Arabidopsis Genes Research Articles

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

BackgroundPolyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain (MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the MBD gene family is still lacking, so it is necessary to conduct a comprehensive analysis.ResultsIn this study, twenty-two, ten and eleven MBD genes were identified in the genome of allotetraploid B. napus and its diploid ancestors, B. rapa and B. oleracea, respectively. Based on the clades of the MBD gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true MBD genes in Brassica existed in only 5 clades. Clade IV and Clade VI were unique in term of MBD genes in dicotyledons. Ka/Ks calculations showed that MBD genes underwent purifying selection in Brassica and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of MBD gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the MBD genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of cis-acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the MBD gene changes, which may be regulated by cis-acting elements and transposable elements. The number imbalance of cis-acting elements and transposable elements in An and Cn subgenomes may also lead to biased An subgenome expression of the MBD gene in B. napus.ConclusionsIn this study, by evaluating the number, structure, phylogeny and expression of the MBD gene in B. napus and its diploid ancestors, we increased the understanding of MBD genes in allopolyploids and provided a reference for future analysis of allopolyploidization.

Comparative analysis of the stellacyanins (SCs) family and focus on drought resistance of PtSC18 in Populus trichocarpa.

Stellacyanin (SC) is a type I (blue) copper protein, which plays a crucial role in plant growth and stress response. However, the comprehensive analysis and functional research of SCs in the woody plant is still lacking. Here, a total of 74 SCs were collected and identified from Arabidopsis, papaya, grape, rice and poplar. Bioinformatics was used to analyze the gene structure, protein structure and evolutionary relationship of 74 genes, especially 19 SCs in Populus trichocarpa. Based on the RNA-seq data, expression pattern of SCs in poplar under cold, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC18 that strongly responded to drought stress was screened. Subcellular localization experiment exhibited that PtSC18 was localized in the nucleus and plasma membrane. Overexpression of PtSC18 enhanced drought tolerance of transgenic Arabidopsis by improving water retention and reducing oxidative damage. Measurements of physiological indicators, including chlorophyll, H2O2, malondialdehyde content, peroxidase and catalase enzyme activities and electrical conductivity, all supported this conclusion. More importantly, PtSC18 enhanced the expression of some stress-related genes in transgenic Arabidopsis. Overall, our results lay a foundation for understanding the structure and function of PtSCs and provide useful gene resources for breeding through genetic engineering.

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits.

DNA methylation is a chromatin modification that plays an essential role in regulating gene expression and genome stability and it is typically associated with gene silencing and heterochromatin. Owing to its heritability, alterations in the patterns of DNA methylation have the potential to provide for epigenetic inheritance of traits. Contemporary epigenomic technologies provide information beyond sequence variation and could supply alternative sources of trait variation for improvement in crops such as sorghum. Yet, compared with other species such as maize and rice, the sorghum DNA methylome is far less well understood. The distribution of CG, CHG, and CHH methylation in the genome is different compared with other species. CG and CHG methylation levels peak around centromeric segments in the sorghum genome and are far more depleted in the gene dense chromosome arms. The genes regulating DNA methylation in sorghum are also yet to be functionally characterised; better understanding of their identity and functional analysis of DNA methylation machinery mutants in diverse genotypes will be important to better characterise the sorghum methylome. Here, we catalogue homologous genes encoding methylation regulatory enzymes in sorghum based on genes in Arabidopsis, maize, and rice. Discovering variation in the methylome may uncover epialleles that provide extra information to explain trait variation and has the potential to be applied in epigenome-wide association studies or genomic prediction. DNA methylation can also improve genome annotations and discover regulatory elements underlying traits. Thus, improving our knowledge of the sorghum methylome can enhance our understanding of the molecular basis of traits and may be useful to improve sorghum performance.

In situ deletions reveal regulatory components for expression of an intracellular immune receptor gene and its co-expressed genes in Arabidopsis.

Intracellular immune receptor nucleotide-binding leucine-rich repeats (NLRs) are highly regulated transcriptionally and post-transcriptionally for balanced plant defense and growth. NLR genes often exist in gene clusters and are usually co-expressed under various conditions. Despite intensive studies of the regulation of NLR proteins, cis-acting elements for NLR gene induction, repression or co-expression are largely unknown due to a larger than usual cis-region for their expression regulation. Here we used the CRISPR/Cas9 genome editing technology to generate a series of in situ deletions at the endogenous location of an NLR gene SNC1 residing in the RPP5 gene cluster. These deletions that made in the wild type and the SNC1 constitutive expressing autoimmune mutant bon1 revealed both positive and negative cis-acting elements for SNC1 expression. Two transcription factors that could bind to these elements were found to have an impact on the expression of SNC1. In addition, co-expression of two genes with SNC1 in the same cluster is found to be mostly dependent on the SNC1 function. Therefore, SNC1 expression is under complex local regulation involving multiple cis-elements and SNC1 itself is a critical regulator of gene expression of other NLR genes in the same gene cluster.

Serratia marcescens PLR enhances lateral root formation through supplying PLR-derived auxin and enhancing auxin biosynthesis in Arabidopsis.

Plant growth promoting rhizobacteria (PGPR) refer to bacteria that colonize the rhizosphere and contribute to plant growth or stress tolerance. To further understand the molecular mechanism by which PGPR exhibit symbiosis with plants, we performed a high-throughput single colony screening from the rhizosphere, and uncovered a bacterium (named promoting lateral root, PLR) that significantly promotes Arabidopsis lateral root formation. By 16S rDNA sequencing, PLR was identified as a novel sub-species of Serratia marcescens. RNA-seq analysis of Arabidopsis integrated with phenotypic verification of auxin signalling mutants demonstrated that the promoting effect of PLR on lateral root formation is dependent on auxin signalling. Furthermore, PLR enhanced tryptophan-dependent indole-3-acetic acid (IAA) synthesis by inducing multiple auxin biosynthesis genes in Arabidopsis. Genome-wide sequencing of PLR integrated with the identification of IAA and its precursors in PLR exudates showed that tryptophan treatment significantly enhanced the ability of PLR to produce IAA and its precursors. Interestingly, PLR induced the expression of multiple nutrient (N, P, K, S) transporter genes in Arabidopsis in an auxin-independent manner. This study provides evidence of how PLR enhances plant growth through fine-tuning auxin biosynthesis and signalling in Arabidopsis, implying a potential application of PLR in crop yield improvement through accelerating root development.

Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 (TabZIP96) under Freezing Stress in Wheat (Triticum aestivum).

The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance.

Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves

The SQUAMOSA promoter-binding protein-like (SPL) family play a key role in guiding the switch of plant growth from juvenile to adult phases. Populus euphratica Oliv. exhibit typical heterophylly, and is therefore an ideal model for studying leaf shape development. To investigate the role and regulated networks of SPLs in the morphogenesis of P. euphratica heteromorphic leaves. In this study, 33 P. euphratica SPL (PeuSPL) genes were identified from P. euphratica genome and transcriptome data. Phylogenetic analysis depicted the classification of these SPL genes into two subgroups. The expression profiles and regulatory networks of P. euphratica SPL genes analysis displayed that major P. euphratica SPL family members gradually increases from linear to broad-ovate leaves, and they were involved in the morphogenesis regulation, stress response, transition from vegetative to reproductive growth, photoperiod, and photosynthesis etc. 14 circRNAs, and 33 lncRNAs can promote the expression of 12 of the P. euphratica SPLs by co-decoying miR156 in heteromorphic leaf morphogenesis. However, it was found that the effect of PeuSPL2-4 and PeuSPL9 in leaf shape development was contrasting to their homologous genes of Arabidopsis. Therefore, it was suggested that the SPL family were evolutionarily conserved for regulation growth, but were varies in different plant for regulation of the organ development.

Functional Differentiation among the Arabidopsis Phosphatidylinositol 4-Phosphate 5-Kinase Genes PIP5K1, PIP5K2 and PIP5K3.

Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) is involved in regulating various cellular processes through the signaling function of its product, phosphatidylinositol (4,5)-bisphosphate. Higher plants encode a large number of PIP5Ks forming distinct clades in their molecular phylogenetic tree. Although biological functions of PIP5K genes have been analyzed intensively in Arabidopsis thaliana, it remains unclear how those functions differ across clades of paralogs. We performed comparative functional analysis of the Arabidopsis genes encoding PIP5K1, PIP5K2 and PIP5K3, of which the first two and the last belong to closely related but distinct clades, to clarify their conserved and/or differentiated functions. Genetic analysis with their single and multiple mutants revealed that PIP5K1 and PIP5K3 have non-overlapping functions, with the former in total plant growth and the latter in root hair elongation, whereas PIP5K2 redundantly functions in both phenomena. This pattern of functional redundancy is explainable in terms of the overlapping pattern of their promoter activities. In transformation rescue experiments, PIP5K3 promoter-directed PIP5K1-YFP completely rescued the short-root-hair phenotype of pip5k3. However, PIP5K3-YFP could substitute for PIP5K1-YFP only partially in rescuing the severe dwarfism of pip5k1pip5k2 when directed by the PIP5K1 promoter. Phylogenetic analysis of angiosperm PIP5Ks revealed that PIP5K3 orthologs have a faster rate of diversification in their amino-acid sequences compared with PIP5K1/2 orthologs after they arose through a eudicot-specific duplication event. These findings suggest that PIP5K3 specialized to promote root hair elongation and lost some of the protein-encoded functions retained by PIP5K1 and PIP5K2, whereas PIP5K1 differentiated from PIP5K2 only in its promoter-directed expression pattern.

Defining the components of the miRNA156-SPL-miR172 aging pathway in pea and their expression relative to changes in leaf morphology

The timing of developmental phase transitions is crucial for plant reproductive success, and two microRNAs (miRNA), miR156 and miR172, are implicated in the control of these changes, together with their respective SQUAMOSA promoter binding–like (SPL) and APETALA2-like (AP2) targets. While their patterns of regulation have been studied in a growing range of species, to date they have not been examined in pea (Pisum sativum), an important legume crop and model species. We analysed the recently released pea genome and defined nine miR156, 21 SPL, four miR172, and five AP2-like genes. Phylogenetic analysis of the SPL genes in pea, Medicago and Arabidopsis confirmed the eight previously defined clades, and identified a ninth potentially legume-specific SPL clade in pea and Medicago. Among the PsSPL, 14 contain a miR156 binding site and all five AP2-like transcription factors in pea include a miR172 binding site. Phylogenetic relationships, expression levels and temporal expression changes identified PsSPL2a/3a/3c/6b/9a/9b/13b/21, PsmiR156d/j and PsmiR172a/d as the most likely of these genes to participate in phase change in pea. Comparisons with leaf morphology suggests that vegetative phase change is unlikely to be definitively marked by a change in leaflet number. In addition, the timing of FT gene induction suggests that the shift from the juvenile to the adult vegetative phase may occur within fourteen days in plants grown under inductive conditions, and calls into question the contribution of miR172/AP2 to the floral transition. This work provides the first insight into the nature of vegetative phase change in pea, and an important foundation for future functional studies.

Wheat TaTIP4;1 Confers Enhanced Tolerance to Drought, Salt and Osmotic Stress in Arabidopsis and Rice.

Tonoplast aquaporins (intrinsic proteins, TIPs) have been indicated to play important roles in plant tolerance to water deficit and salinity. However, the functions of wheat TIPs in response to the stresses are largely unknown. In this study, we observed that transgenic plants overexpressing wheat TaTIP4;1 in Arabidopsis and rice displayed clearly enhanced seed germination and seedling growth under drought, salt and osmotic stress. Compared with wild type plants, Arabidopsis and rice overexpression lines had heightened water contents, reduced leaf water loss, lowered levels of Na+, Na+/K+, H2O2 and malondialdehyde, and improved activities of catalase and/or superoxide dismutase, and increased accumulation of proline under drought, salinity and/or osmotic stresses. Moreover, the expression levels of multiple drought responsive genes clearly elevated upon water dehydration, and the transcription of some salt responsive genes was markedly induced by NaCl treatment in the overexpression lines. Also, the yeast cells containing TaTIP4;1 showed increased tolerance to NaCl and mannitol, and mutation in one of three serines of TaTIP4;1 caused decreased tolerance to the two stresses. These results suggest that TaTIP4;1 serves as an essential positive regulator of seed germination and seedling growth under drought, salt and/or osmotic stress through impacting water relations, ROS balance, the accumulation of Na+ and proline, and stimulating the expression of dozens of stress responsive genes in Arabidopsis and rice. Phosphorylation may modulate the activity of TaTIP4;1.

Understanding the Modus Operandi of Class II KNOX Transcription Factors in Secondary Cell Wall Biosynthesis.

Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are involved in meristem maintenance and/or formation, Class II KNOX TF genes exhibit diverse expression patterns and their precise functions have mostly remained unknown, until recently. The expression patterns of Class II KNOX TF genes in Arabidopsis, namely KNAT3, KNAT4, KNAT5, and KNAT7, suggest that TFs encoded by at least some of these genes, such as KNAT7 and KNAT3, may play a significant role in secondary cell wall formation. Specifically, the expression of the KNAT7 gene is regulated by upstream TFs, such as SND1 and MYB46, while KNAT7 interacts with other cell wall proteins, such as KNAT3, MYB75, OFPs, and BLHs, to regulate secondary cell wall formation. Moreover, KNAT7 directly regulates the expression of some xylan synthesis genes. In this review, we summarize the current mechanistic understanding of the roles of Class II KNOX TFs in secondary cell wall formation. Recent success with the genetic manipulation of Class II KNOX TFs suggests that this may be one of the biotechnological strategies to improve plant feedstocks for bioethanol production.

Identification and characterization of 20S proteasome genes and their relevance to heat/drought tolerance in bread wheat

The genes encoding α- and β-type subunits of 20S proteasome core protease are integral components of 26S proteasome complex in the ubiquitin-proteasome system (UPS). The 20S proteasome represents a catalytic particle that cleaves cytotoxic, denatured, damaged and unwanted proteins in an ATP/ubiquitin-dependent non-lysosomal pathway and is known to impart thermotolerance in model plants. In the present study, we identified 67 genes (including 34 TaPA + 33 TaPB genes) encoding α- and β-subunits of 20S proteasome in bread wheat (Triticum aestivum L.). These genes were distributed on all the 21 wheat chromosomes, majority of them being in triplicate homoeologues. These wheat genes were orthologous to corresponding rice and Arabidopsis genes. Phylogenetic analysis placed these genes in seven clusters, each with one of the seven α (α1-7) and one of the seven β (β1-7) subunits. Expression analysis suggested that 10 of the 67 genes were involved in heat stress response, whereas four genes were involved in drought tolerance at the seedling stage. Nine (9) genes were expressed under both heat and drought suggesting their involvement in response to multiple abiotic stresses. Hopefully, future research on TaPA/TaPB genes, will help in the development of climate resilient wheat cultivars.

The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA

Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes. The co-regulation of clustered genes seems to largely depend on epigenetic reprogramming and three-dimensional chromatin conformation. In this study, we identified the long non-coding RNA (lncRNA) MARneral Silencing (MARS), localized inside the Arabidopsis marneral cluster, which controls the local epigenetic activation of its surrounding region in response to abscisic acid (ABA). MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1 (PRC1) component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binding throughout the cluster in a dose-dependent manner, determining H3K27me3 deposition and chromatin condensation. In response to ABA, MARS decoys LHP1 away from the cluster and promotes the formation of a chromatin loop bringing together the MARNERAL SYNTHASE 1 (MRN1) locus and a distal ABA-responsive enhancer. The enrichment of co-regulated lncRNAs in clustered metabolic genes in Arabidopsis suggests that the acquisition of novel non-coding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways.

Transcript Profiling Analysis and ncRNAs' Identification of Male-Sterile Systems of Brassica campestris Reveal New Insights Into the Mechanism Underlying Anther and Pollen Development.

Male-sterile mutants are useful materials to study the anther and pollen development. Here, whole transcriptome sequencing was performed for inflorescences in three sterile lines of Chinese cabbage (Brassica campestris L. ssp. chinensis Makino, syn. B. rapa ssp. chinensis), the genic male-sterile line (A line), the Polima cytoplasmic male-sterile (CMS) line (P line), and the Ogura CMS line (O line) along with their maintainer line (B line). In total, 7,136 differentially expressed genes (DEGs), 361 differentially expressed long non-coding RNAs (lncRNAs) (DELs), 56 differentially expressed microRNAs (miRNAs) (DEMs) were selected out. Specific regulatory networks related to anther cell differentiation, meiosis cytokinesis, pollen wall formation, and tapetum development were constructed based on the abortion characteristics of male-sterile lines. Candidate genes and lncRNAs related to cell differentiation were identified in sporocyteless P line, sixteen of which were common to the DEGs in Arabidopsis spl/nzz mutant. Genes and lncRNAs concerning cell plate formation were selected in A line that is defected in meiosis cytokinesis. Also, the orthologs of pollen wall formation and tapetum development genes in Arabidopsis showed distinct expression patterns in the three different sterile lines. Among 361 DELs, 35 were predicted to interact with miRNAs, including 28 targets, 47 endogenous target mimics, and five precursors for miRNAs. Two lncRNAs were further proved to be functional precursors for bra-miR156 and bra-miR5718, respectively. Overexpression of bra-miR5718HG in B. campestris slowed down the growth of pollen tubes, caused shorter pollen tubes, and ultimately affected the seed set. Our study provides new insights into molecular regulation especially the ncRNA interaction during pollen development in Brassica crops.

Tomato SlPti5 plays a regulative role in the plant immune response against Botrytis cinerea through modulation of ROS system and hormone pathways

While SlPti5 has been shown to play a crucial role in the regulation of antagonistic genes in Solanum lycopersicum and Arabidopsis against pathogen infection, there have been no comprehensive studies on the effects of SlPti5 on the regulatory response mechanism of reactive oxygen species (ROS) system and hormone pathways during growth and disease resistance of tomato plants. Here, we investigated the function of SlPti5 in the defense response of tomato against Botrytis cinerea utilizing a virus-induced gene silencing (VIGS)-based system. Expression profile analysis showed that SlPti5 was significantly induced upon B. cinerea infection, with high expression levels in the leaves and fruit of tomato. VIGS-based silencing of SlPti5 inhibited early vegetative growth, increased the plant's susceptibility to infection, promoted the development of ROS, affected the expression of genes involved in the ROS scavenging system, and attenuated the expression of genes associated with pathogenesis and the ethylene/jasmonic acid signaling pathways. In sum, our data demonstrated that SlPti5 stimulates the immune response of tomato plant to Botrytis cinerea infection by involving the ethylene (ET)- and jasmonic acid (JA)-mediated pathways and modulating the expression of some key pathogenesis-related (PR) genes.

Transcriptomic analysis of no trichome mutant and identification of new trichome related genes in Arabidopsis

Transcriptomic analysis of no trichome mutant and identification of new trichome related genes in Arabidopsis

Genome-Wide Identification and Characterization of GASA Gene Family in Nicotiana tabacum.

The gibberellic acid stimulated Arabidopsis (GASA) gene family is critical for plant growth, development, and stress response. GASA gene family has been studied in various plant species, however, the GASA gene family in tobacco (Nicotiana tabacum) have not been characterized in detail. In this study, we identified 18 GASA genes in the tobacco genome, which were distributed to 13 chromosomes. All the proteins contained a conserved GASA domain and highly specific 12-cysteine residues at the C-terminus. Phylogenetic analysis divided the NtGASA genes into three well-conserved subfamilies. Synteny analysis suggested that tandem and segmental duplications played an important role in the expansion of the NtGASA gene family. Cis-elements analysis showed that NtGASA genes might influence different phytohormone and stress responses. Tissue expression analysis revealed that NtGASA genes displayed unique or distinct expression patterns in different tissues, suggesting their potential roles in plant growth and development. We also found that the expression of NtGASA genes were mostly regulated by abscisic and gibberellic acid, signifying their roles in the two phytohormone signaling pathways. Overall, these findings improve our understanding of NtGASA genes and provided useful information for further studies on their molecular functions.

Identification and Expression Analysis of the Populus trichocarpa GASA-Gene Family.

The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays an important regulatory role in the growth and development of plants. In this study, we identified 19 GASA genes using bioinformatics-based methods in Populus trichocarpa, and these PtGASA genes could be divided into three categories based on their phylogenetic relationships. Based on an analysis of the structure and motifs of these genes, it was concluded that PtGASA class II members are more conserved than class I and class III members are, and the results of collinearity analysis showed that members of class II are collinearly related in poplar. Expression analysis of Populus trichocarpa roots, stems, and leaves showed that most of the PtGASA genes are expressed at higher levels in the stems or roots than in the leaves; a similar expression pattern was found in Vitis vinifera, indicating that the GASA-family members mainly play a role in the morphogenesis of poplar. Considering the phenomenon of gene amplification, we found that the higher the similarity of homologous genes was, the more similar the expression patterns. This study represents the first whole-genome identification and expression-profile analysis of the GASA-gene family in poplar, a model species, laying a foundation for functional studies of poplar GASA genes and serving as a reference for related research on other woody plant species.

Genome-Wide Identification of the HD-ZIP III Subfamily in Upland Cotton Reveals the Involvement of GhHB8-5D in the Biosynthesis of Secondary Wall in Fiber and Drought Resistance.

A subfamily of transcription factors known as HD-ZIP III plays distinct roles in the secondary cell wall biosynthesis, which could be attributed to the quality of cotton fiber and adaptation to drought stress. In this study, 18 HD-ZIP III genes were identified as genome wide from the upland cotton (Gossypium hirsutum). These genes are distributed on 14 different chromosomes, and all of them have undergone segmental duplications. Numerous cis-elements were identified in the promoter regions, which are related to phytohormone responses and abiotic stresses. Expression profiling of these genes by quantitative real-time (qRT)-PCR illustrated their differential spatial expression, with preferential expression in cotton fiber. Among these genes, GhHB8-5D was predicted to encode a protein that is targeted to the cell nucleus and having self-activation ability. In addition, the ectopic expression of GhHB8-5D or its synonymous mutant GhHB8-5Dm in Arabidopsis resulted in stunted plant growth, curly leaves, and twisted inflorescence stems. Microscopy examination revealed that the morphology of vascular bundles and deposition of secondary wall had substantially altered in stems, which is concomitant with the significant alteration in the transcription levels of secondary wall-related genes in these transgenic Arabidopsis. Further, ectopic expression of GhHB8-5D or GhHB8-5Dm in Arabidopsis also led to significant increase in green seedling rate and reduction in root length relative to wild type when the plants were grown under mimicked drought stress conditions. Taken together, our results may shed new light on the functional roles of GhHB8-5D that is attributable for secondary cell wall thickening in response to drought stress. Such a finding may facilitate a novel strategy for improving plant adaptations to environmental changes via regulating the biosynthesis of secondary cell wall.

Identification of key genes related to flowering by transcriptome of flowering and nonflowering Prunella vulgaris

Prunella vulgaris L. have high medicinal and ornamental values. It blooms in summer and then quickly withers, and there is no research on the regulatory mechanisms of flowering-related genes. Therefore, in this study, the flowering (leaves and spicas) and nonflowering (leaves) parts of P. vulgaris were sequenced with an Illumina HiSeq 4000, and 187 387 transcripts were obtained using Trinity software package. A total of 10 158 differentially expressed genes (DEGs) were found in the leaves of flowering and nonflowering P. vulgaris, with 6 294 upregulated genes and 3 864 downregulated genes. DEGs in leaves of flowering and nonflowering P. vulgaris were mainly annotated for metabolic processes (4 207) in Gene Ontology (GO) and ribosomal pathways (416) in Kyoto Encyclopedia of Genes and Genomes (KEGG). Screening of this set of genes yielded 50 flowering-related unigenes homologous to Arabidopsis genes involved in multiple regulatory pathways related to plant flowering, including autonomous, vernalization, gibberellin, and age pathways. In addition, there are significant differences in the expressions of genes related to flowering, such as PvFLC, PvSOC1, and PvFY, as well as genes involved in plant hormone signal transduction and sugar metabolism. The accuracy and reliability of the transcriptome results were verified by quantitative real-time RT-qPCR analysis of PvGA20OX, PvSVP, PvELF3, PvCRY1, and PvSOC1. Thus, we speculate that the flowering of P. vulgaris is regulated by certain genes related to the flowering regulation pathway and sugar and hormone metabolism pathways. Analysis of the P. vulgaris transcriptome will provide a basis for revealing its flowering mechanism.