Transcriptomic Analyses of Differential Host Responses to Red Rot Pathogen Colletotrichum Falcatum in Sugarcane Through Subtractive Library and NGS Approach

Abstract The fungal pathogen Colletotrichum falcatum causes the stalks, the economically important for sugar extraction. Although, disease management is achieved by cultivating resistant cultivars, the complex polyploidy of sugarcane genome complicates understanding the inheritance of disease resistance. Earlier attempts of using resistant and susceptible varieties to understand host-pathogen interaction resulted in cultivar specific expression of genes due to different genomic background of the varieties. To avoid host background variation in the interaction, suppression subtractive hybridization (SSH) based next generation sequencing technology was utilized in the same cv Co 7805 which behaves differently as incompatible and compatible to two different C. falcatum pathotypes. In the incompatible interaction (ICI) with C. falcatum pathotype Cf87012 (Less virulent, LVir) 10,038 contigs were assembled from ~54,699,263 raw reads. In the compatible interaction (CI) to the C. falcatum pathotype Cf94012 (Virulent, Vir) 4022 contigs were assembled from ~52,509,239 raw reads. The transcripts homologous to CEBiP receptor and transcripts involved in the signals ROS, Ca2+, BR, JA and ABA were exhibited in both the responses. Additionally, MAPK, ET, PI signals and JA amino conjugation related transcripts were found only in ICI. Finally, the temporal gene expression of a total number of 16 transcripts was monitored in qRT-PCR. Most of the transcripts exhibited highest induction in ICI in comparison with CI. Further, more than 17 transcripts specific to the pathogen were found only in CI, indicating that the pathogen colonizes the host tissue whereas it failed to to do so in ICI. Overall, this study has identified for the first time, the differential responses of a single sugarcane host to two different C. falcatum pathotypes and PAMP triggered immunity (PTI) is exhibited in both the responses, but the more efficient effector triggered immunity (ETI) was found only in ICI at the molecular level.

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A Method for Rapid Demineralization of Teeth and Bones

The Open Dentistry Journal ◽

10.2174/1874210601004010223 ◽

2010 ◽

Vol 4 (1) ◽

pp. 223-229 ◽

Cited By ~ 16

Author(s):

Andrew Cho ◽

Shigeki Suzuki ◽

Junko Hatakeyama ◽

Naoto Haruyama ◽

Ashok B Kulkarni

Keyword(s):

Reporter Gene ◽

Gene Expression Pattern ◽

Cell Lineage ◽

Careful Analysis ◽

Lacz Gene ◽

Bone Specimen ◽

Specific Expression ◽

Temporal Gene Expression ◽

Gene And Protein Expression ◽

Tissue Specimens

Tooth and bone specimen require extensive demineralization for careful analysis of cell morphology, as well as gene and protein expression levels. The LacZ gene, which encodes the ß-galactosidase enzyme, is often used as a reporter gene to study gene-structure function, tissue-specific expression by a promoter, cell lineage and fate. This reporter gene is particularly useful for analyzing the spatial and temporal gene expression pattern, by expressing the LacZ gene under the control of a promoter of interest. To analyze LacZ activity, and the expression of other genes and their protein products in teeth and bones, it is necessary to carry out a complete demineralization of the specimen before cutting sections. However, strong acids, such as formic acid used for tooth demineralization, destroy the activities of enzymes including those of ß-galactosidase. Therefore, most protocols currently use mild acids such as 0.1 M ethylene diamine tetra-acetic acid (EDTA) for demineralization of tooth and bone specimen, which require a longer period of treatment for complete demineralization. A method by which hard tissue specimens such as teeth and bones can be rapidly, but gently, decalcified is necessary to save time and effort. Here, we report a suitable method for rapid demineralization of mouse teeth in 0.1M EDTA at 42˚C without any loss of ß-galactosidase activity.

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Differential Regulation of Defense-Related Gene Expression in Response to Red Rot Pathogen Colletotrichum falcatum Infection in Sugarcane

Applied Biochemistry and Biotechnology ◽

10.1007/s12010-013-0346-4 ◽

2013 ◽

Vol 171 (2) ◽

pp. 488-503 ◽

Cited By ~ 10

Author(s):

P. T. Prathima ◽

M. Raveendran ◽

K. K. Kumar ◽

P. R. Rahul ◽

V. Ganesh Kumar ◽

...

Keyword(s):

Gene Expression ◽

Differential Regulation ◽

Red Rot ◽

Colletotrichum Falcatum ◽

Related Gene ◽

Defense Related Gene

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Molecular and physiological characterization of the effects of auxin-enriched rootstock on grafting

Horticulture Research ◽

10.1038/s41438-021-00509-y ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Longmei Zhai ◽

Xiaomin Wang ◽

Dan Tang ◽

Qi Qi ◽

Huseyin Yer ◽

...

Keyword(s):

Callus Formation ◽

Ethylene Biosynthesis ◽

Union Formation ◽

Biosynthetic Gene ◽

Graft Union ◽

Specific Expression ◽

Physiological Characterization ◽

Graft Healing ◽

Expression Of Genes ◽

Or Gene

AbstractsGrafting is a highly useful technique, and its success largely depends on graft union formation. In this study, we found that root-specific expression of the auxin biosynthetic gene iaaM in tobacco, when used as rootstock, resulted in more rapid callus formation and faster graft healing. However, overexpression of the auxin-inactivating iaaL gene in rootstocks delayed graft healing. We observed increased endogenous auxin levels and auxin-responsive DR5::GUS expression in scions of WT/iaaM grafts compared with those found in WT/WT grafts, which suggested that auxin is transported upward from rootstock to scion tissues. A transcriptome analysis showed that auxin enhanced graft union formation through increases in the expression of genes involved in graft healing in both rootstock and scion tissues. We also observed that the ethylene biosynthetic gene ACS1 and the ethylene-responsive gene ERF5 were upregulated in both scions and rootstocks of the WT/iaaM grafts. Furthermore, exogenous applications of the ethylene precursor ACC to the junction of WT/WT grafts promoted graft union formation, whereas application of the ethylene biosynthesis inhibitor AVG delayed graft healing in WT/WT grafts, and the observed delay was less pronounced in the WT/iaaM grafts. These results demonstrated that elevated auxin levels in the iaaM rootstock in combination with the increased auxin levels in scions caused by upward transport/diffusion enhanced graft union formation and that ethylene was partially responsible for the effects of auxin on grafting. Our findings showed that grafting success can be enhanced by increasing the auxin levels in rootstocks using transgenic or gene-editing techniques.

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Molecular and pathological characterization of isolates of Colletotrichum falcatum Went. causing red rot in sugarcane

Agricultural Research Journal ◽

10.5958/2395-146x.2021.00034.x ◽

2021 ◽

Vol 58 (2) ◽

pp. 224-231

Author(s):

Anuradha ◽

Lenika Kashyap ◽

Rajinder Kumar ◽

Paramjit Singh

Keyword(s):

Red Rot ◽

Colletotrichum Falcatum

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Investigation of allele-specific expression of genes involved in adipogenesis and lipid metabolism suggests complex regulatory mechanisms of PPARGC1A expression in porcine fat tissues

BMC Genetics ◽

10.1186/s12863-018-0696-6 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Monika Stachowiak ◽

Izabela Szczerbal ◽

Krzysztof Flisikowski

Keyword(s):

Lipid Metabolism ◽

Regulatory Mechanisms ◽

Specific Expression ◽

Allele Specific Expression ◽

Expression Of Genes ◽

Allele Specific

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Transcriptome changes reveal the genetic mechanisms of the reproductive plasticity of workers in lower termites

BMC Genomics ◽

10.1186/s12864-019-6037-y ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Chenxu Ye ◽

Humaira Rasheed ◽

Yuehua Ran ◽

Xiaojuan Yang ◽

Lianxi Xing ◽

...

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Molecular Mechanisms ◽

Environmental Changes ◽

Mapk Pathway ◽

Specific Expression ◽

Expression Of Genes ◽

Genetic Mechanisms ◽

Ecological Success ◽

Reproductive Plasticity

Abstract Background The reproductive plasticity of termite workers provides colonies with tremendous flexibility to respond to environmental changes, which is the basis for evolutionary and ecological success. Although it is known that all colony members share the same genetic background and that differences in castes are caused by differences in gene expression, the pattern of the specific expression of genes involved in the differentiation of workers into reproductives remains unclear. In this study, the isolated workers of Reticulitermes labralis developed into reproductives, and then comparative transcriptomes were used for the first time to reveal the molecular mechanisms underlying the reproductive plasticity of workers. Results We identified 38,070 differentially expressed genes and found a pattern of gene expression involved in the differentiation of the workers into reproductives. 12, 543 genes were specifically upregulated in the isolated workers. Twenty-five signal transduction pathways classified into environmental information processing were related to the differentiation of workers into reproductives. Ras functions as a signalling switch regulates the reproductive plasticity of workers. The catalase gene which is related to longevity was up-regulated in reproductives. Conclusion We demonstrate that workers leaving the natal colony can induce the expression of stage-specific genes in the workers, which leads to the differentiation of workers into reproductives and suggests that the signal transduction along the Ras-MAPK pathway crucially controls the reproductive plasticity of the workers. This study also provides an important model for revealing the molecular mechanism of longevity changes.

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Potential of plant extracts in combination with bacterial antagonist treatment as biocontrol agent of red rot of sugarcane

Canadian Journal of Microbiology ◽

10.1139/w06-126 ◽

2007 ◽

Vol 53 (2) ◽

pp. 196-206 ◽

Cited By ~ 14

Author(s):

V. Jayakumar ◽

R. Bhaskaran ◽

S. Tsushima

Keyword(s):

Plant Extracts ◽

Field Experiments ◽

Curcuma Longa ◽

Saccharum Officinarum ◽

Red Rot ◽

Colletotrichum Falcatum ◽

Similar Response ◽

Red Rot Disease ◽

Leaf Extracts ◽

Rot Disease

Plant extracts and antifungal microorganisms were tested singly and in combination for biocontrol of sugarcane red rot disease ( Colletotrichum falcatum ) using two sugarcane ( Saccharum officinarum L.) cultivars, CoC671 and CoC92061, in pot and field experiments. Leaf extracts of Abrus precatorius and Bassia latifolia and the rhizome extract of Curcuma longa reduced Colletotrichum falcatum mycelial growth by 80%, 58%, and 57%, respectively. Although sugarcane- planting materials (setts) treated individually with either Pseudomonas fluorescens Md1 or A. precatorius in pot experiments had the lowest incidences of red rot, 20.1% and 24.2%, respectively, none of the plant extracts were effective in the field. In contrast, when the two varieties were tested separately in two field locations, the setts treated with A. precatorius in combination with a spray or soil application of P. fluorescens Md1 had the lowest incidence of red rot in both locations, e.g., 3.1% and 3.4% incidence for CoC92061 in one location, and had a similar response to the chemical control. The results suggest the applicability of plant-based extracts for the suppression of sugarcane red rot disease in the field as an environment-friendly tool in combination with antagonists.

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History of Herbicide-Tolerant Crops, Methods of Development and Current State of the Art – Emphasis on Glyphosate Tolerance

Weed Technology ◽

10.1017/s0890037x00035934 ◽

1992 ◽

Vol 6 (3) ◽

pp. 626-634 ◽

Cited By ~ 44

Author(s):

Ganesh M. Kishore ◽

Stephen R. Padgette ◽

Robert T. Fraley

Keyword(s):

Weed Management ◽

Effective Means ◽

Shikimate Pathway ◽

Management Program ◽

Crop Plants ◽

Epsp Synthase ◽

Glyphosate Tolerance ◽

Specific Expression ◽

Expression Of Genes ◽

Wide Range

Weed management is an integral part of agriculture; weeds lower both productivity and quality of agricultural products. A combination of mechanical, chemical, biological, and cultural methods is expected to deliver a sustainable weed management program for the next two decades. While chemical methods offer the most cost effective means of weed management, crop selectivity has hampered the use of the best chemicals for weed management. Recent progress in gene technology has facilitated the introduction and expression of genes to confer a wide range of traits to crop plants. Application of this technology has resulted in the development of crop plant genotypes that are resistant to a specific herbicide. This article describes the progress that has been made by our group toward the introduction of glyphosate tolerance to crop plants. Glyphosate [N-(phosphonomethyl)glycine] kills plants due to inhibition of the biosynthesis of aromatic compounds via the shikimate pathway. Our approach for introduction of glyphosate tolerance is based on insertion and expression in plants of a gene encoding a glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, a key enzyme of the shikimate pathway. The wild type enzyme present in plants is susceptible to inhibition glyphosate; variants of EPSP synthase have been produced that are less susceptible to inhibition by glyphosate. Expression of genes encoding these variants has been shown to confer glyphosate tolerance to plants. The degree of glyphosate tolerance is related to the tolerance characteristics of the EPSP synthase variant, its substrate activity, targeting to the plastid, and the level of expression of the variant gene. The tissue specificity of expression of the variant EPSP synthase has also been shown to be critical since glyphosate is a systemic herbicide and is translocated to many growing points within the plant. Our studies on glyphosate tolerance have substantially enhanced our understanding of the mode-of-action of glyphosate, the shikimate pathway, and protein sorting within plant cells, as well as developmental and tissue specific expression of genes in plants. Commercial use of glyphosate tolerance technology is expected to affect positively, the weed management arsenal available to the farmers, the sustainability of farm land and groundwater, and promote the use of a “soft” herbicide.

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Gene Expression Profiling Indicated Diverse Functions and Characteristics of Core Genes in Pea Aphid

Insects ◽

10.3390/insects11030186 ◽

2020 ◽

Vol 11 (3) ◽

pp. 186

Author(s):

Ruizheng Tian ◽

Yixiao Huang ◽

Balachandar Balakrishnan ◽

Maohua Chen

Keyword(s):

Expression Profiling ◽

Insect Pest ◽

Transcriptome Profiling ◽

Pea Aphid ◽

Biological Processes ◽

Specific Expression ◽

The Core ◽

Expression Of Genes ◽

Pea Aphids ◽

Core Genes

The pea aphid is a global insect pest, and variable phenotypes can be produced by pea aphids in the same genotype in response to changes in external environmental factors. However, detailed dynamic gene regulation networks and the core markers involved in different biological processes of pea aphids have not yet been reported. In this study, we obtained the published genomic and transcriptomic data, and performed transcriptome profiling of five pea aphid morphs (winged asexual female, wingless asexual female, wingless sexual female, winged male and wingless male) from each of three pea aphid genotypes, i.e., the transcriptomes from a total of 15 types of pea aphids were analyzed and the type-specific expression of genes in five different morphs was identified. The expression profiling was verified by quantitative real-time PCR (qPCR) analysis. Moreover, we determined the expression features and co-expression networks of highly variable genes. We also used the ARACNe method to obtain 263 core genes related to different biological pathways. Additionally, eight of the identified genes were aligned with transcription factor families, indicating that they act as transcription factors and regulate downstream genes. Furthermore, we found reliable markers using random forest methodology to distinguish different morphs of pea aphids. Our study provides a systematic and comprehensive approach for analyzing the core genes that may play important roles in a multitude of biological processes from the insect transcriptomes.

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