SPDE: a multi-functional software for sequence processing and data extraction.

SUMMARY: Sequence Processing and Data Extraction (SPDE) has eight modules comprising 100 basic functions ranging from sequence extraction, format conversion to data reorganization and mining, and all of these functions can be completed by point-and-click icons. SPDE also incorporates eight public analyses tools; thus, SPDE is a comprehensive bioinformatics platform for big biological data analysis. AVAILABILITY AND IMPLEMENTATION: SPDE built by Python can run on 32-bit, 64-bit Windows and MacOS systems. It can be downloaded from https://github.com/simon19891216/SPDEv1.2.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Auxin-Induced SaARF4 Downregulates SaACO4 to Inhibit Lateral Root Formation in Sedum alfredii Hance.

Lateral root (LR) formation promotes plant resistance, whereas high-level ethylene induced by abiotic stress will inhibit LR emergence. Considering that local auxin accumulation is a precondition for LR generation, auxin-induced genes inhibiting ethylene synthesis may thus be important for LR development. Here, we found that auxin response factor 4 (SaARF4) in Sedum alfredii Hance could be induced by auxin. The overexpression of SaARF4 decreased the LR number and reduced the vessel diameters. Meanwhile, the auxin distribution mode was altered in the root tips and PIN expression was also decreased in the overexpressed lines compared with the wild-type (WT) plants. The overexpression of SaARF4 could reduce ethylene synthesis, and thus, the repression of ethylene production decreased the LR number of WT and reduced PIN expression in the roots. Furthermore, the quantitative real-time PCR, chromatin immunoprecipitation sequencing, yeast one-hybrid, and dual-luciferase assay results showed that SaARF4 could bind the promoter of 1-aminocyclopropane-1-carboxylate oxidase 4 (SaACO4), associated with ethylene biosynthesis, and could downregulate its expression. Therefore, we concluded that SaARF4 induced by auxin can inhibit ethylene biosynthesis by repressing SaACO4 expression, and this process may affect auxin transport to delay LR development.

A Single Amino Acid Change in Nramp6 from Sedum Alfredii Hance Affects Cadmium Accumulation.

SaNramp6 in Sedum alfredii encodes a membrane-localized metal transporter. We isolated the SaNramp6h allele from the hyperaccumulating ecotype (HE) of S. alfredii. When this allele was expressed in transgenic yeast and Arabidopsis thaliana, it enhanced their cadmium (Cd) sensitivity by increased Cd transport and accumulation. We isolated another allele, SaNramp6n, from a nonhyperaccumulating ecotype (NHE) of S. alfredii. Amino acid sequence comparisons revealed three amino acid differences between SaNramp6h and SaNramp6n. We investigated the Cd transport activity of the Nramp6 allele, and determined which residues are essential for the transport activity. We conducted structure-function analyses of SaNramp6 based on site-directed mutagenesis and functional assays of the mutants in yeast and Arabidopsis. The three residues that differed between SaNramp6h and SaNramp6n were mutated. Only the L157P mutation of SaNramp6h impaired Cd transport. The other mutations, S218N and T504A, did not affect the transport activity of SaNramp6h, indicating that these residues are not essential for metal selectivity. Transgenic plants overexpressing SaNramp6hL157P showed altered metal accumulation in shoots and roots. Our results suggest that the conserved site L157 is essential for the high metal transport activity of SaNramp6h. This information may be useful for limiting or increasing Cd transport by other plant natural resistance associated macrophage protein (NRAMP) proteins.

Genome-Wide Identification of the Expansin Gene Family and Its Potential Association with Drought Stress in Moso Bamboo.

Expansins, a group of cell wall-loosening proteins, are involved in cell-wall loosening and cell enlargement in a pH-dependent manner. According to previous study, they were involved in plant growth and abiotic stress responses. However, information on the biological function of the expansin gene in moso bamboo is still limited. In this study, we identified a total of 82 expansin genes in moso bamboo, clustered into four subfamilies (α-expansin (EXPA), ß-expansin (EXPB), expansin-like A (EXLA) and expansin-like B (EXPB)). Subsequently, the molecular structure, chromosomal location and phylogenetic relationship of the expansin genes of Phyllostachys edulis (PeEXs) were further characterized. A total of 14 pairs of tandem duplication genes and 31 pairs of segmented duplication genes were also identified, which may promote the expansion of the expansin gene family. Promoter analysis found many cis-acting elements related to growth and development and stress response, especially abscisic acid response element (ABRE). Expression pattern revealed that most PeEXs have tissue expression specificity. Meanwhile, the expression of some selected PeEXs was significantly upregulated mostly under abscisic acid (ABA) and polyethylene glycol (PEG) treatment, which implied that these genes actively respond to expression under abiotic stress. This study provided new insights into the structure, evolution and function prediction of the expansin gene family in moso bamboo.

cDNA Library for Mining Functional Genes in Sedum alfredii Hance Related to Cadmium Tolerance and Characterization of the Roles of a Novel SaCTP2 Gene in Enhancing Cadmium Hyperaccumulation.

Heavy metal contamination presents serious threats to living organisms. Functional genes related to cadmium (Cd) hypertolerance or hyperaccumulation must be explored to enhance phytoremediation. Sedum alfredii Hance is a Zn/Cd cohyperaccumulator exhibiting abundant genes associated with Cd hypertolerance. Here, we developed a method for screening genes related to Cd tolerance by expressing a cDNA-library for S. alfredii Hance. Yeast functional complementation validated 42 of 48 full-length genes involved in Cd tolerance, and the majority of them were strongly induced in roots and exhibited diverse expression profiles across tissues. Coexpression network analysis suggested that 15 hub genes were connected with genes involved in metabolic processes, response to stimuli, and metal transporter and antioxidant activity. The functions of a novel SaCTP2 gene were validated by heterologous expression in Arabidopsis, responsible for retarding chlorophyll content decrease, maintaining membrane integrity, promoting reactive oxygen species (ROS) scavenger activities, and reducing ROS levels. Our findings suggest a highly complex network of genes related to Cd hypertolerance in S. alfredii Hance, accomplished via the antioxidant system, defense genes induction, and the calcium signaling pathway. The proposed cDNA-library method is an effective approach for mining candidate genes associated with Cd hypertolerance to develop genetically engineered plants for use in phytoremediation.

Identification and expression analysis of salt-responsive genes using a comparative microarray approach in Salix matsudana.

Salt stress exerts negative effects on plant growth, development and yields, with roots being the primary site of both perception and damage. Salix matsudana (Chinese willow) is tolerant of high salinity. However, genes associated with this trait were rarely characterized. Therefore, we first performed salt-stress treatment on S. matsudana plants, then identified differentially expressed genes by comparison of salt-treated roots and untreated controls using microarray analysis. A total of 403 salt-responsive genes were identified, of which 239 were repressed and 164 were up-regulated. Functional classification analysis revealed that these genes belonged to families encoding proteins involved in metabolism, regulation of transcription, signal transduction, hormone responses, abiotic stress responses, and other processes related to growth and development. This suggested that when S. matsudana was confronted with salt stress, coordinated adjustments are made to physiological and biochemical processes, which would then allow more resources to be allocated to protective mechanisms to avoid salt injury. The expression patterns of representative genes were further validated and the diversity of the temporal profiles indicated that a combination of several genes and the initiation of diverse pathways performed functions in S. matsudana salt tolerance. This work represents the first study employing microarrays to investigate salt tolerance in S. matsudana. The data presented herein enhance our understanding of the molecular mechanisms of S. matsudana responses to salinity stress and lay the groundwork for genetic engineering strategies to improve stress tolerance of agronomically important species.

Isolation of salt stress-related genes from Aspergillus glaucus CCHA by random overexpression in Escherichia coli.

The halotolerant fungus Aspergillus glaucus CCHA was isolated from the surface of wild vegetation around a saltern with the salinity range being 0-31%. Here, a full-length cDNA library of A. glaucus under salt stress was constructed to identify genes related to salt tolerance, and one hundred clones were randomly selected for sequencing and bioinformatics analysis. Among these, 82 putative sequences were functionally annotated as being involved in signal transduction, osmolyte synthesis and transport, or regulation of transcription. Subsequently, the cDNA library was transformed into E. coli cells to screen for putative salt stress-related clones. Five putative positive clones were obtained from E. coli cells grown on LB agar containing 1 M NaCl, on which they showed rapid growth compared to the empty vector control line. Analysis of transgenic Arabidopsis thaliana lines overexpressing CCHA-2142 demonstrated that the gene conferred increased salt tolerance to plants as well by protecting the cellular membranes, suppressing the inhibition of chlorophyll biosynthesis. These results highlight the utility of this A. glaucus cDNA library as a tool for isolating and characterizing genes related to salt tolerance. Furthermore, the identified genes can be used for the study of the underlying biology of halotolerance.

Genome-wide characterization and gene expression analyses of ALDH gene family in response to drought stress in moso bamboo (Phyllostachys edulis).

Aldehyde dehydrogenase (ALDH) superfamily, comprising enzymes dependent on NAD+ or NADP+, plays an important role in controlling plant growth and development, as well as in responsing to phytohormone and environmental stress. These enzymes possess the ability to prevent toxic effects of aldehydes by converting them into their corresponding carboxylic acids. However, the potential function of ALDH genes in moso bamboo (Phyllostachys edulis) remains largely unknown. In this study, the ALDH gene superfamily in moso bamboo was analyzed through genome-wide screening, the evolutionary relationship of expansion genes was conducted. Tissue-specific expression patterns of ALDH genes were observed in 26 different tissues. Plant hormone and environmental stress responsive cis-elements were identified in the promoter of ALDH genes, which were supported by public databases data on the expression patterns under various abiotic stresses and hormone treatments. ALDH activity was increased in moso bamboo seedlings exposed to drought, compared to control condition. Furthermore, PeALDH2B2 was found to physically interact with PeGPB1 in response to drought. Overall, the study provides a comprehensive analysis of the ALDH family in moso bamboo and contributes to our understanding of the function of ALDH genes in growth, development, and adaptation to drought stresses.

Expression profile of miRNAs in Populus cathayana L. and Salix matsudana Koidz under salt stress.

Soil salinization can lead to environmental and ecological problems worldwide. Abiotic stressors, including salinity, are suspected to regulate microRNA (miRNA) expression. Plants exposed to such abiotic stressors express specific miRNAs, which are genes encoding small non-coding RNAs of 20-24 nucleotides. miRNAs are known to exist widely in plant genomes, and are endogenous. A previous study used miRNA microarray technology and poly(A) polymerase-mediated qRT-PCR technology to analyze the expression profile of miRNAs in two types of plants, Populus cathayana L. (salt-sensitive plants) and Salix matsudana Koidz (highly salinity-tolerant plants), both belonging to the Salicaceae family. miRNA microarray hybridization revealed changes in expression of 161 miRNAs P. cathayana and 32 miRNAs in S. matsudana under salt stress. Differences in expression indicate that the same miRNA has different expression patterns in salt-sensitive plants and salt-tolerant plants under salt stress. These indicate that changes in expression of miRNAs might function as a response to varying salt concentrations. To examine this, we used qRT-PCR to select five miRNA family target genes involved in plant responses to salt stress. Upon saline treatment, the expressions of both ptc-miR474c and ptc-miR398b in P. cathayana were down-regulated, but were up-regulated in S. matsudana. Expression of the miR396 family in both types of plants was suppressed. Furthermore, we have analyzed the different expression patterns between P. cathayana and S. matsudana. Findings of this study can be utilized in future investigations of post-transcriptional gene regulation in P. cathayana and S. matsudana under saline stress.

A comprehensive analysis of the floral transition in ma bamboo (Dendrocalamus latiflorus) reveals the roles of DlFTs involved in flowering.

Bamboo has a unique flowering characteristics of long and unpredictable vegetative period, which differs from annual herbs and perennial woody plants. In order to understand the molecular regulatory mechanism of bamboo flowering, a comprehensive study was conducted in ma bamboo (Dendrocalamus latiflorus Munro), including morphological, physiological and transcriptiome analyses. Differentially expressed genes related to the flowering pathway were identified by comparative transcriptome analysis. DlFT1, a homologous gene of FT/Hd3a, was significantly upregulated in flowering bamboo. Direct differentiation of spikelets from calli occurred and the downstream gene AP1 was upregulated in the transgenic bamboo overexpressing DlFT1. Transgenic rice overexpressing DlFT1 showed a strong early flowering phenotype. DlFT1 and DlTFL1 could interact with DlFD, and DlTFL1 delayed flowering. It is presumed that DlTFL1 plays an antagonistic role with DlFT1 in ma bamboo. In addition, the expression of DlFT1 was regulated by DlCO1, indicating that a CO-FT regulatory module might exist in ma bamboo. These results suggest that DlFT1 is a florigen candidate gene with conservative function in promoting flowering. Interestingly, the results have shown for the first time that DlFT2 can specifically interact with E3 ubiquitin ligase WAV3, while DlFT3 transcripts are mainly nonsense splicing. These findings provide better understanding of the roles of the florigen gene in bamboo and lay a theoretical basis for regulating bamboo flowering in the future.

An Efficient Genetic Transformation and CRISPR/Cas9-Based Genome Editing System for Moso Bamboo (Phyllostachys edulis).

Moso bamboo (Phyllostachys edulis) is the most important monopodial bamboo species worldwide. Without a genetic transformation system, it is difficult to verify the functions of genes controlling important traits and conduct molecular breeding in moso bamboo. Here, we established a plant regeneration system from immature embryos. Calli were induced on MS medium added 4-6 mg⋅L-1 2,4-dichlorophenoxyacetic acid (2,4-D) with high efficiency (>60%). A plant growth regulator combination of 0.5 mg⋅L-1 1-naphthylacetic acid (NAA), 2.0 mg⋅L-1 6-benzylaminopurine (BAP), and 3.0 mg⋅L-1 zeatin (ZT) was suitable for shoot differentiation, and the shoot induction frequency was increased to 43% after 0.5 mg⋅L-1 abscisic acid (ABA) pretreatment. An effective antibiotic screening concentration was determined by hygromycin sensitivity test. We further optimized the Agrobacterium concentration and added vacuum infiltration for infection, which improves the transient expression efficiency. A genetic transformation system was established for the first time in moso bamboo, with the transformation efficiency of approximately 5%. To optimize genome editing, two endogenous U3 small nuclear RNA (snRNA) promoters were isolated and used to drive small guide RNA (sgRNA) expression. The results showed that the PeU3.1 promoter exhibited higher efficiency, and it was used for subsequent genome editing. Finally, homozygous pds1pds2 mutants were obtained by an efficient CRISPR/Cas9 genome-editing system. These technical systems will be conducive to gene functional validation and accelerate the molecular breeding process of moso bamboo.

TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro).

Ma bamboo (Dendrocalamus latiflorus Munro) is the most widely cultivated clumping bamboo in Southern China and is valuable for both consumption and wood production. The development of bamboo shoots involving the occurrence of lateral buds is unique, and it affects both shoot yield and the resulting timber. Plant-specific TCP transcription factors are involved in plant growth and development, particularly in lateral bud outgrowth and morphogenesis. However, the comprehensive information of the TCP genes in Ma bamboo remains poorly understood. In this study, 66 TCP transcription factors were identified in Ma bamboo at the genome-wide level. Members of the same subfamily had conservative gene structures and conserved motifs. The collinear analysis demonstrated that segmental duplication occurred widely in the TCP transcription factors of Ma bamboo, which mainly led to the expansion of a gene family. Cis-acting elements related to growth and development and stress response were found in the promoter regions of DlTCPs. Expression patterns revealed that DlTCPs have tissue expression specificity, which is usually highly expressed in shoots and leaves. Subcellular localization and transcriptional self-activation experiments demonstrated that the five candidate TCP proteins were typical self-activating nuclear-localized transcription factors. Additionally, the transcriptome analysis of the bamboo shoot buds at different developmental stages helped to clarify the underlying functions of the TCP members during the growth of bamboo shoots. DlTCP12-C, significantly downregulated as the bamboo shoots developed, was selected to further verify its molecular function in Arabidopsis. The DlTCP12-C overexpressing lines exhibited a marked reduction in the number of rosettes and branches compared with the wild type in Arabidopsis, suggesting that DlTCP12-C conservatively inhibits lateral bud outgrowth and branching in plants. This study provides useful insights into the evolutionary patterns and molecular functions of the TCP transcription factors in Ma bamboo and provides a valuable reference for further research on the regulatory mechanism of bamboo shoot development and lateral bud growth.

Anatomical Characteristics and Variation Mechanisms on the Thick-Walled and Dwarfed Culm of Shidu Bamboo (Phyllostachys nidularia f. farcta).

Stable culm variants are valuable and important material for the study of culm development in bamboo plants. However, to date, there are few reports on the mechanism of variation of these bamboo variants. Phyllostachys nidularia f. farcta (Shidu bamboo) is a bamboo variant with stable phenotypes such as a dwarf culm with a thickened wall. In this study, we systematically investigated the cytological characteristics and underlying mechanism of morphological variation in culms of this variant using anatomical, mathematical statistical, physiological, and genomic methods. The anatomical observation and statistical results showed that the lateral increase of ground tissue in the inner layer of culm wall and the enlargement of vascular bundles are the anatomical essence of the wall thickening of Shidu bamboo; the limited elongation of fiber cells and the decrease in the number of parenchyma cells longitudinally are probably the main causes of the shortening of its internodes. A number of genes involved in the gibberellin synthesis pathway and in the synthesis of cell wall components are differentially expressed between the variant and its prototype, Ph. nidularia, and may play an important role in determining the phenotype of internode shortening in Shidu bamboo. The decrease in gibberellin content and the content of the major chemical components of the cell wall of Shidu bamboo confirmed the results of the above transcriptome. In addition, the variation in culm morphology in Shidu bamboo had little effect on the volume of the culm wall of individual internodes, suggesting that the decrease in the total number of internodes and the decrease in dry matter content (lignin, cellulose, etc.) may be the main factor for the sharp decline in culm biomass of Shidu bamboo.

Transporters and ascorbate-glutathione metabolism for differential cadmium accumulation and tolerance in two contrasting willow genotypes.

Salix matsudana Koidz is a low cadmium (Cd)-accumulating willow, whereas its cultivated variety, Salix matsudana var. matsudana f. umbraculifera Rehd., is a high Cd-accumulating and tolerant willow (HCW). The physiological and molecular mechanisms underlying differential Cd accumulation and tolerance in the two Salix species are poorly understood. Here, we confirmed that the differential Cd translocation capacity from roots to the shoots leads to the differential Cd accumulation in their aboveground parts between these two willow genotypes. Cadmium accumulation happens preferentially in the transport pathway, and Cd is mainly located in the vacuolar, cell wall and intercellular space in HCW bark by cadmium location analysis at tissue and subcellular levels. Comparative transcriptome analysis revealed that higher expressions of several metal transporter genes (ATP-binding cassette transporters, K+ transporters/channels, yellow stripe-like proteins, zinc-regulated transporter/iron-regulated transporter-like proteins, etc.) are involved in root uptake and translocation capacity in HCW; meanwhile, ascorbate-glutathione metabolic pathways play essential roles in Cd detoxification and higher tolerance of the Cd-accumulator HCW. These results lay the foundation for further understanding the molecular mechanisms of Cd accumulation in woody plants and provide new insights into molecular-assisted-screening woody plant varieties for phytoremediation.

Identification and functional characterization of ABCC transporters for Cd tolerance and accumulation in Sedum alfredii Hance.

Cd is one of the potential toxic elements (PTEs) exerting great threats on the environment and living organisms and arising extensive attentions worldwide. Sedum alfredii Hance, a Cd hyperaccumulator, is of great importance in studying the mechanisms of Cd hyperaccumulation and has potentials for phytoremediation. ATP-binding cassette sub-family C (ABCC) belongs to the ABC transporter family, which is deemed to closely associate with multiple physiological processes including cellular homeostasis, metal detoxification, and transport of metabolites. In the present work, ten ABCC proteins were identified in S. alfredii Hance, exhibiting uniform domain structure and divergently clustering with those from Arabidopsis. Tissue-specific expression analysis indicated that some SaABCC genes had significantly higher expression in roots (Sa23221 and Sa88F144), stems (Sa13F200 and Sa14F98) and leaves (Sa13F200). Co-expression network analysis using these five SaABCC genes as hub genes produced two clades harboring different edge genes. Transcriptional expression profiles responsive to Cd illustrated a dramatic elevation of Sa14F190 and Sa18F186 genes. Heterologous expression in a Cd-sensitive yeast cell line, we confirmed the functions of Sa14F190 gene encoding ABCC in Cd accumulation. Our study performed a comprehensive analysis of ABCCs in S. alfredii Hance, firstly mapped their tissue-specific expression patterns responsive to Cd stress, and characterized the roles of Sa14F190 genes in Cd accumulation.

SaHsfA4c From Sedum alfredii Hance Enhances Cadmium Tolerance by Regulating ROS-Scavenger Activities and Heat Shock Proteins Expression.

The heat shock transcription factor (Hsf) family, an important member in plant stress response, affects cadmium (Cd) tolerance in plants. In this study, we identified and functionally characterized a transcript of the Hsf A4 subgroup from Sedum alfredii. Designated as SaHsfA4c, the open reading frame was 1,302 bp long and encoded a putative protein of 433 amino acids containing a complete DNA-binding domain (DBD). Heterologous expression of SaHsfA4c in yeast enhanced Cd stress tolerance and accumulation, whereas expression of the alternatively spliced transcript InSaHsfA4c which contained an intron and harbored an incomplete DBD, resulted in relatively poor Cd stress tolerance and low Cd accumulation in transgenic yeast. The function of SaHsfA4c under Cd stress was characterized in transgenic Arabidopsis and non-hyperaccumulation ecotype S. alfredii. SaHsfA4c was able to rescue the Cd sensitivity of the Arabidopsis athsfa4c mutant. SaHsfA4c reduced reactive oxygen species (ROS) accumulation and increased the expression of ROS-scavenging enzyme genes and Hsps in transgenic lines. The present results suggest that SaHsfA4c increases plant resistance to stress by up-regulating the activities of ROS-scavenging enzyme and the expression of Hsps.

Molecular breeding of water lily: engineering cold stress tolerance into tropical water lily.

Water lilies (order Nymphaeales) are rich in both economic and cultural values. They grow into aquatic herbs, and are divided into two ecological types: tropical and hardy. Although tropical water lilies have more ornamental and medicinal values compared to the hardy water lily, the study and utilization of tropical water lilies in both landscaping and pharmaceutical use is greatly hindered due to their limited planting area. Tropical water lilies cannot survive the winter in areas beyond 24.3°N latitude. Here, the transgenic pipeline through the pollen-tube pathway was generated for water lily for the first time. To improve cold stress tolerance of tropical water lilies, a gene encoding choline oxidase (CodA) driven by a cold stress-inducible promoter was transformed into a tropical water lily through the pollen-tube transformation. Six independent transgenic lines were tested for survival rate during two winter seasons from 2015 to 2017 in Hangzhou (30.3°N latitude). PCR and southern blot detection revealed that the CodA gene had been integrated into the genome. Reverse transcription PCR showed that CodA gene was induced after cold stress treatment, and further quantitative real-time PCR revealed different expressions among six 4 lines and line 3 had the highest expression. Multiple physiological experiments showed that after cold stress treatment, both the conductivity and malondialdehyde (MDA) levels from transgenic plants were significantly lower than those of non-transgenic plants, whereas the content of betaine and the activity of superoxide dismutase, catalase, and peroxidase were higher than those from non-transgenic plants. These results suggest that expression of exogenous CodA gene significantly improved the cold stress tolerance of tropical water lilies through a wide range of physiological alterations. Our results currently expanded a six-latitude cultivating area of the tropical water lilies. These results not only illuminate the bright future for water lily breeding but will also facilitate the functional genomic studies.

Overexpressing the Sedum alfredii Cu/Zn Superoxide Dismutase Increased Resistance to Oxidative Stress in Transgenic Arabidopsis.

Superoxide dismutase (SOD) is a very important reactive oxygen species (ROS)-scavenging enzyme. In this study, the functions of a Cu/Zn SOD gene (SaCu/Zn SOD), from Sedum alfredii, a cadmium (Cd)/zinc/lead co-hyperaccumulator of the Crassulaceae, was characterized. The expression of SaCu/Zn SOD was induced by Cd stress. Compared with wild-type (WT) plants, overexpression of SaCu/Zn SOD gene in transgenic Arabidopsis plants enhanced the antioxidative defense capacity, including SOD and peroxidase activities. Additionally, it reduced the damage associated with the overproduction of hydrogen peroxide (H2O2) and superoxide radicals (O2•-). The influence of Cd stress on ion flux across the root surface showed that overexpressing SaCu/Zn SOD in transgenic Arabidopsis plants has greater Cd uptake capacity existed in roots. A co-expression network based on microarray data showed possible oxidative regulation in Arabidopsis after Cd-induced oxidative stress, suggesting that SaCu/Zn SOD may participate in this network and enhance ROS-scavenging capability under Cd stress. Taken together, these results suggest that overexpressing SaCu/Zn SOD increased oxidative stress resistance in transgenic Arabidopsis and provide useful information for understanding the role of SaCu/Zn SOD in response to abiotic stress.

Selection of suitable reference genes for quantitative real-time PCR gene expression analysis in Salix matsudana under different abiotic stresses.

Salix matsudana is a deciduous, rapidly growing willow species commonly cultivated in China, which can tolerate drought, salt, and heavy metal stress conditions. Selection of suitable reference genes for quantitative real-time PCR is important for normalizing the expression of the key genes associated with various stresses. To validate suitable reference genes, we selected 11 candidate reference genes (five traditional housekeeping genes and six novel genes) and analyzed their expression stability in various samples, including different tissues and under different abiotic stress treatments. The expression of these genes was determined using five programs-geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder. The results showed that α-TUB2 (alpha-tubulin 2) and DnaJ (chaperone protein DnaJ 49) were the most stable reference genes across all the tested samples. We measured the expression profiles of the defense response gene SmCAT (catalase) using the two most stable and one least stable reference genes in all samples of S. matsudana. The relative quantification of SmCAT varied greatly according to the different reference genes. We propose that α-TUB2 and DnaJ should be the preferred reference genes for normalization and quantification of transcript levels in future gene expression studies in willow species under various abiotic stress conditions.

Phenotypic and Comparative Transcriptome Analysis of Different Ploidy Plants in Dendrocalamus latiflorus Munro.

Elucidating the differences in gene expression profiles of plants with different ploidy levels and how they affect phenotypic traits is vital to allow genetic improvement of plants such as Ma bamboo (Dendrocalamus latiflorus Munro). We previously obtained triploid (2n = 3X = 36), hexaploid (2n = 6X = 72), and dodecaploid (2n = 12X = 144) Ma bamboo plants from embryogenic callus by anther culturing. Phenotypic differences between these plants appeared to be correlated with differences in ploidy. Here, we performed transcriptome profiling and sequencing of anther-regenerated plants and F1 seedlings of different ploidy levels using RNA-Seq technology. Pair-wise comparisons of the four resulting libraries revealed 8,396 differentially expressed genes. These differentially expressed genes were annotated, functionally classified, and partially validated. We found that the chromosome doubling led to substantially up- or down-regulation of genes that were involved in cell growth and differentiation; the polyploidy levels altered the anatomical, physiological and growth characteristics, such as leaf thickness, fusoid cell and stomatal size, shoot number, photosynthesis and respiration rate and so on. Additionally, two candidate genes, EXPB3 and TCP with potenitial regulatory roles in cell division and differentiation, were identified through gene coexpresseion network analysis. These results highlight the significance of potential applications of polyploidy, and provide valuable information for the genetic breeding of bamboo species.