Genes In Xylem Research Articles

Combined Use of Phenotype-Based and Genome-Informed Approaches Identified a Unique Fusarium oxysporum f. sp. cubense Isolate in Hawaii.

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is a serious disease that threatens banana production worldwide. It is a long-standing problem in Hawaii, but previously, there was little knowledge of the causal pathogen. We isolated a strain of Foc, named Foc-UH, from a field experiencing the disease epidemic in Hawaii. Infection assays of a diverse panel of 26 banana clones, including varieties used for differentiating pathogen races and fruit production, revealed that Foc-UH has a race 1 pathogenic phenotype with an intermediate race 2 virulence and revealed the differential resistance of varieties to infection. Separate phylogenetic analyses using the barcoding regions of three nuclear genes, seven complete nuclear genes, and single-nucleotide polymorphisms within conserved whole-genome protein coding sequences placed Foc-UH into recently proposed taxonomic frameworks relevant to Foc and the F. oxysporum species complex. Screening of the 99.7% complete draft genome identified five secreted in xylem (SIX) gene homologs: SIX1d, SIX1f, SIX9a, SIX9b, and SIX13a. This profile is similar to that of several race 1 isolates except for the absence of SIX4 and SIX6. Foc-UH was morphologically dissimilar to the nearest related isolates. Altogether, this study identified a unique isolate that causes banana Fusarium wilt, which represents the first characterization of the causal pathogen in Hawaii. The findings and genomic resources generated in this study are expected to guide banana breeding and cultivar deployment in Hawaii and beyond and contribute to further understanding of the pathogenicity and evolutionary systematics of Foc.

Insight into growth and wood properties based on QTL and eQTL mapping in Populus deltoides ‘Danhong’ × Populus simonii ‘Tongliao1’

Poplar is a short-rotation cultivated energy tree species, and analysis of genetic regulation of gene expression at the seedling stage is important for understanding phenotypic variation in growth rate and wood quality. However, the genetic regulation of xylem gene expression is still poorly understood. We determined transcriptomes of developing xylem of Populus deltoides ‘Danhong’, P. simonii ‘Tongliao1’ and F1 hybrids of them to explore the variations in the landscape transcriptome and its genetic basis. Through quantitative trait locus (QTL) and expression QTL (eQTL) analysis, we identified 237 QTLs, 48,019 cis-eQTLs and 2,184,889 trans-eQTLs contributing to the whole-genome transcriptome variation in poplar. Trans-acting effects play major role in expression regulation. We identified 38 eQTL hotspots, among which the A/T base mutation in PdCaM247 3′UTR in hot12654 influenced the wood basic density and regulated the expression of QTL major genes (YEATS and IQD32) and secondary cell wall related genes. Transgenic poplar with overexpressing PdCaM247 presented an increase of the secondary xylem. Yeast two-hybrid analysis revealed that PdCaM247 interacted with the secondary cell wall regulator MYB156. This study generates a large genetic resource for studying xylem development and provides new insights into the genetic basis of secondary cell wall regulatory networks.

IDENTIFICATION OF THE CELL WALL SYNTHESIS GENES IN BETULA PENDULA

This study aims to provide information on Betula pendulacell wall synthesis genes regarding their potential physiological roles and the molecular mechanism associated. Here we identified 46 gene models in 7 gene families that encode cellulose synthase and related enzymes of B. pendula, and the transcript abundance of these genes in xylem, root, leaf, and flower tissues also be determined. Based on these RNA-seq data, we have identified 8 genes that most likely participate in cell wall synthesis, which include 3 cellulose synthase genes and 5cellulose synthase-like genes. In parallel, a gene co-expression network was also constructed based on transcriptome sequencing. These analyses will help decipher the genetic information of B.pendulacell wall synthesis genes and alter its wood structureon the cellular level.

Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during the plant’s growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula Roth. Background and Objectives: The cell cycle factors not only influence cell cycles progression together, but also regulate accretion, division, and differentiation of cells, and then regulate growth and development of the plant. In this study, we identified the putative cell cycle genes in the B. pendula genome, based on the annotated cell cycle genes in Arabidopsis thaliana (L.) Heynh. It can be used as a basis for further functional research. Materials and Methods: RNA-seq technology was used to determine the transcription abundance of all cell cycle genes in xylem, roots, leaves, and floral tissues. Results: We identified 59 cell cycle gene models in the genome of B. pendula, with 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1, and BpWEE1. Conclusions: By combining phylogenetic analysis and tissue-specific expression data, we identified 17 core cell cycle genes in the Betulapendula genome.

A single-cell analysis of the Arabidopsis vegetative shoot apex.

The shoot apical meristem allows for reiterative formation of new aerial structures throughout the life cycle of a plant. We use single-cell RNA sequencing to define the cellular taxonomy of the Arabidopsis vegetative shoot apex at the transcriptome level. We find that the shoot apex is composed of highly heterogeneous cells, which can be partitioned into 7 broad populations with 23 transcriptionally distinct cell clusters. We delineate cell-cycle continuums and developmental trajectories of epidermal cells, vascular tissue, and leaf mesophyll cells and infer transcription factors and gene expression signatures associated with cell fate decisions. Integrative analysis of shoot and root apical cell populations further reveals common and distinct features of epidermal and vascular tissues. Our results, thus, offer a valuable resource for investigating the basic principles underlying cell division and differentiation in plants at single-cell resolution.

Effector Profiles of Endophytic Fusarium Associated with Asymptomatic Banana (Musa sp.) Hosts.

During the infection of a host, plant pathogenic fungi secrete small proteins called effectors, which then modulate the defence response of the host. In the Fusarium oxysporum species complex (FOSC), the secreted in xylem (SIX) gene effectors are important for host-specific pathogenicity, and are also useful markers for identifying the various host-specific lineages. While the presence and diversity of the SIX genes has been explored in many of the pathogenic lineages of F. oxysporum, there is a limited understanding of these genes in non-pathogenic, endophytic isolates of F. oxysporum. In this study, universal primers for each of the known SIX genes are designed and used to screen a panel of endophytically-associated Fusarium species isolated from healthy, asymptomatic banana tissue. SIX gene orthologues are identified in the majority of the Fusarium isolates screened in this study. Furthermore, the SIX gene profiles of these endophytic isolates do not overlap with the SIX genes present in the pathogenic lineages of F. oxysporum that are assessed in this study. SIX gene orthologues have not been commonly identified in Fusarium species outside of the FOSC nor in non-pathogenic isolates of F. oxysporum. The results of this study indicate that the SIX gene effectors may be more broadly distributed throughout the Fusarium genus than previously thought. This has important implications for understanding the evolution of pathogenicity in the FOSC.

Identification of putative lignin biosynthesis genes in Betula pendula

We identified 15 genes encoding enzymes for phenylpropanoid biosynthesis in the genome of birch by combining phylogenetic analysis and tissue-specific expression data. Lignin is one of the most abundant terrestrial biopolymers and is essential for plant structure and defense. An essential step in lignin formation is phenylpropanoid synthesis, we identified 120 gene models in 10 protein families encoding enzymes for phenylpropanoid biosynthesis in the genome of Betula pendula. The transcript abundance was determined for all 120 genes in xylem, root, leaf, and flower tissues using RNA-seq technology. We identified 15 genes that likely encode phenylpropanoid biosynthesis enzymes during wood formation. Ten of these genes are evolutionarily conserved compared to the lignin genes in Populus trichocarpa.

Comparison of Secreted in Xylem (SIX) genes in two fusarium wilt pathogens of ornamental palms

Fusarium oxysporum ff. sp. canariensis (Foc) and palmarum (Fop) cause lethal fusarium wilt on ornamental palms. Foc infects Phoenix canariensis and has a worldwide presence, whereas Fop primarily infects Washingtonia robusta and Syagrus romanzoffiana and is currently primarily restricted to Florida (USA). A Secreted in Xylem (SIX) gene profile was obtained for Fop and Foc isolates from the USA. SIX1, SIX7, SIX10 and SIX12 were detected in most Foc isolates and, with the exception of SIX12, with minimal sequence polymorphism. SIX8 and SIX9 were detected in all Fop isolates, with no sequence polymorphism. SIX10 was also present in seven of the Fop isolates. Phylogenetic trees were constructed using EF-1α‐, SIX1, SIX7 and SIX10 gene sequences from this study and previously derived sequences from Foc isolates obtained in Australia, the Canary Islands and Japan. The topology of the housekeeping EF‐1α gene indicated Foc is polyphyletic, with the Australian isolates separating into a distinct group from all other Foc isolates. However, the topologies of SIX1, SIX7 and SIX10 phylogenetic trees for Foc indicate monophyly. As has been proposed previously, this suggests the core genome of Foc evolved into a separate lineage after the SIX genes were conserved within the whole genome. This study is the first to generate SIX12 sequences for Foc. Interestingly, the topology of the SIX12 phylogenetic tree suggests polyphyly. For Fop, the topologies of the EF‐1α, SIX8 and SIX9 phylogenetic trees support monophyly. The distinct SIX gene profile and EF‐1α sequence of Fop demonstrates an independent evolutionary origin from Foc.

Fungal canker pathogens trigger carbon starvation by inhibiting carbon metabolism in poplar stems

Carbon starvation is the current leading hypothesis of plant mortality mechanisms under drought stress; recently, it is also used to explain tree die-off in plant diseases. However, the molecular biology of the carbon starvation pathway is unclear. Here, using a punch inoculation system, we conducted transcriptome and physiological assays to investigate pathogen response in poplar stems at the early stages of Botryosphaeria and Valsa canker diseases. Transcriptome assays showed that the majority of differentially expressed genes (DEGs) in stem phloem and xylem, such as genes involved in carbon metabolism and transportation, aquaporin genes (in xylem) and genes related to the biosynthesis of secondary metabolites and the phenylpropanoid pathway (related to lignin synthesis), were downregulated at 7 days after inoculation (DAI). Results also showed that the expression of the majority of disease-resistance genes upregulated in poplar stems, which may be connected with the downregulation expression of the majority of WRKY family genes. Physiological assays showed that transpiration rate decreased but WUE (water use efficiency) increased the 3 and 7 DAI, while the net photosynthetic rate decreased at 11 DAI in Botryosphaeria infected poplars (ANOVA, P < 0.05). The NSC (non-structural carbohydrates) content assays showed that the soluble sugar content of stem phloem samples increased at 3, 7, and 11 DAI that might due to the impede of pathogen infection. However, soluble sugar content of stem xylem and root samples decreased at 11 DAI; in contrast, the starch content unchanged. Therefore, results revealed a chronological order of carbon related molecular and physiological performance: declination of genes involved in carbon and starch metabolism first (at least at 7 DAI), declination of assimilation and carbon reserve (at 11 DAI) second. Results implied a potential mechanism that affects the host carbon reserve, by directly inhibiting the expression of genes involved in carbon metabolism and transport.

Characterization of Cellulose synthase-like D (CSLD) family revealed the involvement of PtrCslD5 in root hair formation in Populus trichocarpa

Cellulose synthase-like D (CSLD) family was characterized for their expression and functions in Populus trichocarpa. Ten members, PtrCslD1-10, were identified in the P. trichocarpa genome, and they belong to 4 clades by phylogenetic tree analysis. qRT-PCR and promoter:GUS assays in Arabidopsis and P. trichocarpa displayed divergent expression patterns of these 10 PtrCSLD genes in root hairs, root tips, leaves, vascular tissues, xylem and flowers. Among PtrCslD2, PtrCslD4, PtrCslD5, PtrCslD6, and PtrCslD8 that all exhibited expression in root hairs, only PtrCslD5 could restore the root hairless phenotype of the atcsld3 mutant, demonstrating that PtrCslD5 is the functional ortholog of AtCslD3 for root hair formation. Our results suggest more possible functions for other PtrCslD genes in poplar.

Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine (Pinus taeda L.) based on transcriptome analyses

Loblolly pine (Pinus taeda L.) is one of the most important species for oleoresin (a mixture of terpenoids) in South China. The high oleoresin content of loblolly pine is associated with resistance to bark beetles and other economic benefits. In this study, we conducted transcriptome analyses of loblolly pine secondary xylem to gain insight into the genes involved in terpenoid biosynthesis. A total of 372 unigenes were identified as being critical for oleoresin production, including genes for ATP-binding cassette (ABC) transporters, the cytochrome P450 (CYP) protein family, and terpenoid backbone biosynthesis enzymes. Six key genes involved in terpenoid biosynthetic pathways were selected for multiple sequence alignment, conserved motif prediction, and phylogenetic and expression profile analyses. The protein sequences of all six genes exhibited a higher degree of sequence conservation, and upstream genes were relatively more conserved than downstream genes in terpenoid biosynthetic pathways. The N-terminal regions of these sequences were less conserved than the C-terminal ends, as the N-terminals were quite diverse in both length and composition. The phylogenetic analyses revealed that most genes originated from gene duplication after species divergence, and partial genes exhibited incomplete lineage sorting. In addition, the expression profile analyses showed that all six genes exhibited high expression levels during the high-oleoresin-yielding phase.

Analysis of public RNA-seq data in studies of flax fiber biogenesis

Abstract In this work we used publicly available raw RNA-seq data to elucidate mechanisms of flax fiber biogenesis by measuring expression of cell-wall related genes (cellulose synthase, cellulose synthase-like and chitinase-like genes) in stem of flax (Linum usitatissimum cv. Bethune). Using public RNA-sequence data we have quantified and characterised the expression of the specific cell-wall genes in the top, middle and bottom parts of the Bethune flax stem. The most prominent findings are: Secondary cell-wall cellulose synthase (CesA) genes are expressed differentially in phloem and xylem in all parts of Bethune stem, in contrast with primary cell-wall cellulose synthase genes. Total expression level of cellulose synthase-like (Csl) genes is tissue invariant (although, CslG and CslE are differentially expressed) and smaller than the total expression of cellulose synthase genes. The CslD2D3 subgroup dominates total expression of CslD genes in both xylem and phloem. Expression levels of all expressed chitinase-like (Ctl) genes are tissue dependent in all parts of stem. Total expression level of chitinase-like genes is much higher than expression of cellulose synthase and cellulose synthase-like genes in both tissues.

RNAi-mediated silencing of the Arabidopsis thaliana ULCS1 gene, encoding a WDR protein, results in cell wall modification impairment and plant infertility

Ubiquitin mediated protein degradation constitutes one of the most complex post translational gene regulation mechanisms in eukaryotes. This fine-tuned proteolytic machinery is based on a vast number of E3 ubiquitin ligase complexes that mark target proteins with ubiquitin. The specificity is accomplished by a number of adaptor proteins that contain functional binding domains, including the WD40 repeat motif (WDRs). To date, only few of these proteins have been identified in plants. An RNAi mediated silencing approach was used here to functionally characterize the Arabidopsis thaliana ULCS1 gene, which encodes for a small molecular weight WDR protein. AtULCS1 interacts with the E3Cullin Ring Ligase subunit DDB1a, regulating most likely the degradation of specific proteins involved in the manifestation of diverse developmental events. Silencing of AtULCS1 results in sterile plants with pleiotropic phenotypes. Detailed analysis revealed that infertility is the outcome of anther indehiscence, which in turn is due to the impairment of the plants to accomplish secondary wall modifications. Furthermore, IREGULAR XYLEM gene expression and lignification is diminished in anther endothecium and the stem vascular tissue of the silenced plants. These data underline the importance of AtULCS1 in plant development and reproduction.

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures.

Summary Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes.Microarray analyses were used to: identify and functionally characterize groups of co‐expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation.We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue‐based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC‐7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup‐shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation.Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure.

Transcriptome sequencing and profiling of expressed genes in phloem and xylem of ramie (Boehmeria nivea L. Gaud).

Ramie (Boehmeria nivea L. Gaud) is a highly versatile herbaceous plant which is widely cropped in southern China. The success of this herbaceous plant relies on wide use in modern industry. Understanding the profiling of expressed genes in phloem and xylem of ramie is crucial for improving its industrial performance. Herein, we uncover the transcriptome profile in phloem and xylem in present study. Using Illumina paired-end sequencing technology, 57 million high quality reads were generated. De novo assembly yielded 87,144 unigenes with an average length of 635 bp. By sequence similarity searching for public databases, a total of 32,541 (41.77%) unigenes were annotated for their function. Among these genes, 57,873 (66.4%) and 28,678 (32.9%) unigenes were assigned to categories of Gene Ontology and Orthologous Groups database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 18,331 (21.0%) unigenes were mapped to 125 pathways. The metabolic pathways were assigned the most unigene (4,793, 26.2%). Furthermore, Pol II and Pol III subunits as well as the genes of Galactose metabolism pathway had higher expression in phloem compared to xylem. In addition, fatty acid metabolism pathway genes showed more abundant in xylem than phloem. These results suggest that high activities of RNA synthesis and Galactose metabolism pathway promises fiber synthesis in phloem. The present study is the initial exploration to uncover the fiber biosynthesis difference between phloem and xylem in ramie through the analysis of deep sequencing data.

Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus.

BackgroundNitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In this study, we analyzed the effects of contrasting nitrogen fertilization treatments on the phenotypes of fast growing Eucalyptus hybrids (E. urophylla x E. grandis) with a special focus on xylem secondary cell walls and global gene expression patterns.ResultsHistological observations of the xylem secondary cell walls further confirmed by chemical analyses showed that lignin was reduced by luxuriant fertilization, whereas a consistent lignin deposition was observed in trees grown in N-limiting conditions. Also, the syringyl/guaiacyl (S/G) ratio was significantly lower in luxuriant nitrogen samples. Deep sequencing RNAseq analyses allowed us to identify a high number of differentially expressed genes (1,469) between contrasting N treatments. This number is dramatically higher than those obtained in similar studies performed in poplar but using microarrays. Remarkably, all the genes involved the general phenylpropanoid metabolism and lignin pathway were found to be down-regulated in response to high N availability. These findings further confirmed by RT-qPCR are in agreement with the reduced amount of lignin in xylem secondary cell walls of these plants.ConclusionsThis work enabled us to identify, at the whole genome level, xylem genes differentially regulated by N availability, some of which are involved in the environmental control of xylogenesis. It further illustrates that N fertilization can be used to alter the quantity and quality of lignocellulosic biomass in Eucalyptus, offering exciting prospects for the pulp and paper industry and for the use of short coppices plantations to produce second generation biofuels.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0256-9) contains supplementary material, which is available to authorized users.

Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus

Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus

Distinct cinnamoyl CoA reductases involved in parallel routes to lignin in Medicago truncatula

Cinnamoyl CoA reductases (CCR) convert hydroxycinnamoyl CoA esters to their corresponding cinnamyl aldehydes in monolignol biosynthesis. We identified two CCR genes in the model legume Medicago truncatula. CCR1 exhibits preference for feruloyl CoA, but CCR2 prefers caffeoyl and 4-coumaroyl CoAs, exhibits sigmoidal kinetics with these substrates, and is substrate-inhibited by feruloyl and sinapoyl CoAs. M. truncatula lines harboring transposon insertions in CCR1 exhibit drastically reduced growth and lignin content, whereas CCR2 knockouts grow normally with moderate reduction in lignin levels. CCR1 fully and CCR2 partially complement the irregular xylem gene 4 CCR mutation of Arabidopsis. The expression of caffeoyl CoA 3-O-methyltransferase (CCoAOMT) is up-regulated in CCR2 knockout lines; conversely, knockout of CCoAOMT up-regulates CCR2. These observations suggest that CCR2 is involved in a route to monolignols in Medicago whereby coniferaldehyde is formed via caffeyl aldehyde which then is 3-O-methylated by caffeic acid O-methyltransferase.

Cis-acting elements analysis and function detection of xylem specific promoter from Populus

The cis-acting elements of JCesAP, YCesAP, and MDCesAP were analyzed by the PLACE database, the results showed that three sequences all had a core element and upstream promoter element containing TATA-box and CAAT-box. The sequences related xylem-specific and wound-defense functions were found in YCesAP and MDCesAP; and the “core xylem gene set” in JCesAP, indicating that three sequences were xylem-specific and provided with wound-defense functions. Meanwhile, some other elements were also detected, including some tissue-specific elements and some regulative ones that were induced by light, temperature, and water. For investigating their functions, three sequences of JCesAP, YCesAP, and MDCesAP were respectively combined with the report gene GFP, and those reconstructed GFP genes were respectively transferred into the genome of Populus tomentose by Agrobacterium-mediated transformation method. The detected results of GFP expressions in hygromycin B resistant calli of P. tomentosa showed that three sequences all possessed the promoter functions with tissue-specific characteristics.

Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes

As a step toward a comprehensive description of lignin biosynthesis in Populus trichocarpa, we identified from the genome sequence 95 phenylpropanoid gene models in 10 protein families encoding enzymes for monolignol biosynthesis. Transcript abundance was determined for all 95 genes in xylem, leaf, shoot and phloem using quantitative real-time PCR (qRT-PCR). We identified 23 genes that most probably encode monolignol biosynthesis enzymes during wood formation. Transcripts for 18 of the 23 are abundant and specific to differentiating xylem. We found evidence suggesting functional redundancy at the transcript level for phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), p-hydroxycinnamoyl-CoA:quinate shikimate p-hydroxycinnamoyltransferase (HCT), caffeoyl-CoA O-methyltransferase (CCoAOMT) and coniferyl aldehyde 5-hydroxylase (CAld5H). We carried out an enumeration-based motif identification and discriminant analysis on the promoters of all 95 genes. Five core motifs correctly discriminate the 18 xylem-specific genes from the 77 non-xylem genes. These motifs are similar to promoter elements known to regulate phenylpropanoid gene expression. This work suggests that genes in monolignol biosynthesis are regulated by multiple motifs, often related in sequence.