Small RNA and methylation responses in susceptible and tolerant landraces of cassava infected with South African cassava mosaic virus

Differences in the 3' intergenic region and the V2 protein of two sequence variants of tomato curly stunt virus play an important role in disease pathology in Nicotiana benthamiana

Tomato production in South Africa is threatened by the emergence of tomato curly stunt virus (ToCSV), a monopartite Begomovirus transmitted by the whitefly vector Bemisia tabaci (Genn.). We investigated the role of sequence differences present in the 3' intergenic region (IR) and the V2 coding region on the differing infectivity of ToCSV sequence variant isolates V30 and V22 in the model host Nicotiana benthamiana. Using virus mutant chimeras, we determined that the development of the upward leaf roll symptom phenotype is mediated by sequence differences present in the 3' IR containing the TATA-associated composite element. Sequence differences present in the V2 coding region are responsible for modulating disease severity and symptom recovery in V22-infected plants. Serine substitution of V22 V2 Val27 resulted in a significant increase in disease severity with reduced recovery, the first study to demonstrate the importance of this V2 residue in disease development. Two putative ORFs, C5 and C6, were identified using in silico analysis and detection of an RNA transcript spanning their coding region suggests that these ORFs may be transcribed during infection. Additional virus-derived RNA transcripts spanning multiple ORFs and crossing the boundaries of recognised polycistronic transcripts, as well as the origin of replication within the IR, were detected in ToCSV-infected plants providing evidence of bidirectional readthrough transcription. From our results, we conclude that the diverse responses of the model host to ToCSV infection is influenced by select sequence differences and our findings provide several avenues for further investigation into the mechanisms behind these responses to infection.

High throughput sRNA sequencing revealed gene regulatory role mediated by pathogen-derived small RNAs during Sri Lankan Cassava Mosaic Virus infection in Cassava

Small RNA (sRNA) mediated gene regulation during Sri Lankan Cassava Mosaic Virus (SLCMV) infection was studied from the Indian Cassava Cultivar H226. Our study generated high throughput sRNA dataset of 23.64 million reads from the control and SLCMV infected H226 leaf libraries. mes-miR9386 was detected as the most prominent miRNA expressed in control and infected leaf. Among the differentially expressed miRNAs, mes-miR156, mes- miR395 and mes-miR535a/b showed significant down regulation in the infected leaf. Genome-wide analysis of the three small RNA profiles revealed critical role of virus-derived small RNAs (vsRNAs) from the infected leaf tissues of H226. The vsRNAs were mapped to the bipartite SLCMV genome and high expression of siRNAs generated from the virus genomic region encoding AV1/AV2 genes in the infected leaf pointed towards the susceptibility of H226 cultivars to SLCMV. Furthermore, the sRNA reads mapped to the antisense strand of the SLCMV ORFs was higher than the sense strand. These vsRNAs were potential to target key host genes involved in virus interaction such as aldehyde dehydrogenase, ADP-ribosylation factor1 and ARF1-like GTP-binding proteins. The sRNAome-assisted analysis also revealed the origin of virus-encoded miRNAs from the SLCMV genome in the infected leaf. These virus-derived miRNAs were predicted to have hair-pin like secondary structures, and have different isoforms. Moreover, our study revealed that the pathogen sRNAs play a critical role in the infection process in H226 plants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03494-2.

Differential miRNA profiles in South African cassava mosaic virus-infected cassava landraces reveal clues to susceptibility and tolerance to cassava mosaic disease

Specific miRNA families are involved in susceptibility or antiviral immunity in plants. Manihot esculenta Crantz (cassava) is a perennial plant that is an important food security crop in sub-Saharan Africa. Cassava is susceptible to several begomoviruses that cause cassava mosaic disease (CMD). In this study, we investigated the leaf miRNAome response in a tolerant (TME3) and susceptible (T200) cassava landrace challenged with South African cassava mosaic virus. RNAseq was performed on leaf samples at 12, 32 and 67 days post infection (dpi), representing early, symptomatic and late persistent stages of CMD infection. Significantly, distinct profiles of conserved miRNA family expression between the T200 and TME3 landraces at the three infection stages were observed. Notably at 12 days post SACMV infection, TME3 exhibited significant downregulation (log2fold<2.0) of 42 %, compared to 9% in T200, of the conserved miRNA families. This demonstrates an overall early response to SACMV in TME3 prior to symptom appearance not observed in T200, and expression of a large cohort of miRNA-regulated genes. Notably, at early infection, downregulation of mes-miR162 and 168 that target antiviral posttransriptional gene silencing (PTGS) regulators DCL1 and AGO1, respectively, was observed in TME3, and AGO1 and DCL1 expression was higher compared to T200 post infection. Early rapid responses prior to symptom development, including RNA silencing, may be key to establishing the tolerance/recovery phenotype exhibited by TME3 landrace later on at 67 dpi. At recovery, TME3 was hallmarked by a highly significant down-regulation of mes-miR167. MiR167 targets an auxin responsive factor which plays a role in auxin signaling and adaptive responses to stress, suggesting the importance of the auxin signaling in recovery of SACMV-induced symptoms. The gene targets of these miRNAs and their associated networks may provide clues to the molecular basis of CMD tolerance in perennial hosts such as cassava.

Olea Europaea Geminivirus: A Novel Bipartite Geminivirid Infecting Olive Trees

In 2014, high-throughput sequencing of libraries of total DNA from olive trees allowed the identification of two geminivirus-like contigs. After conventional resequencing of the two genomic DNAs, their analysis revealed they belonged to the same viral entity, for which the provisional name of Olea europaea geminivirus (OEGV) was proposed. Although DNA-A showed a genome organization similar to that of New World begomoviruses, DNA-B had a peculiar ORF arrangement, consisting of a movement protein (MP) in the virion sense and a protein with unknown function on the complementary sense. Phylogenetic analysis performed either on full-length genome or on coat protein, replication associated protein (Rep), and MP sequences did not endorse the inclusion of this virus in any of the established genera in the family Geminiviridae. A survey of 55 plants revealed that the virus is widespread in Apulia (Italy) with 91% of the samples testing positive, although no correlation of OEGV with a disease or specific symptoms was encountered. Southern blot assay suggested that the virus is not integrated in the olive genome. The study of OEGV-derived siRNA obtained from small RNA libraries of leaves and fruits of three different cultivars, showed that the accumulation of the two genomic components is influenced by the plant genotype while virus-derived-siRNA profile is in line with other geminivirids reported in literature. Single-nucleotide polymorphism (SNP) analysis unveiled a low intra-specific variability.

RNA silencing of South African cassava mosaic virus in transgenic cassava expressing AC1/AC4 hp- RNA induces tolerance

Cassava mosaic disease (CMD), caused by geminiviruses, is a major hurdle to cassava production. Due to the heterozygous nature of cassava, breeding for virus resistance is difficult, but cassava has been shown to be a good candidate for genetic engineering using RNA interference (RNAi). T This study reports on the ability of a transgene-derived RNA hairpin, homologous to an overlapping region of the SACMV replication associated protein and putative virus suppressor of silencing protein (AC1/AC4), to confer tolerance in the CMD-susceptible model cassava cultivar 60444. Three of the fourteen transgenic lines expressing SACMV AC1/AC4 hairpin-derived siRNAs showed decreased symptoms and viral loads compared to untransformed control plants. Expression of SACMV AC1/AC4 homologous siRNAs showed that this tolerance is most likely associated with post-transcriptional gene silencing of the virus. This is the first report of targeting the overlapping AC1 and AC4 genes of SACMV conferring CMD tolerance in cassava.

Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato

Geminiviruses are plant ssDNA viruses that replicate through dsDNA intermediates and form minichromosomes which carry the same epigenetic marks as the host chromatin. During the infection, geminiviruses are targets of the post-transcriptional and transcriptional gene silencing machinery. To obtain insights into the connection between virus-derived small RNAs (vsRNAs), viral genome methylation and gene expression, we obtained the transcriptome, sRNAome and methylome from the geminivirus Tomato yellow leaf curl virus-infected tomato plants. The results showed accumulation of transcripts just at the viral ORFs, while vsRNAs spanned the entire genome, showing a prevalent accumulation at regions where the viral ORFs overlapped. The viral genome was not homogenously methylated showing two highly methylated regions located in the C1 ORF and around the intergenic region (IR). The compilation of those results showed a partial correlation between vsRNA accumulation, gene expression and DNA methylation. We could distinguish different epigenetic scenarios along the viral genome, suggesting that in addition to its function as a plant defence mechanism, DNA methylation could have a role in viral gene regulation. To our knowledge, this is the first report that shows integrative single-nucleotide maps of DNA methylation, vsRNA accumulation and gene expression from a plant virus.

Cassava Mosaic and Brown Streak Diseases: Current Perspectives and Beyond

Cassava is the fourth largest source of calories in the world but is subject to economically important yield losses due to viral diseases, including cassava brown streak disease and cassava mosaic disease. Cassava mosaic disease occurs in sub-Saharan Africa and the Asian subcontinent and is associated with nine begomovirus species, whereas cassava brown streak disease has to date been reported only in sub-Saharan Africa and is caused by two distinct ipomovirus species. We present an overview of key milestones and their significance in the understanding and characterization of these two major diseases as well as their associated viruses and whitefly vector. New biotechnologies offer a wide range of opportunities to reduce virus-associated yield losses in cassava for farmers and can additionally enable the exploitation of this valuable crop for industrial purposes. This review explores established and new technologies for genetic manipulation to achieve desired traits such as virus resistance.

The Search for Resistance to Cassava Mosaic Geminiviruses: How Much We Have Accomplished, and What Lies Ahead

The cassava mosaic disease (CMD), which occurs in all cassava growing regions of Africa and the Indian subcontinent, is caused by cassava mosaic geminiviruses (CMGs). CMGs are considered to be the most damaging vector-borne plant pathogens. So far, the most successful approach used to control these viruses has been the transfer of a polygenic recessive resistance locus, designated CMD1, from wild cassava to cassava cultivars. Further progress in harnessing natural resistance to contain CMGs has come from the discovery of the dominant monogenic resistance locus, CMD2, in some West African cassava cultivars. CMD2 has been combined with CMD1 through genetic crosses. Because of the limitations of the cassava breeding approach, especially with regard to time required to produce a variety and the loss of preferred agronomic attributes, efforts have been directed toward the deployment of genetic engineering approaches. Most of these approaches have been centered on RNA silencing strategies, developed mainly in the model plant Nicotiana benthamiana. Early RNA silencing platforms assessed for CMG resistance have been use of viral genes for co-suppression, antisense suppression or for hairpin RNAs-mediated gene silencing. Here, progress and challenges in the deployment of these approaches in the control of CMGs are discussed. Novel functional genomics approaches with potential to overcome some of the drawbacks of the current strategies are also discussed.

Differential response of cassava genotypes to infection by cassava mosaic geminiviruses

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Cassava genotypes respond differently to infection by cassava mosaic geminiviruses.

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Cassava mosaic disease resistant loci prompt recovery from systemic infection.

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CMD symptoms are directly correlated with contents of viral DNA and virus specific small RNAs.

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CMD infected plants abundantly accumulate 21–24 nt of virus specific small RNAs.

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VsRNAs heterogeneously map the entire virus genome in both polarities.

Mitigation of cassava mosaic disease (CMD) focuses on the introgression of resistance imparted by the polygenic recessive (CMD1), dominant monogenic (CMD2) and CMD3 loci. The mechanism(s) of resistance they impart, however, remain unknown. Two CMD susceptible and nine CMD resistant cassava genotypes were inoculated by microparticle bombardment with infectious clones of African cassava mosaic virus Cameroon strain (ACMV-CM) and the Kenyan strain K201 of East African cassava mosaic virus (EACMV KE2 [K201]). Genotypes carrying the CMD1 (TMS 30572), CMD2 (TME 3, TME 204 and Oko-iyawo) and CMD3 (TMS 97/0505) resistance mechanisms showed high levels of resistance to ACMV-CM, with viral DNA undetectable by PCR beyond 7 days post inoculation (dpi). In contrast, all genotypes initially developed severe CMD symptoms and accumulated high virus titers after inoculation with EACMV KE2 (K201). Resistant genotypes recovered to become asymptomatic by 65 dpi with no detectable virus in newly formed leaves. Genotype TMS 97/2205 showed highest resistance to EACMV KE2 (K201) with <30% of inoculated plants developing symptoms followed by complete recovery by 35 dpi. Deep sequencing of small RNAs confirmed production of 21–24 nt virus derived small RNAs (vsRNA) that mapped to cover the entire ACMV-CM and EACMV KE2 (K201) viral genomes in both polarities, with hotspots seen within gene coding regions. In resistant genotypes, total vsRNAs were most abundant at 20 and 35 dpi but reduced significantly upon recovery from CMD. In contrast, CMD susceptible genotypes displayed abundant vsRNAs throughout the experimental period. The percentage of vsRNAs reads ranked by class size were 21nt (45%), 22 nt (28%) and 24 nt (18%) in all genotypes studied. The number of vsRNA reads directly correlated with virus titer and CMD symptoms.