Golden trumpet (
Allamanda cathartica
) plants were observed to exhibit mottling and distortion symptoms on leaves. The genome of an associated begomovirus (Al-K1) was amplified by rolling-circle ...amplification, cloned, and sequenced. The viral genome consisted of two circular ssDNA molecules, and the organization of the ORFs was similar to those of DNA-A and DNA-B components of bipartite begomoviruses. The size of DNA-A (KC202818) and DNA-B (MG969497) of the begomovirus was 2772 and 2690 nucleotides, respectively. Sequence analysis revealed that the DNA-A and DNA-B components shared the highest sequence identity with duranta leaf curl virus (MN537564, 87.8%) and cotton leaf curl Alabad virus (MH760452, 81.0%), respectively. Interestingly, the Al-K1 isolate shared significantly less nucleotide sequence identity with allamanda leaf curl virus (EF602306, 71.6%), the only monopartite begomovirus reported previously in golden trumpet from China. Al-K1 shared less than 91% sequence identity with other begomoviruses, and hence, according to the latest ICTV guidelines for species demarcation of begomoviruses, Al-K1 is proposed to be a member of a new species, and we propose the name "allamanda leaf mottle distortion virus" (AllLMoDV-IN-Al_K1-12) for this virus. AllLMoDV was detected in various golden trumpet samples from different locations by PCR with specific primers based on the genome sequence determined in this study. Our study provides evidence of the occurrence of a new bipartite begomovirus in a perennial ornamental plant in India.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (
) and ...tryptamine 5-hydroxylase (
) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (
) and acetyl-serotonin methyltransferase (
) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of
and
, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Aims, including the rationale
Salinity and drought are the two major stresses limiting the productivity of economically important crops such as Glycine max (soybean). The incidence of these stresses ...during the pod development stages affects the quality and quantity of seeds, which compromise the yield of soybean. The miR164:NAC module has been shown to play a critical role in regulating the response to salt and drought stress in several plant species. However, biological role of miR164:NAC module in salt stress in soybean is not fully understood.
Methods
In this study, we identified 215 salt responsive miRNAs, using miScript miRNA array with a sensitive and a tolerant soybean genotype, William82 and INCASoy36, respectively. The targets of these salt regulated miRNAs were searched in the degradome datasets.
Key results
It was found that four salt stress deregulated miRNAs targeted the NAC transcription factor and among these miR164k and miR408d showed antagonistic expression in the two soybean genotypes. The expression of miR164k was higher in salt tolerant INCASoy36 as compared to salt sensitive William82, under unstressed conditions. However under salt stress, miR164k was downregulated in INCASoy36 (−2.65 fold), whereas it was upregulated in William82 (4.68 fold). A transient co‐expression assay validated that gma‐miR164k directs the cleavage of GmNAC1 transcript. Bioinformatics analysis revealed that the regulation of NAC transcription factor family by members of miR164 family is conserved across many species. The dynamic expression profiles of miR164 and NAC‐TFs were captured in different tissues of rice, tobacco, and two soybean genotypes under drought and salt stress conditions.
Main conclusion
Collectively, our results suggest that genetically determined dynamic modulation of the conserved miR164:NAC‐TF module may play an important role in determining the adaptive response of plants to stress.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to ...negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and
-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant-virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.
Plants can adapt to different environmental conditions and can survive even under very harsh conditions. They have developed elaborate networks of receptors and signaling components, which modulate ...their biochemistry and physiology by regulating the genetic information. Plants also have the abilities to transmit information between their different parts to ensure a holistic response to any adverse environmental challenge. One such phenomenon that has received greater attention in recent years is called stress priming. Any milder exposure to stress is used by plants to prime themselves by modifying various cellular and molecular parameters. These changes seem to stay as memory and prepare the plants to better tolerate subsequent exposure to severe stress. In this review, we have discussed the various ways in which plants can be primed and illustrate the biochemical and molecular changes, including chromatin modification leading to stress memory, with major focus on thermo-priming. Alteration in various hormones and their subsequent role during and after priming under various stress conditions imposed by changing climate conditions are also discussed.
Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at ...the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage. They also play an important role in regulating plant’s response to salt-stress. In this work we adopted the approach of comparative and integrated data-mining to understand the miRNA-mediated regulation of salt-stress in rice. We profiled and compared the miRNA regulations using natural varieties and transgenic lines with contrasting behaviors in response to salt-stress. The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRNAs, their targets and the associated metabolic pathways. The analysis revealed the modulation of many biological pathways, which are involved in salt-tolerance and play an important role in plant phenotype and physiology. The end modifications of the miRNAs were also studied in our analysis and isomiRs having a dynamic role in salt-tolerance mechanism were identified.
The recent thrust in research has projected the type II clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR-Cas9) system as an avant-garde plant genome editing ...tool. It facilitates the induction of site-specific double-stranded DNA cleavage by the RNA-guided DNA endonuclease (RGEN), Cas9. Elimination, addition, or alteration of sections in DNA sequence besides the creation of a knockout genotype (CRISPRko) is aided by the CRISPR-Cas9 system in its wild form (wtCas9). The inactivation of the nuclease domain generates a dead Cas9 (dCas9), which is capable of targeting genomic DNA without scissoring it. The dCas9 system can be engineered by fusing it with different effectors to facilitate transcriptional activation (CRISPRa) and transcriptional interference (CRISPRi). CRISPR-Cas thus holds tremendous prospects as a genome-manipulating stratagem for a wide gamut of crops. In this article, we present a brief on the fundamentals and the general workflow of the CRISPR-Cas system followed by an overview of the prospects of bioinformatics in propelling CRISPR-Cas research with a special thrust on the available databases and algorithms/web-accessible applications that have aided in increasing the usage and efficiency of editing. The article also provides an update on the current regulatory landscape in different countries on the CRISPR-Cas edited plants to emphasize the far-reaching impact of the genomic editing technology.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
NAC genes comprise one of the largest families of plant transcription regulators that are known to play crucial roles in various developmental processes and stress responses. Evolutionary expansion ...of the gene family in land plants probably added to the functional diversity of the gene family. The ongoing research has analyzed the differential expression patterns of the NAC transcription factors under various stresses for determining their plausible role during adaptive stress response in plants. However, the complex molecular mechanism regulating NAC gene expression and function is still elusive. The discovery of miRNAs, as a novel class of regulatory factors, has shed new light on the regulatory mechanisms that define the functional domains of the transcription factors. In this context studies on miRNA-mediated regulation of NAC gene expression in plant development have provided critical evidence for multi-layered control of the transcription factors. The review describes the divergent role of NAC transcription factors, which were initially thought to be only involved in vasculature development in plants. The structural features of the NAC transcription factors and the evolution of the gene family have also been discussed. Special focus is placed on the regulation of NAC-TFs by miRNAs to understand the developmental networks operating in the plants in response to abiotic stress and hormone cues.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Plants have an inherent mechanism for perceiving drought stress and respond through a series of physiological, cellular and molecular changes for maintaining physiological water balance. It has been ...shown that nitrogen (N) and phosphate (P) can help to improve plant tolerance to water limitation by increasing the activities of the photosynthetic machinery and antioxidant enzymes. Maize is highly sensitive to drought stress, especially at the seedling stage. In this study, we used four maize genotypes (HKI-161, HKI-193-1, HQPM-1 and HQPM-7) and studied the effect of N and P application on response to drought stress and recovery at germination and seedling stage. We show that application of N and P had no effect on rate of germination but increased the seedling growth, chlorophyll content, malondialdehyde levels, proline, anthocyanin content, gas exchange parameters and antioxidant enzymes (APX, CAT and GR) during drought stress. The variation in the effect was visible across genotypes, but the observed changes indicate improved drought stress tolerance in the maize seedlings. During drought recovery, seedlings of HKI-161 and HKI-193-1 genotype that did not receive N and/or P treatment or that were pre-supplemented with only P showed rapid transition to flowering stages. Seedlings pretreated with N showed comparatively late transition to flowering. The HQPM-1 seedlings, which received N treatment moved to flowering stage while HQPM-7 seedlings showed only normal vegetative growth under all treatment conditions. Molecular analysis identified 2016 transcripts that are differentially expressed in the drought tolerant and susceptible genotypes. About 947 transcripts showed >3-fold change in expression and were expressed during stress tolerant genotype. Transcripts coding for proteins in P and N metabolism were identified within the drought regulated transcripts. The analysis showed that transcripts related to P metabolism were expressed during stress and recovery phases in the susceptible genotype while transcripts related to N metabolism were down regulated during drought stress and recovery stages in all the genotypes.
Rice plants often encounter high temperature stress, but the associated coping strategies are poorly understood. It is known that a prior shorter exposure to high temperature, called thermo-priming, ...generally results in better adaptation of the plants to subsequent exposure to high temperature stress. High throughput sequencing of transcript and small RNA libraries of rice seedlings primed with short exposure to high temperature followed by high temperature stress and from plants exposed to high temperature without priming was performed. This identified a number of transcripts and microRNAs (miRs) that are induced or down regulated. Among them osa-miR531b, osa-miR5149, osa-miR168a-5p, osa-miR1846d-5p, osa-miR5077, osa-miR156b-3p, osa-miR167e-3p and their respective targets, coding for heat shock activators and repressors, showed differential expression between primed and non-primed plants. These findings were further validated by qRT-PCR. The results indicate that the miR-regulated heat shock proteins (HSPs)/heat shock transcription factors (HSFs) may serve as important regulatory nodes which are induced during thermo-priming for plant survival and development under high temperatures.
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