Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease

Abstract

Cassava mosaic begomoviruses (CMBs) cause cassava mosaic disease (CMD) across Africa and the Indian subcontinent. Like all members of the geminivirus family, CMBs have small, circular single-stranded DNA genomes. We report here the discovery of two novel DNA sequences, designated SEGS-1 and SEGS-2 (for sequences enhancing geminivirus symptoms), that enhance symptoms and break resistance to CMD. The SEGS are characterized by GC-rich regions and the absence of long open reading frames. Both SEGS enhanced CMD symptoms in cassava (Manihot esculenta Crantz) when coinoculated with African cassava mosaic virus (ACMV), East African cassava mosaic Cameroon virus (EACMCV), or East African cassava mosaic virus-Uganda (EACMV-UG). SEGS-1 also overcame resistance of a cassava landrace carrying the CMD2 resistance locus when coinoculated with EACMV-UG. Episomal forms of both SEGS were detected in CMB-infected cassava but not in healthy cassava. SEGS-2 episomes were also found in virions and whiteflies. SEGS-1 has no homology to geminiviruses or their associated satellites, but the cassava genome contains a sequence that is 99% identical to full-length SEGS-1. The cassava genome also includes three sequences with 84 to 89% identity to SEGS-2 that together encompass all of SEGS-2 except for a 52-bp region, which includes the episomal junction and a 26-bp sequence related to alphasatellite replication origins. These results suggest that SEGS-1 is derived from the cassava genome and facilitates CMB infection as an integrated copy and/or an episome, while SEGS-2 was originally from the cassava genome but now is encapsidated into virions and transmitted as an episome by whiteflies.IMPORTANCE Cassava is a major crop in the developing world, with its production in Africa being second only to maize. CMD is one of the most important diseases of cassava and a serious constraint to production across Africa. CMD2 is a major CMD resistance locus that has been deployed in many cassava cultivars through large-scale breeding programs. In recent years, severe, atypical CMD symptoms have been observed occasionally on resistant cultivars, some of which carry the CMD2 locus, in African fields. In this report, we identified and characterized two DNA sequences, SEGS-1 and SEGS-2, which produce similar symptoms when coinoculated with cassava mosaic begomoviruses onto a susceptible cultivar or a CMD2-resistant landrace. The ability of SEGS-1 to overcome CMD2 resistance and the transmission of SEGS-2 by whiteflies has major implications for the long-term durability of CMD2 resistance and underscore the need for alternative sources of resistance in cassava.

Cassava mosaic disease: a review of a threat to cassava production in Zambia

“…Another potential factor in disease expression is the presence of subviral agents called sequence enhancing geminivirus symptoms (SEGS) (formerly satellite DNA molecules). These satellite DNA molecules are known to modulate replication and symptom expression of their helper virus (Maredza et al 2016;Ndunguru et al 2016). SEGS associated with cassava begomoviruses have been shown to enhance severe symptoms and break down plant resistance (Ndunguru et al 2008).…”

Multiple morphogenic culture systems cause loss of resistance to cassava mosaic disease

“…Reliance on a single gene mechanism, however, risks evolution of the pathogen to overcome the resistance. Indeed, breakdown of CMD2-mediated resistance was reported recently under greenhouse conditions by Ndunguru, et al [ 7 ]. Advanced biotechnologies in cassava rely on induction of somatic embryogenesis to generate the totipotent tissues utilized for transgene integration and delivery of gene editing reagents [ 8 , 9 ].…”

An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing

“…The supernatant was subjected to 0.22 M filtration 9 followed by DNase I digestion (2.5 U for h at 37°C). Virion DNA was isolated using the QIAamp MinElute Virus Spin Kit (Qiagen, Hilden, Germany) (Ndunguru et al, 2016;Ng et al, 2011;Rosario et al, 2015).…”