera. Flow cytometry estimates that this nuclear genome is approximately 1,802 Mbp per haploid genome (±16 SD). The BAC library contains 73,728 clones, a 4.8-fold genome coverage, with an average insert size of 117 kb, a chloroplast DNA content of 0.2%, and little to no bacterial sequences nor empty vector content clones. As a test of the utility of this BAC library, we screened the library with six single/low-copy genic probes. We obtained at least two positive clones for each gene and confirmed the clones by DNA sequencing. A total of 182 paired end sequences were obtained from 96 of the BAC clones. Using BLAST searches, we found that 25% of the BAC end sequences were similar to DNA sequences in GenBank. Of these, 68% shared sequence with transposable elements and 25% with genes from other taxa. This result closely reflected the content of random sequences obtained from a small insert genomic library for L. tulipifera, indicating that the BAC library construction process was not biased. The first genomic DNA sequences for Liriodendron genes are also reported. All the Liriodendron genomic sequences described in this paper have been deposited in the GenBank data library. The end sequences from shotgun genomic clones and BAC clones are under accession DU169330–DU169684. Partial sequences of Gigantea, Frigida, LEAFY, cinnamyl alcohol dehydrogenase, 4-coumarate:CoA ligase, and phenylalanine ammonia-lyase genes are under accession DQ223429–DQ223434.
Huogen Li - One of the best experts on this subject based on the ideXlab platform.
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transcriptomic and microstructural analyses in Liriodendron tulipifera linn reveal candidate genes involved in nectary development and nectar secretion
BMC Plant Biology, 2019Co-Authors: Huogen LiAbstract:Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of nectaries, the mechanism of nectar secretion and the molecular mechanism of nectary development in Liriodendron remain poorly understood. In this study, we examined the nectary surface cells and change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select appropriate samples for subsequent research. Transcriptome sequencing was of the top and middle parts of immature nectaries and the middle part of mature and postsecretory nectaries in L. tulipifera was performed. We evaluated the expression profiles of 21 DEGs that are closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. L. tulipifera nectaries are starch-storing nectaries and are located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb of clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02–79.77% efficiency. In total, 26,955 DEGs were identified by performing six pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. We evaluated the nectary development and secretion processes comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that nectaries play important roles in flavonoid synthesis and petal color presentation.
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interspecies evolutionary divergence in Liriodendron evidence from the nucleotide variations of lcdhn like gene
BMC Evolutionary Biology, 2018Co-Authors: Yanli Cheng, Huogen LiAbstract:Liriodendron is a genus of Magnoliaceae, which consists of two relict species, Liriodendron chinense and L. tulipifera. Although the morphologies are highly similar, the two species exhibit different adaptive capacity. Dehydrins (DHNs) are abiotic stresses resistant proteins in planta, which are associated with adaptive evolution. To better understand the evolution divergence between L. chinense and L. tulipifera and how DHN genes are associated with adaptation evolution, we firstly investigated the DNA polymorphisms of the LcDHN-like gene in 21 L. chinense and 6 L. tulipifera populations. A 707 bp LcDHN-like gene was cloned, which included a 477 bp open reading frame (ORF) and coding 158 amino acids. 311 LcDHN-like gDNA sequences were obtained from 70 L. chinense and 35 L. tulipifera individuals. The AMOVA and phylogenetic relationship analysis showed significant differences between the two species. A higher genetic diversity was observed in L. tulipifera compared to L. chinense, in consistent with the higher adaptive capacity of L. tulipifera. Our data also suggested that the LcDHN-like genes’ polymorphisms were under neutral mutation and purifying selection model in the L. chinense and L. tulipifera populations, respectively. The distinct expanding range and rate between the two species, haplotypes shared only in L.chinense’s nearby populations, and wide dispersals in L. tulipifera could contribute to the obscure east-west separation in L. chinense and entirely unordered phylogeny in L. tulipifera. The completely separated nonsynonymous substitution at position 875 and the higher range scope of aliphatic index in L. tulipifera populations may be related with its higher adaptive capacity. Taken together, our study suggests LcDHN-like gene is a potential mark gene responsible for adaptive evolution divergence in Liriodendron. Significant differences and completely distinct haplogroups between L. chinense and L. tulipifera showed that the two species have evolved into different directions. The more widely distribution, earlier haplogroups divergence events, and richer SNPs variations in L. tulipifera could imply its stronger adaptation in this species. And potential effect of the allelic variations in LcDHN-like gene may reflect the difference of water stress and chill tolerance between L. chinense and L. tulipifera, which could provide some information for further adaption evolution studies of Liriodendron.
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relationship between parental genetic distance and offspring s heterosis for early growth traits in Liriodendron implication for parent pair selection in cross breeding
New Forests, 2016Co-Authors: Huogen Li, Jing YeAbstract:Parent-pair selection is one of crucial factors that generate progenies with strong heterosis in tree cross-breeding programmes. In our Liriodendron breeding programme, we conducted a very effective strategy on selecting elite parental combinations with strong heterosis on the basis of a large number of crosses and progeny tests. In the past two decades, we have conducted dozens of interspecies crosses in Liriodendron and the hybrids with good performance have been broadly planted for both ornamental and industrial utilization in southern China. In contrast to the application, the genetic mechanism of heterosis in Liriodendron still remains unknown. Genetic distance is one key parameter which has been considered for parent-pair selection. Here, we reported the relationship between parental genetic distance and offspring heterosis by analyzing early growth traits of progenies from intra- and inter-specific crosses in Liriodendron. The genetic distances among 13 parental trees were assessed based on polymorphisms generated from 24 microsatellites loci. Offspring heterosis was estimated based on a 6-year-old progeny test. No significant correlations were found between parental genetic distance and offspring heterosis. However, we found that the offspring heterosis of growth reached the maximum value when parental genetic distance was 1.07, which was validated in another batch of crosses based on 2-year-old growth. Our findings may be helpful for the future parent-pair selection in Liriodendron cross-breeding programmes.
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de novo transcriptome analysis of Liriodendron chinense petals and leaves by illumina sequencing
Gene, 2014Co-Authors: Ying Yang, Meng Xu, Jie Wang, Huogen LiAbstract:Liriodendron chinense (Hemsl.) Sarg is an endangered species and occupies a pivotal position in phylogenetic studies of flowering plants, while its genomic resources are limited. In this study, we performed transcriptome sequencing for L. chinense petals and leaves using the Illumina paired-end sequencing technique. Approximately 17.02-Gb clean reads were obtained, and de novo assembly generated 87,841 unigenes, with an average length of 778 bp. Of these, there were 65,535 (74.61%) unigenes with significant similarity to publically available plant protein sequences. There were 3386 genes identified as significant differentially expressed between petals and leaves, among them 2969 (87.68%) were up-regulated and 417 (12.31%) down-regulated in petals. Metabolic pathway analysis revealed that 25 unigenes were predicted to be responsible for the biosynthesis of carotenoids, with 7 genes differentially expressed between these two tissues. This report is the first to identify genes associated with carotenoid biosynthesis in Liriodendron and represents a valuable resource for future genomic studies on the endangered species L. chinense.
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est ssrs development and paternity analysis for Liriodendron spp
New Forests, 2010Co-Authors: Meng Xu, Huogen LiAbstract:Liriodendron are ideal plants for research on mating system, systemic evolution and population genetics. Here we report the development and application of a set of simple sequence repeat (SSR) markers derived from expressed sequence tags (ESTs) of L. tulipifera. In total, 176 primer pairs were developed and yielded 132 EST-SSR markers that amplified clear SSR bands with genomic DNA of L. tulipifera. Transferability of these EST-SSR markers to related species and genera was further examined. Twelve highly informative loci screened from 132 EST-SSR markers were applied to explore the effective pollen dispersal patterns and male reproductive success of Liriodendron. A provenance trial population of Liriodendron comprised 12 L. chinense (Hemsl.) Sarg provenances and 5 L. tulipifera provenances. The four maternal trees were randomly sampled as tested maternal trees in the population. Paternities of 220 open-pollination progenies from 4 maternal trees above were potentially identified by means of paternity analysis, of which 138 progenies (accounting for 62.7%) were assigned to 49 male parents at the 95% confidence level. The cumulative exclusion probability of 12 EST-SSR loci was 98.5%. The average effective pollen dispersal distance of pollen donors ranged from 15 to 35 m, with the maximum dispersal distance of 77 m. There were obvious male reproductive success differences among individuals, ranging from 0 to 10.9%. The cumulative male reproductive success of individuals within 35 m radius around the known maternal trees reached 51.4%. Diversiform mating patterns, including selfing, intra-species mating and interspecies mating, coexisted in the occasion of open-pollination in Liriodendron.
Jinhui Chen - One of the best experts on this subject based on the ideXlab platform.
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transcriptome analysis and metabolic profiling reveal the key role of carotenoids in the petal coloration of Liriodendron tulipifera
Horticulture research, 2020Co-Authors: Lingfeng Hu, Jinhui ChenAbstract:Liriodendron tulipifera, also known as tuliptree, is a popular ornamental horticultural plant with extraordinary tulip-shaped flowers characterized by an orange band near their base. The mechanisms underlying petal band-specific pigmentation during L. tulipifera flower development are unclear. Here, we combined nontargeted and targeted metabolomics and transcriptomics to identify a pathway cascade leading to carotenoid biosynthesis that is specifically activated in the petal band. The comparative analysis of carotenoid metabolites between L. tulipifera and Liriodendron hybrids indicates that γ-carotene, a rare carotene in plants, is the most likely orange pigment responsible for the coloration of the petal band. Phenotypic and transcriptomic analyses of developing petals reveal that the band area is first predefined by the loss of green color. Later, the band is maintained by locally activating and repressing carotenoid and chlorophyll biosynthesis genes, respectively. Two rate-limiting genes of carotene biosynthesis, carotenoid isomerase (CRTISO) and epsilon lycopene cyclase (e-LCY), encode the core enzymes responsible for petal band-specific orange pigmentation in L. tulipifera. In particular, a putative additional e-LCY copy specific to L. tulipifera may contribute to the distinct petal coloration pattern, compared with L. chinense. Taken together, our work provides a first glimpse of the metabolome and transcriptome dynamics in tuliptree flower coloration and provides a valuable resource for flower breeding or metabolic engineering as well as for understanding flower evolution in an early woody angiosperm.
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Genetic Diversity and Differentiation of Relict Plant Liriodendron Populations Based on 29 Novel EST-SSR Markers
Forests, 2019Co-Authors: Xiaofei Long, Yuhao Weng, Yu Sheng, Lanhua Guan, Jinhui ChenAbstract:Surviving relict populations of species that were more widespread in ancient times can teach us a lot, such as evolution and genetic differentiation. One such relict plant is Liriodendron, of which populations remain in China (L. chinense (Hemsl.) Sarg.) and the USA (L. tulipifera L.). Studying the genetic structure of these populations would give insight into the genetic differentiation and the breeding strategy. In this work, we developed and characterized 29 novel simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) from hybrid Liriodendron (Liriodendron chinense × tulipifera) callus. In total, 29 SSRs with perfect primer-designed were used to assess genetic diversity and differentiation. The set of polymorphic EST-SSR loci was identified in 48 Liriodendron individuals, represented by 35 individuals sampled from 14 provenances of L. chinense and 13 individuals sampled from 5 provenances of L. tulipifera. Our results indicated that L. chinense populations possess slightly higher genetic diversity than L. tulipifera populations. Based on genetic distances, 48 Liriodendron individuals clustered into three groups (the eastern China L. chinense, the western China L. chinense and L. tulipifera), although the STRUCTURE analysis of the Liriodendron populations revealed just two clear genetic clusters (L. chinense and L. tulipifera). Among these 29 novel markers, ESSR119 showed an obvious species-specific characteristic which can be very useful in marker-assisted selection (MAS). In general, all these EST-SSR markers may have agronomic potential and constitute a basis for future studies on the identification, innovation, and even preservation of Liriodendron germplasms.
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Liriodendron genome sheds light on angiosperm phylogeny and species pair differentiation
Nature plants, 2019Co-Authors: Jinhui Chen, Pengkai Wang, Xiaofei Long, Yu Sheng, Xuanmin Guang, Chenxi Zhao, Linfeng Yang, Yanwei Zhou, Haibin Xu, Jin ZhangAbstract:The genus Liriodendron belongs to the family Magnoliaceae, which resides within the magnoliids, an early diverging lineage of the Mesangiospermae. However, the phylogenetic relationship of magnoliids with eudicots and monocots has not been conclusively resolved and thus remains to be determined1–6. Liriodendron is a relict lineage from the Tertiary with two distinct species—one East Asian (L. chinense (Hemsley) Sargent) and one eastern North American (L. tulipifera Linn)—identified as a vicariad species pair. However, the genetic divergence and evolutionary trajectories of these species remain to be elucidated at the whole-genome level7. Here, we report the first de novo genome assembly of a plant in the Magnoliaceae, L. chinense. Phylogenetic analyses suggest that magnoliids are sister to the clade consisting of eudicots and monocots, with rapid diversification occurring in the common ancestor of these three lineages. Analyses of population genetic structure indicate that L. chinense has diverged into two lineages—the eastern and western groups—in China. While L. tulipifera in North America is genetically positioned between the two L. chinense groups, it is closer to the eastern group. This result is consistent with phenotypic observations that suggest that the eastern and western groups of China may have diverged long ago, possibly before the intercontinental differentiation between L. chinense and L. tulipifera. Genetic diversity analyses show that L. chinense has tenfold higher genetic diversity than L. tulipifera, suggesting that the complicated regions comprising east–west-orientated mountains and the Yangtze river basin (especially near 30° N latitude) in East Asia offered more successful refugia than the south–north-orientated mountain valleys in eastern North America during the Quaternary glacial period. A high-quality reference genome for the plant Liriodendron chinense places magnoliids as sister to the clade consisting of eudicots and monocots. Population genomic analyses unravel the evolution of two distinct species in the genus Liriodendron.
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Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation
Nature plants, 2018Co-Authors: Jinhui Chen, Pengkai Wang, Yu Sheng, Xuanmin Guang, Chenxi Zhao, Linfeng Yang, Yanwei ZhouAbstract:The genus Liriodendron belongs to the family Magnoliaceae, which resides within the magnoliids, an early diverging lineage of the Mesangiospermae. However, the phylogenetic relationship of magnoliids with eudicots and monocots has not been conclusively resolved and thus remains to be determined1–6. Liriodendron is a relict lineage from the Tertiary with two distinct species—one East Asian (L. chinense (Hemsley) Sargent) and one eastern North American (L. tulipifera Linn)—identified as a vicariad species pair. However, the genetic divergence and evolutionary trajectories of these species remain to be elucidated at the whole-genome level7. Here, we report the first de novo genome assembly of a plant in the Magnoliaceae, L. chinense. Phylogenetic analyses suggest that magnoliids are sister to the clade consisting of eudicots and monocots, with rapid diversification occurring in the common ancestor of these three lineages. Analyses of population genetic structure indicate that L. chinense has diverged into two lineages—the eastern and western groups—in China. While L. tulipifera in North America is genetically positioned between the two L. chinense groups, it is closer to the eastern group. This result is consistent with phenotypic observations that suggest that the eastern and western groups of China may have diverged long ago, possibly before the intercontinental differentiation between L. chinense and L. tulipifera. Genetic diversity analyses show that L. chinense has tenfold higher genetic diversity than L. tulipifera, suggesting that the complicated regions comprising east–west-orientated mountains and the Yangtze river basin (especially near 30° N latitude) in East Asia offered more successful refugia than the south–north-orientated mountain valleys in eastern North America during the Quaternary glacial period. A high-quality reference genome for the plant Liriodendron chinense places magnoliids as sister to the clade consisting of eudicots and monocots. Population genomic analyses unravel the evolution of two distinct species in the genus Liriodendron.
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establishment of transient gene expression systems in protoplasts from Liriodendron hybrid mesophyll cells
PLOS ONE, 2017Co-Authors: Zhenyu Chen, Pengkai Wang, Liming Yang, Guangping Wang, Dandan Wang, Suchan Liao, Tielong Cheng, Jinhui ChenAbstract:Liriodendron is a genus of the magnolia family comprised of two flowering tree species that produce hardwoods of great ecological and economic value. However, only a limited amount of genetic research has been performed on the Liriodendron genus partly because transient or stable transgenic trees have been difficult to produce. In general, transient expression systems are indispensable for rapid, high-throughput screening and systematic characterization of gene functions at a low cost; therefore, development of such a system for Liriodendron would provide a necessary step forward for research on Magnoliaceae and other woody trees. Herein, we describe an efficient and rapid protocol for preparing protoplasts from the leaf mesophyll tissue of a Liriodendron hybrid and an optimized system for polyethylene glycol-mediated transient transfection of the protoplasts. Because the leaves of the Liriodendron hybrid are waxy, we formulated an enzyme mix containing 1.5% (w/v) Cellulase R-10, 0.5% (w/v) Macerozyme R-10, and 0.1% (w/v) Pectolyase Y-23 to efficiently isolate protoplasts from the Liriodendron hybrid leaf mesophyll tissue in 3 h. We optimized Liriodendron protoplast transfection efficiency by including 20 μg plasmid DNA per 104 protoplasts, a transformation time of 20 min, and inclusion of 20% (w/v) polyethylene glycol 4000. After integrating the Liriodendron WOX1 gene into pJIT166-GFP to produce a WOX1-GFP fusion product and transfecting it into isolated protoplasts, LhWOX1-GFP was found to localize to the nucleus according to its green fluorescence.
Jim Leebensmack - One of the best experts on this subject based on the ideXlab platform.
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an est database for Liriodendron tulipifera l floral buds the first est resource for functional and comparative genomics in Liriodendron
Tree Genetics & Genomes, 2008Co-Authors: Haiying Liang, John E Carlson, Jim Leebensmack, Kerr P Wall, Lukas A Mueller, Matyas Buzgo, Lena LandherrAbstract:Liriodendron tulipifera L. was selected by the Floral Genome Project for identification of new genes related to floral diversity in basal angiosperms. A large, non-normalized cDNA library was constructed from premeiotic and meiotic floral buds and sequenced to generate a database of 9,531 high-quality expressed sequence tags. These sequences clustered into 6,520 unigenes, of which 5,251 were singletons, and 1,269 were in contigs. Homologs of genes regulating many aspects of flower development were identified, including those for organ identity and development, cell and tissue differentiation, and cell-cycle control. Almost 5% of the transcriptome consisted of homologs to known floral gene families. Homologs of most of the genes involved in cell-wall construction were also recovered. This provides a new opportunity for comparative studies in lignin biosynthesis, a trait of key importance in the evolution of land plants and in the utilization of fiber from economically important tree species, such as Liriodendron. Also of note is that 1,089 unigenes did not match any sequence in the public databases, including the complete genomes of Arabidopsis, rice, and Populus. Some of these novel genes might be unique in basal angiosperm species and, when better characterized, may be informative for understanding the origins of diverged gene families. Thus, the Liriodendron expressed sequence tag database and library will help bridge our understanding of the mechanisms of flower initiation and development that are shared among basal angiosperms, eudicots, and monocots, and provide new opportunities for comparative analysis of gene families across angiosperm species.
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development of a bac library for yellow poplar Liriodendron tulipifera and the identification of genes associated with flower development and lignin biosynthesis
Tree Genetics & Genomes, 2007Co-Authors: Haiying Liang, Jim Leebensmack, Eric Fang, Jeffrey P Tomkins, David A Kudrna, K Arumuganathan, Shaying Zhao, Scott E SchlarbaumAbstract:Liriodendron tulipifera L., a member of the Magnoliaceae, occupies an important phylogenetic position as a basal angiosperm that has retained numerous putatively ancestral morphological characters, and thus has often been used in studies of the evolution of flowering plants and of specific gene families. However, genomic resources for these early branching angiosperm lineages are very limited. In this study, we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from L. tulipifera. Flow cytometry estimates that this nuclear genome is approximately 1,802 Mbp per haploid genome (±16 SD). The BAC library contains 73,728 clones, a 4.8-fold genome coverage, with an average insert size of 117 kb, a chloroplast DNA content of 0.2%, and little to no bacterial sequences nor empty vector content clones. As a test of the utility of this BAC library, we screened the library with six single/low-copy genic probes. We obtained at least two positive clones for each gene and confirmed the clones by DNA sequencing. A total of 182 paired end sequences were obtained from 96 of the BAC clones. Using BLAST searches, we found that 25% of the BAC end sequences were similar to DNA sequences in GenBank. Of these, 68% shared sequence with transposable elements and 25% with genes from other taxa. This result closely reflected the content of random sequences obtained from a small insert genomic library for L. tulipifera, indicating that the BAC library construction process was not biased. The first genomic DNA sequences for Liriodendron genes are also reported. All the Liriodendron genomic sequences described in this paper have been deposited in the GenBank data library. The end sequences from shotgun genomic clones and BAC clones are under accession DU169330–DU169684. Partial sequences of Gigantea, Frigida, LEAFY, cinnamyl alcohol dehydrogenase, 4-coumarate:CoA ligase, and phenylalanine ammonia-lyase genes are under accession DQ223429–DQ223434.
Scott E Schlarbaum - One of the best experts on this subject based on the ideXlab platform.
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ltucad1 is a cinnamyl alcohol dehydrogenase ortholog involved in lignin biosynthesis in Liriodendron tulipifera l a basal angiosperm timber species
Plant Molecular Biology Reporter, 2013Co-Authors: Yi Xu, Shivegowda Thammannagowda, Tina P Thomas, Parastoo Azadi, Scott E Schlarbaum, Haiying LiangAbstract:Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis and catalyzes the final step in the synthesis of monolignols. Seven CAD homologs (LtuCAD1 to LtuCAD7) have been previously identified from a basal angiosperm species Liriodendron tulipifera L., which is an important timber tree species with significant ecological and economic values. The phylogenetic analysis indicates that LtuCAD1 is the only Liriodendron CAD grouped with the bona fide CADs, the primary CAD genes involved in lignification. In this study, the predicted protein sequence of LtuCAD1 was found to have conserved domains and the same key determinant site with the bona fide CADs in other plant species. Additionally, LtuCAD1 had the highest expression level in xylem as revealed by quantitative RT-PCR analysis. The expression of beta-glucuronidase (GUS) driven by the LtuCAD1 promoter was largely localized in vascular tissues in Arabidopsis. In stem cross sections, GUS staining was found exclusively in xylem and phloem. When expressed in the Arabidopsis cad4 cad5 double mutant, LtuCAD1 was able to restore the total lignin content and decrease the S/G lignin ratio. Our data indicate that LtuCAD1 is a CAD ortholog involved in lignin biosynthesis in Liriodendron.
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investigation of genome structure of a cinnamyl alcohol dehydrogenase locus in a basal angiosperm hardwood species Liriodendron tulipifera l reveals low synteny
Journal of Systematics and Evolution, 2011Co-Authors: X U Yi, Scott E Schlarbaum, Haiying LiangAbstract:Abstract Basal angiosperms contain a wide diversity of floral and growth forms and gave rise to the largest recent angiosperm lineages. As none of the basal angiosperm genomes has been sequenced, examining large bacterial artificial chromosome (BAC) inserts remains the main approach to providing a first glimpse of the structure and organization of their genomes. In this study, we sequenced a 126.9âkbp BAC contig harboring a cinnamyl alcohol dehydrogenase gene (LtuCAD1) in a basal angiosperm species, Liriodendron tulipifera L., an important timber tree species with significant ecological and economic values. A key enzyme in lignin biosynthesis, CAD catalyzes the final step in the synthesis of monolignols. We carried out phylogenetic analyses of seven fullâlength CAD family genes (LtuCAD1â7) obtained from a comprehensive Liriodendron expressed sequence tag dataset. The phylogenetic tree suggests that LtuCAD1 is the primary CAD gene involved in lignifications as it is the only Liriodendron CAD grouped with the bona fide CADs class. As well as the LtuCAD1, the BAC contig contained fragmented sequences for one integrase, eight hypothetical proteins, two gagâpol polyproteins, one RNase H family protein, and one chromatin binding protein. Comparative analysis with other angiosperm species suggests that the genomic segment in this BAC has undergone frequent arrangement. This study is our initial step in identifying and understanding lignin biosynthesis genes from basal angiosperm species. Such knowledge can help bridge the information gap between hardwood (angiosperm) and softwood (gymnosperm) species and benefit potential breeding and biotechnology application for enhanced production of biomass and digestibility in L. tulipifera.
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development of a bac library for yellow poplar Liriodendron tulipifera and the identification of genes associated with flower development and lignin biosynthesis
Tree Genetics & Genomes, 2007Co-Authors: Haiying Liang, Jim Leebensmack, Eric Fang, Jeffrey P Tomkins, David A Kudrna, K Arumuganathan, Shaying Zhao, Scott E SchlarbaumAbstract:Liriodendron tulipifera L., a member of the Magnoliaceae, occupies an important phylogenetic position as a basal angiosperm that has retained numerous putatively ancestral morphological characters, and thus has often been used in studies of the evolution of flowering plants and of specific gene families. However, genomic resources for these early branching angiosperm lineages are very limited. In this study, we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from L. tulipifera. Flow cytometry estimates that this nuclear genome is approximately 1,802 Mbp per haploid genome (±16 SD). The BAC library contains 73,728 clones, a 4.8-fold genome coverage, with an average insert size of 117 kb, a chloroplast DNA content of 0.2%, and little to no bacterial sequences nor empty vector content clones. As a test of the utility of this BAC library, we screened the library with six single/low-copy genic probes. We obtained at least two positive clones for each gene and confirmed the clones by DNA sequencing. A total of 182 paired end sequences were obtained from 96 of the BAC clones. Using BLAST searches, we found that 25% of the BAC end sequences were similar to DNA sequences in GenBank. Of these, 68% shared sequence with transposable elements and 25% with genes from other taxa. This result closely reflected the content of random sequences obtained from a small insert genomic library for L. tulipifera, indicating that the BAC library construction process was not biased. The first genomic DNA sequences for Liriodendron genes are also reported. All the Liriodendron genomic sequences described in this paper have been deposited in the GenBank data library. The end sequences from shotgun genomic clones and BAC clones are under accession DU169330–DU169684. Partial sequences of Gigantea, Frigida, LEAFY, cinnamyl alcohol dehydrogenase, 4-coumarate:CoA ligase, and phenylalanine ammonia-lyase genes are under accession DQ223429–DQ223434.