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Sequences enhancing cassava mosaic disease symptoms occur in the cassava genome and are associated with South African cassava mosaic virus infection

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An Expression of Concern to this article was published on 27 April 2016

An Erratum to this article was published on 24 March 2016

Abstract

Cassava is an important food security crop in Sub-Saharan Africa. Two episomal begomovirus-associated sequences, named Sequences Enhancing Geminivirus Symptoms (SEGS1 and SEGS2), were identified in field cassava affected by the devastating cassava mosaic disease (CMD). The sequences reportedly exacerbated CMD symptoms in the tolerant cassava landrace TME3, and the model plants Arabidopsis thaliana and Nicotiana benthamiana, when biolistically co-inoculated with African cassava mosaic virus-Cameroon (ACMV-CM) or East African cassava mosaic virus-UG2 (EACMV-UG2). Following the identification of small SEGS fragments in the cassava EST database, the intention of this study was to confirm their presence in the genome, and investigate a possible role for these sequences in CMD. We report that multiple copies of varying lengths of both SEGS1 and SEGS2 are widely distributed in the sequenced cassava genome and are present in several other cassava accessions screened by PCR. The endogenous SEGS1 and SEGS2 are in close proximity or overlapping with cassava genes, suggesting a possible role in regulation of specific biological processes. We confirm the expression of SEGS in planta using EST data and RT-PCR. The sequence features of endogenous SEGS (iSEGS) are unique but resemble non-autonomous transposable elements (TEs) such as MITEs and helitrons. Furthermore, many SEGS-associated genes, some involved in virus–host interactions, are differentially expressed in susceptible (T200) and tolerant TME3) cassava landraces infected by South African cassava mosaic virus (SACMV) of susceptible (T200) and tolerant (TME3) cassava landraces. Abundant SEGS-derived small RNAs were also present in mock-inoculated and SACMV-infected T200 and TME3 leaves. Given the known role of TEs and associated genes in gene regulation and plant immune responses, our observations are consistent with a role of these DNA elements in the host’s regulatory response to geminiviruses.

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Acknowledgments

This project was supported by Grants from the National Research Foundation Competitive Grant and the International Center for Genetic Engineering and Biotechnology, Trieste. ATM was supported by Claude Leon Foundation and NRF-South Africa. We would like to thank Dr. Louis Bengyella for assistance in the phylogenetic analysis.

Conflict of interest

The authors declare no conflict of interest.

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Authors and Affiliations

  1. School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, Wits, 2050, South Africa

    A. T. Maredza, F. Allie & M. E. C. Rey

  2. Department of Systems Biology, Columbia University in the City of New York, 1130 St Nicholas Avenue, New York, NY, USA

    G. Plata

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  1. A. T. Maredza
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  2. F. Allie
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  3. G. Plata
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Correspondence to M. E. C. Rey.

Additional information

Communicated by K. Gruden.

Small RNA-Seq data reported are available in the European Nucleotide Archive under the accession number PRJEB8495.

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438_2015_1049_MOESM1_ESM.pdf

Online Resources 1 Single-primer amplified fragment from healthy cassava is similar to episomal SEGS1. Online Resource 2 iSEGS1 elements in the cassava genome. Online Resource 3 iSEGS2 elements in the cassava genome. Online Resource 4 Large fragments homologous to SEGS1 found in the cassava genome. Online Resource 5 Large fragments homologous to SEGS2 found in the cassava genome. Online Resource 6 Mapping of TIRs in episomal and integrated SEGS and prediction of secondary structures (Mfold). Online Resource 7 Gene ontologies (GO) annotations of iSEGS-associated genes grouped as “upstream of iSEGS”, “downstream of iSEGS” or “overlapping with iSEGS”. Online Resource 8 iSEGS fragments detected in cassava-expressed sequence tags. Online Resource 9 Cassava ESTs carrying fragments that are homologous to iSEGS1. Online Resource 10 Cassava ESTs carrying fragments that are homologous to iSEGS2. Online Resource 11 Expression of genes proximal to iSEGS1 comparing two cultivars infected with SACMV. Online Resource 12 Expression of genes proximal to iSEGS2 comparing two cultivars infected with SACMV. Online Resource 13 Small RNA sequence data and mapping of sRNAs to SEGS (PDF 3450 kb)

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Maredza, A.T., Allie, F., Plata, G. et al. Sequences enhancing cassava mosaic disease symptoms occur in the cassava genome and are associated with South African cassava mosaic virus infection. Mol Genet Genomics 291, 1467–1485 (2016). https://doi.org/10.1007/s00438-015-1049-z

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