Understanding sugarcane defence responses during the initial phase of Colletotrichum falcatum pathogenesis by suppression subtractive hybridization (SSH)

Sathyabhama, M.; Viswanathan, R.; Nandakumar, Madhumitha; Malathi, P.; Sundar, A. Ramesh

doi:10.1016/j.pmpp.2015.07.003

Cited by 24 publications

(12 citation statements)

References 51 publications

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“…The pressure test software WebCT is used for system test, which enables the server and client to work normally as stated in [10]. The data results displayed on the client's page reflect the system's ability to meet the customer requirements in the early stage of the design process.…”

Section: System Test Results and Discussionmentioning

confidence: 99%

The Construction of Intelligent English Teaching Model Based on Artificial Intelligence

Li¹

2017

Int. J. Emerg. Technol. Learn.

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Abstract-In order to build a modernized tool platform that can help students improve their English learning efficiency according to their mastery of knowledge and personality, this paper develops an online intelligent English learning system that uses Java and artificial intelligence language Prolog as the software system. This system is a creative reflection of the thoughts of expert system in artificial intelligence. Established on the Struts Spring Hibernate lightweight JavaEE framework, the system modules are coupled with each other in a much lower degree, which is convenient to future function extension. Combined with the idea of expert system in artificial intelligence, the system developed appropriate learning strategies to help students double the learning effect with half the effort; Finally, the system takes into account the forgetting curve of memory, on which basis the knowledge that has been learned will be tested periodically, intending to spare students' efforts to do a sea of exercises and obtain better learning results. Keywords-Artificial intelligence, foreign language teaching, intelligent learning IntroductionFor a long time, the traditional way of teaching English has been widely criticized for various problems and deficiencies, and the crisis often means turning point. With the advancement of the integration of information technology and English curriculum, artificial intelligence also serves as a tool for the optimization of secondary school English teaching.[1] provides a new platform for the creation of an intelligent and personalized English teaching environment.In this paper, a teaching aid system is designed based on artificial intelligence and the forgetting law of human brains [2]. This system can review English vocabulary and knowledge points lest they are forgotten over time, so as to improve learning efficiency and provide targeted learning contents [3]. Through practical research, the system is proved with certain application value and referential meanings for the methods alike.

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Section: System Test Results and Discussionmentioning

confidence: 99%

The Construction of Intelligent English Teaching Model Based on Artificial Intelligence

Li¹

2017

Int. J. Emerg. Technol. Learn.

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“…This proves the involvement and possible role of secretory pathway in HR-PCD. In a typical R-Avr gene interaction, few rapidly elicited proteins like Avr9/Cf9 are reported and in sugarcane, the transcript was found upregulated in the resistant cultivar (Sathyabhama et al 2015). Avr9/Cf-9-induced F-Box1 (ACIF1; ACRE189) is an F-box protein with a leucine-rich-repeat domain found in a screen to identify proteins involved in Cf9-mediated ETI in N. benthamiana (Rowland et Similarly, in this study, a few Ub-ligases are upregulated only in the ICI and a speci c F-box and DNA damage binding proteins were found only in the CI (Table 3).…”

Section: Discussionmentioning

confidence: 99%

“…The whole genome and transcriptome of C. falcatum were sequenced using Illumina Hi-Seq 2500 (Viswanathan et al 2016, Prasanth et al 2017). Earlier we adopted suppression subtractive hybridization (SSH) strategy to identify the time speci c and initial defense responses of sugarcane during C. falcatum pathogenesis which hypothesized involvement of jasmonic acid (JA), ethylene (ET), reactive oxygen species (ROS), phosphoinositide (PI) and calcium (Ca 2+ ) signals in disease resistance (Sathyabhama et al 2015(Sathyabhama et al , 2016. The previous transcriptomic studies, a set of sugarcane cultivars varying in red rot resistance, either a resistant or a susceptible host were used to determine differential transcripts upregulated during C. falcatum pathogenesis (Pratima et al 2013.…”

Section: Introductionmentioning

confidence: 99%

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

Sathyabhama

Viswanathan

Prasanth

et al. 2021

Preprint

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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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“…The differential expression of the chitinase gene in red rot resistant and susceptible sugarcane cultivars was monitored through qRT-PCR (21). Subsequently molecular tools like differential display, subtractive libraries and NGS platforms were deployed to understand differential expression of defense/resistant genes and upregulation of genes during biotrophic phase (7,8,9,22). Further, the involvement of jasmonic acid (JA), ethylene (ET), reactive oxygen species (ROS), phosphoinositide (PI) and calcium (Ca 2+ ) signals in the red rot resistance was hypothesized (9,23).…”

Section: Discussionmentioning

confidence: 99%

“…To understand molecular basis of the host-pathogen interaction differential display RT-PCR was initially used to identify transcripts differentially regulated during interaction in sugarcane and suspension cells (7,8) Further, subtractive libraries were established to identify time speci c and initial defense responses of sugarcane during C. falcatum pathogenesis (9). Besides to understand the pathogen biology in detail, the genome of C. falcatum was sequenced to be 48.16 MB in size with 12,270 genes (10).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Sugarcane in Response to Colletotrichum Falcatum Infection Reveals Repertoire of Transcription Factors and Host Targets

Prasanth

Viswanathan

Malathi

et al. 2021

Preprint

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Background - Sugarcane (Saccharum spp hybrid), an important C4 perennial plantation crop, globally grown for white sugar and ethanol production. Red rot caused by Colletotrichum falcatum is one of the most important threats affecting sugarcane productivity in many countries including India.Materials and Methods - Comprehensive understanding is very much needed to define their transcription level differences and their key regulatory genes during interaction of sugarcane with C. falcatum. To compute and evaluate the molecular mechanism in sugarcane, transcriptome analysis of sugarcane challenged with C. falcatum was sequenced using Hi-Seq 2500 and gene expression profiles were generated by qRT-PCR assays in both compatible and incompatible interactions after challenge inoculation of C. falcatum in sugarcane.Results - A total of 15,728,914 reads were aligned to 48,935 unigenes using BOWTIE 2; the unigenes were annotated using BLASTX and found that 39,895 unigenes were annotated and 22,025 were unigenes with respect to host species, 8,830 with respect to Colletotrichum spp and 9,040 were found to be novel genes. A total of 243 transcription factors (TFs) were found to be predicted in sugarcane challenged with C. falcatum and those TFs were divided into 45 specific families. WRKY, MYB, NAC, bHLH and AUX/IAA transcription factors were found to be abundant which are considered to be key regulators in controlling wide range of molecular events such as defense response, oxidative stimuli, host signalling and triggering disease resistance. In addition, a lot of stress related genes and genes involved in gene ontological and KEGG pathway were significantly affected due to C. falcatum infection. Quantative real time PCR assays carried out to validate reliability of observed expression patterns in sugarcane in response to C. falcatum infection illustrates first transcriptome wide in planta identification and analysis of TF repertoire in the host pathogen interaction.Conclusion - The results of this study provide a benchmark discovery in finding host targets and provide tissue specific data set of genes that express in response to C. falcatum in sugarcane and also a complete analysis of main group of genes that significantly enriched under this condition. This is the first comprehensive work provides basis for the further studies to dissect role of TFs at molecular level in sugarcane defense to fungal pathogens.

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Understanding sugarcane defence responses during the initial phase of Colletotrichum falcatum pathogenesis by suppression subtractive hybridization (SSH)

Cited by 24 publications

References 51 publications

The Construction of Intelligent English Teaching Model Based on Artificial Intelligence

The Construction of Intelligent English Teaching Model Based on Artificial Intelligence

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

Transcriptome Analysis of Sugarcane in Response to Colletotrichum Falcatum Infection Reveals Repertoire of Transcription Factors and Host Targets

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