Identification and Expression Analyses of Invertase Genes in Moso Bamboo Reveal Their Potential Drought Stress Functions

Invertases (INVs) can irreversibly hydrolyze sucrose into fructose and glucose, which play principal roles in carbon metabolism and responses to various stresses in plants. However, little is known about the INV family in bamboos, especially their potential function in drought stress. In this study, 29 PeINVs were identified in moso bamboo (Phyllostachys edulis). They were clustered into alkaline/neutral invertase (NINV) and acid invertase (AINV) groups based on the gene structures, conserved motifs, and phylogenetic analysis results. The collinearity analysis showed nine segmental duplication pairs within PeINVs, and 25 pairs were detected between PeINVs and OsINVs. PeINVs may have undergone strong purification selection during evolution, and a variety of stress and phytohormone-related regulatory elements were found in the promoters of PeINVs. The tissue-specific expression analysis showed that PeINVs were differentially expressed in various moso bamboo tissues, which suggested that they showed functional diversity. Both the RNA-seq and quantitative real-time PCR results indicated that four PeINVs were significantly upregulated under drought stress. Co-expression network and Pearson’s correlation coefficient analyses showed that these PeINVs co-expressed positively with sugar and water transport genes (SWTGs), and the changes were consistent with sugar content. Overall, we speculate that the identified PeINVs are spatiotemporally expressed, which enables them to participate in moso bamboo growth and development. Furthermore, PeINVs, together with SWTGs, also seem to play vital roles in the response to drought stress. These results provide a comprehensive information resource for PeINVs, which will facilitate further study of the molecular mechanism underlying PeINVs involvement in the response to drought stress in moso bamboo.

Download Full-text

Genome-wide analysis of fatty acid desaturase genes in rice (Oryza sativa L.)

Scientific Reports ◽

10.1038/s41598-019-55648-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Zhiguo E ◽

Chen Chen ◽

Jinyu Yang ◽

Hanhua Tong ◽

Tingting Li ◽

...

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Unsaturated Fatty Acids ◽

Oryza Sativa L ◽

Expression Patterns ◽

Rice Genome ◽

Regulatory Elements ◽

Segmental Duplications ◽

Specific Expression ◽

Gene Structures

AbstractFatty acid desaturases can catalyze saturated or unsaturated fatty acids to form a double bond at various locations in the hydrocarbon chain. In the present study, a total of 20 full-length desaturase genes were identified from rice genome. An exhaustive analysis was performed to describe their chromosomal locations, gene structures, phylogeny, cis-regulatory elements, sub-cellular localizations and expression patterns. The rice desaturase genes were distributed on ten of 12 chromosomes and phylogenetically classified into six subfamilies with the Arabidopsis counterparts, FAB2, FAD2, FAD3/7/8, FAD6, DES1 and SLD1. Among of them, 9 members were expanded via chromosomal tandem or segmental duplications. The gene structures and motif constituents were evolutionarily conserved in the same subfamilies. The majority of desaturase genes showed tissue-specific expression patterns and response to abiotic stresses and hormones based on microarray data and qRT-PCR analyses. This study will provide useful clues for functional validation of desaturase genes and contribute to produce nutritionally important fatty acids by genetic modification in rice.

Download Full-text

Genome-Wide Identification of Sultr Genes in Malus domestica and Low Sulfur-Induced MhSultr3;1a to Increase Cysteine-Improving Growth

Frontiers in Plant Science ◽

10.3389/fpls.2021.748242 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mi Xun ◽

Jianfei Song ◽

Junyuan Shi ◽

Jiaqi Li ◽

Yujia Shi ◽

...

Keyword(s):

Malus Domestica ◽

Higher Plants ◽

Expression Patterns ◽

Regulatory Elements ◽

Promoter Regions ◽

Specific Expression ◽

Essential Nutrient ◽

Function Characterization ◽

Gene Structures ◽

Low Sulfur

Sulfur is an essential nutrient for plant growth and development. Sulfate transporters (Sultrs) are critical for sulfate (SO42-) uptake from the soil by the roots in higher plants. However, knowledge about Sultrs in apples (Malus domestica) is scarce. Here, nine putative MdSultrs were identified and classified into two groups according to the their phylogenetic relationships, gene structures, and conserved motifs. Various cis-regulatory elements related to abiotic stress and plant hormone responsiveness were found in the promoter regions of MdSultrs. These MdSultrs exhibited tissue-specific expression patterns and responded to low sulfur (S), abscisic acid (ABA), indole-3-acetic acid (IAA), and methyl jasmonate (MeJA), wherein MdSultr3;1a was especially expressed in the roots and induced by low S. The uptake of SO42- in cultivated apples depends on the roots of its rootstock, and MhSultr3;1a was isolated from Malus hupehensis roots used as a rootstock. MhSultr3;1a shared 99.85% homology with MdSultr3;1a and localized on the plasma membrane and nucleus membrane. Further function characterization revealed that MhSultr3;1a complemented an SO42- transport-deficient yeast mutant and improved the growth of yeast and apple calli under low S conditions. The MhSultr3;1a-overexpressing apple calli had a higher fresh weight compared with the wild type (WT) under a low-S treatment because of the increased SO42- and cysteine (Cys) content. These results demonstrate that MhSultr3;1a may increase the content of SO42- and Cys to meet the demands of S-containing compounds and improve their growth under S-limiting conditions.

Download Full-text

Genome-Wide Identification of Tomato Golden 2-Like Transcription Factors and Abiotic Stress Related Members Screening

10.21203/rs.3.rs-1007193/v1 ◽

2021 ◽

Author(s):

Ziyu Wang ◽

Junfang Liu ◽

Haiyan Zhao ◽

Xuying Sun ◽

Tairu Wu ◽

...

Keyword(s):

Transcription Factors ◽

Abiotic Stresses ◽

Regulatory Elements ◽

Biosynthesis Pathway ◽

Rna Seq ◽

Promoter Regions ◽

Multiple Functions ◽

Genome Wide ◽

Comprehensive Information ◽

Motif Composition

Abstract Background: Golden 2-Like (G2-like) transcription factors play an important role in plant development. However, the roles of these G2-like regulatory genes in response to abiotic stresses in tomato are not well understood.Results: In this study, we identified 66 putative G2-like genes in tomato (Solanum lycopersicum) and classified them into 5 groups (I to V) according to gene structure, motif composition and phylogenetic analysis. The G2-like genes were unevenly distributed across all 12 chromosomes. There were nine pairs of duplicated gene segments and four tandem duplicated SlGlk genes. Analysis of the cis-regulatory elements (CREs) showed that the promoter regions of SlGlks contain many kinds of stress- and hormone-related CREs. Based on RNA-seq, SlGlks were expressed in response to three abiotic stresses. Thirty-six differentially expressed SlGlks were identified; these genes have multiple functions according to Gene Ontology (GO) analysis and are enriched mainly in the zeatin biosynthesis pathway. Further studies exhibited that silencing SlGlk16 in tomato would reduce drought stress tolerance by earlier wilted, lower superoxide dismutase (SOD), peroxidase (POD) activities, less Pro contents and more MDA contents. Conclusion: Overall, the results of this study provide comprehensive information on G2-like transcription factors and G2-like genes that may be expressed in response to abiotic stresses.

Download Full-text

Morphological, Physiological and Biochemical Responses of Poplar Plants to Drought Stress

Journal of AgriSearch ◽

10.21921/jas.5.3.7 ◽

2018 ◽

Vol 5 (03) ◽

Author(s):

ARADHNA KUMARI ◽

IM KHAN ◽

ANIL KUMAR SINGH ◽

SANTOSH KUMAR SINGH

Keyword(s):

Water Stress ◽

Drought Stress ◽

Biochemical Parameters ◽

Sugar Content ◽

Soluble Sugar ◽

Field Capacity ◽

Drought Event ◽

Total Biomass ◽

Biochemical Responses ◽

Physiological And Biochemical

Poplar clone Kranti was selected to assess the morphological, physiological and biochemical responses under drought at different levels of water stress, as it is a common clone used to be grown in Uttarakhand for making paper and plywood. The cuttings of Populus deltoides L. (clone Kranti) were exposed to four different watering regimes (100, 75, 50 and 25% of the field capacity) and changes in physiological and biochemical parameters related with drought tolerance were recorded. Alterations in physiological (i.e. decrease in relative water content) and biochemical parameters (i.e. increase in proline and soluble sugar content and build-up of malondialdehyde by-products) occurred in all the three levels of water stress, although drought represented the major determinant. Drought treatments (75%, 50% and 25% FC) decreased plant height, radial stem diameter, harvest index, total biomass content and RWC in all the three watering regimes compared to control (100% FC). Biochemical parameters like proline, soluble sugar and MDA content increased with severity and duration of stress, which helped plants to survive under severe stress. It was analyzed that for better wood yield poplar seedlings should avail either optimum amount of water (amount nearly equal to field capacity of soil) or maximum withdrawal up to 75% of field capacity up to seedling establishment period (60 days). Furthermore, this study manifested that acclimation to drought stress is related with the rapidity, severity, and duration of the drought event of the poplar species.

Download Full-text

Identification and Expression Profiling of Nonphosphorus Glycerolipid Synthase Genes in Response to Abiotic Stresses in Dendrobium catenatum

Plants ◽

10.3390/plants10061204 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1204

Author(s):

Xinqiao Zhan ◽

Yichun Qian ◽

Bizeng Mao

Keyword(s):

Salt Stress ◽

Drought Stress ◽

Expression Profiling ◽

Abiotic Stresses ◽

Membrane Lipids ◽

Chinese Herb ◽

Growth Stages ◽

Limited Information ◽

Gene Structures ◽

Functional Investigation

Dendrobium catenatum, a valuable Chinese herb, frequently experiences abiotic stresses, such as cold and drought, under natural conditions. Nonphosphorus glycerolipid synthase (NGLS) genes are closely linked to the homeostasis of membrane lipids under abiotic stress in plants. However, there is limited information on NGLS genes in D. catenatum. In this study, a total of eight DcaNGLS genes were identified from the D. catenatum genome; these included three monogalactosyldiacylglycerol synthase (DcaMGD1, 2, 3) genes, two digalactosyldiacylglycerol synthase (DcaDGD1, 2) genes, and three sulfoquinovosyldiacylglycerol synthase (DcaSQD1, 2.1, 2.2) genes. The gene structures and conserved motifs in the DcaNGLSs showed a high conservation during their evolution. Gene expression profiling showed that the DcaNGLSs were highly expressed in specific tissues and during rapid growth stages. Furthermore, most DcaNGLSs were strongly induced by freezing and post-freezing recovery. DcaMGD1 and DcaSQDs were greatly induced by salt stress in leaves, while DcaDGDs were primarily induced by salt stress in roots. Under drought stress, most DcaNGLSs were regulated by circadian rhythms, and DcaSQD2 was closely associated with drought recovery. Transcriptome analysis also revealed that MYB might be regulated by circadian rhythm and co-expressed with DcaNGLSs under drought stress. These results provide insight for the further functional investigation of NGLS and the regulation of nonphosphorus glycerolipid biosynthesis in Dendrobium.

Download Full-text

Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Joseph Tomlinson ◽

Shawn W. Polson ◽

Jing Qiu ◽

Juniper A. Lake ◽

William Lee ◽

...

Keyword(s):

Broiler Chickens ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Detection Tool ◽

Commercial Broiler ◽

Significant Phenomenon ◽

Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

Download Full-text

Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis)

Scientific Reports ◽

10.1038/s41598-021-95899-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bin Huang ◽

Zhinuo Huang ◽

Ruifang Ma ◽

Jialu Chen ◽

Zhijun Zhang ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Heat Shock ◽

Gene Family ◽

Regulatory Elements ◽

Moso Bamboo ◽

Naphthalene Acetic Acid ◽

Plant Responses ◽

Heat Stress Response ◽

Regulatory Pathways

AbstractHeat shock transcription factors (HSFs) are central elements in the regulatory network that controls plant heat stress response. They are involved in multiple transcriptional regulatory pathways and play important roles in heat stress signaling and responses to a variety of other stresses. We identified 41 members of the HSF gene family in moso bamboo, which were distributed non-uniformly across its 19 chromosomes. Phylogenetic analysis showed that the moso bamboo HSF genes could be divided into three major subfamilies; HSFs from the same subfamily shared relatively conserved gene structures and sequences and encoded similar amino acids. All HSF genes contained HSF signature domains. Subcellular localization prediction indicated that about 80% of the HSF proteins were located in the nucleus, consistent with the results of GO enrichment analysis. A large number of stress response–associated cis-regulatory elements were identified in the HSF upstream promoter sequences. Synteny analysis indicated that the HSFs in the moso bamboo genome had greater collinearity with those of rice and maize than with those of Arabidopsis and pepper. Numerous segmental duplicates were found in the moso bamboo HSF gene family. Transcriptome data indicated that the expression of a number of PeHsfs differed in response to exogenous gibberellin (GA) and naphthalene acetic acid (NAA). A number of HSF genes were highly expressed in the panicles and in young shoots, suggesting that they may have functions in reproductive growth and the early development of rapidly-growing shoots. This study provides fundamental information on members of the bamboo HSF gene family and lays a foundation for further study of their biological functions in the regulation of plant responses to adversity.

Download Full-text

Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽

10.1186/s12864-021-07601-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhiwei Chen ◽

Longhua Zhou ◽

Panpan Jiang ◽

Ruiju Lu ◽

Nigel G. Halford ◽

...

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Regulatory Elements ◽

Gene Promoters ◽

Related Protein ◽

Rna Seq ◽

Response Elements ◽

Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

Download Full-text

Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽

10.3390/plants10071465 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1465

Author(s):

Ramon de Koning ◽

Raphaël Kiekens ◽

Mary Esther Muyoka Toili ◽

Geert Angenon

Keyword(s):

Common Bean ◽

Seed Development ◽

Expression Analysis ◽

De Novo ◽

Expression Patterns ◽

Gene Families ◽

Rna Seq ◽

Raffinose Family Oligosaccharides ◽

Specific Expression ◽

Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

Download Full-text

Replicate sequencing libraries are important for quantification of allelic imbalance

Nature Communications ◽

10.1038/s41467-021-23544-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Asia Mendelevich ◽

Svetlana Vinogradova ◽

Saumya Gupta ◽

Andrey A. Mironov ◽

Shamil R. Sunyaev ◽

...

Keyword(s):

Allelic Imbalance ◽

False Positive Rate ◽

Error Rates ◽

Differential Analysis ◽

Rna Seq ◽

Specific Expression ◽

Technical Noise ◽

Specific Analysis ◽

Positive Rate ◽

Allele Specific

AbstractA sensitive approach to quantitative analysis of transcriptional regulation in diploid organisms is analysis of allelic imbalance (AI) in RNA sequencing (RNA-seq) data. A near-universal practice in such studies is to prepare and sequence only one library per RNA sample. We present theoretical and experimental evidence that data from a single RNA-seq library is insufficient for reliable quantification of the contribution of technical noise to the observed AI signal; consequently, reliance on one-replicate experimental design can lead to unaccounted-for variation in error rates in allele-specific analysis. We develop a computational approach, Qllelic, that accurately accounts for technical noise by making use of replicate RNA-seq libraries. Testing on new and existing datasets shows that application of Qllelic greatly decreases false positive rate in allele-specific analysis while conserving appropriate signal, and thus greatly improves reproducibility of AI estimates. We explore sources of technical overdispersion in observed AI signal and conclude by discussing design of RNA-seq studies addressing two biologically important questions: quantification of transcriptome-wide AI in one sample, and differential analysis of allele-specific expression between samples.

Download Full-text