Dynamic Transcriptome Profiling of Bean Common Mosaic Virus (BCMV) Infection in Common Bean (Phaseolus Vulgaris L.)

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2016 Aug 13

PMID 27515794

Citations 17

Authors

Kathleen Martin

Jugpreet Singh

John H Hill

Steven A Whitham

Steven B Cannon

Affiliations

Soon will be listed here.

Abstract

Background: Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties that distinguish the pathogenicity types with respect to the viral strains. The molecular responses in Phaseolus to BCMV infection have not yet been well characterized.

Results: We report the transcriptional responses of a widely susceptible variety of common bean (Phaseolus vulgaris L., cultivar 'Stringless green refugee') to two BCMV strains, in a time-course experiment. We also report the genome sequence of a previously unreported BCMV strain. The interaction with the known strain NL1-Iowa causes moderate symptoms and large transcriptional responses, and the newly identified strain (Strain 2 or S2) causes severe symptoms and moderate transcriptional responses. The transcriptional profiles of host plants infected with the two isolates are distinct, and involve numerous differences in splice forms in particular genes, and pathway specific expression patterns.

Conclusions: We identified differential host transcriptome response after infection of two different strains of Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris L.). Virus infection initiated a suite of changes in gene expression level and patterns in the host plants. Pathways related to defense, gene regulation, metabolic processes, photosynthesis were specifically altered after virus infection. Results presented in this study can increase the understanding of host-pathogen interactions and provide resources for further investigations of the biological mechanisms in BCMV infection and defense.

Citing Articles

Comprehensive transcriptomic analysis reveals turnip mosaic virus infection and its aphid vector Myzus persicae cause large changes in gene regulatory networks and co-transcription of alternative spliced mRNAs in Arabidopsis thaliana.

Herath V, Casteel C, Verchot J BMC Plant Biol. 2025; 25(1):128.

PMID: 39885390 PMC: 11780806. DOI: 10.1186/s12870-024-06014-3.

Integrated transcriptome and microRNA sequencing analyses reveal gene responses in poplar leaves infected by the novel pathogen bean common mosaic virus (BCMV).

Wang L, Zhang W, Shen W, Li M, Fu Y, Li Z Front Plant Sci. 2023; 14:1163232.

PMID: 37396641 PMC: 10308444. DOI: 10.3389/fpls.2023.1163232.

Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration.

Jha U, Nayyar H, Chattopadhyay A, Beena R, Lone A, Naik Y Front Plant Sci. 2023; 14:1183505.

PMID: 37229109 PMC: 10204772. DOI: 10.3389/fpls.2023.1183505.

Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B.

Zhong X, Yang L, Li J, Tang Z, Wu C, Zhang L Virol J. 2022; 19(1):182.

PMID: 36357910 PMC: 9650830. DOI: 10.1186/s12985-022-01890-3.

Identification of stably expressed reference genes for expression studies in using mass spectrometry-based label-free quantification.

Cheng S, Ku Y, Cheung M, Lam H Front Plant Sci. 2022; 13:1001920.

PMID: 36247637 PMC: 9557097. DOI: 10.3389/fpls.2022.1001920.

References

Marquez Y, Brown J, Simpson C, Barta A, Kalyna M . Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 2012; 22(6):1184-95. PMC: 3371709. DOI: 10.1101/gr.134106.111. View

Ishihama N, Yoshioka H . Post-translational regulation of WRKY transcription factors in plant immunity. Curr Opin Plant Biol. 2012; 15(4):431-7. DOI: 10.1016/j.pbi.2012.02.003. View

Naderpour M, Lund O, Larsen R, Johansen E . Potyviral resistance derived from cultivars of Phaseolus vulgaris carrying bc-3 is associated with the homozygotic presence of a mutated eIF4E allele. Mol Plant Pathol. 2010; 11(2):255-63. PMC: 6640476. DOI: 10.1111/j.1364-3703.2009.00602.x. View

Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S . KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011; 39(Web Server issue):W316-22. PMC: 3125809. DOI: 10.1093/nar/gkr483. View

Nuruzzaman M, Manimekalai R, Sharoni A, Satoh K, Kondoh H, Ooka H . Genome-wide analysis of NAC transcription factor family in rice. Gene. 2010; 465(1-2):30-44. DOI: 10.1016/j.gene.2010.06.008. View

Adams M, Antoniw J, Beaudoin F . Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol. 2010; 6(4):471-87. DOI: 10.1111/j.1364-3703.2005.00296.x. View

Sturn A, Quackenbush J, Trajanoski Z . Genesis: cluster analysis of microarray data. Bioinformatics. 2002; 18(1):207-8. DOI: 10.1093/bioinformatics/18.1.207. View

Staiger D, Brown J . Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell. 2013; 25(10):3640-56. PMC: 3877812. DOI: 10.1105/tpc.113.113803. View

Trapnell C, Pachter L, Salzberg S . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105-11. PMC: 2672628. DOI: 10.1093/bioinformatics/btp120. View

10.

Haas B, Papanicolaou A, Yassour M, Grabherr M, Blood P, Bowden J . De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013; 8(8):1494-512. PMC: 3875132. DOI: 10.1038/nprot.2013.084. View

11.

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

12.

Jada B, Soitamo A, Siddiqui S, Murukesan G, Aro E, Salakoski T . Multiple different defense mechanisms are activated in the young transgenic tobacco plants which express the full length genome of the Tobacco mosaic virus, and are resistant against this virus. PLoS One. 2014; 9(9):e107778. PMC: 4171492. DOI: 10.1371/journal.pone.0107778. View

13.

Martin K, Hill J, Cannon S . Occurrence and Characterization of Bean common mosaic virus Strain NL1 in Iowa. Plant Dis. 2019; 98(11):1593. DOI: 10.1094/PDIS-07-14-0673-PDN. View

14.

Bent A . Plant Disease Resistance Genes: Function Meets Structure. Plant Cell. 1996; 8(10):1757-1771. PMC: 161313. DOI: 10.1105/tpc.8.10.1757. View

15.

DeLuca D, Levin J, Sivachenko A, Fennell T, Nazaire M, Williams C . RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012; 28(11):1530-2. PMC: 3356847. DOI: 10.1093/bioinformatics/bts196. View

16.

Chen L, Song Y, Li S, Zhang L, Zou C, Yu D . The role of WRKY transcription factors in plant abiotic stresses. Biochim Biophys Acta. 2011; 1819(2):120-8. DOI: 10.1016/j.bbagrm.2011.09.002. View

17.

Ambawat S, Sharma P, Yadav N, Yadav R . MYB transcription factor genes as regulators for plant responses: an overview. Physiol Mol Biol Plants. 2014; 19(3):307-21. PMC: 3715649. DOI: 10.1007/s12298-013-0179-1. View

18.

Lu J, Du Z, Kong J, Chen L, Qiu Y, Li G . Transcriptome analysis of Nicotiana tabacum infected by Cucumber mosaic virus during systemic symptom development. PLoS One. 2012; 7(8):e43447. PMC: 3429483. DOI: 10.1371/journal.pone.0043447. View

19.

Yang C, Guo R, Jie F, Nettleton D, Peng J, Carr T . Spatial analysis of arabidopsis thaliana gene expression in response to Turnip mosaic virus infection. Mol Plant Microbe Interact. 2007; 20(4):358-70. DOI: 10.1094/MPMI-20-4-0358. View

20.

Feng X, Myers J, Karasev A . Bean common mosaic virus Isolate Exhibits a Novel Pathogenicity Profile in Common Bean, Overcoming the bc-3 Resistance Allele Coding for the Mutated eIF4E Translation Initiation Factor. Phytopathology. 2015; 105(11):1487-95. DOI: 10.1094/PHYTO-04-15-0108-R. View