The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed

Abstract

Endogenous viral sequences are essentially ‘fossil records’ that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements found within the nuclear genomes of various Nicotiana species. Although other ssDNA virus-like sequences are included within the draft genomes of various plant species, it is not entirely certain that these are not contaminants. The Nicotiana geminivirus-related DNA elements therefore remain the only definitively proven instances of endogenous plant ssDNA virus sequences. Here, we characterize two new classes of endogenous plant virus sequence that are also apparently derived from ancient geminiviruses in the genus Begomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in the Dioscorea spp. of the Enantiophyllum clade. We used fluorescence in situ hybridization to confirm that the EGV1 sequences are integrated in the D. alata genome and showed that one or two ancestral EGV sequences likely became integrated more than 1.4 million years ago during or before the diversification of the Asian and African Enantiophyllum Dioscorea spp. Unexpectedly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. Further, the detection in D. alata of EGV gene transcripts, small 21–24 nt RNAs that are apparently derived from these transcripts, and expressed Rep proteins, provides evidence that some EGV genes are possibly still functionally expressed in at least some of the Enantiophyllum clade species.

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

“…Similar to caulimovirids, ssDNA viruses of the family Geminiviridae have also been able to get integrated in their host plant genomes ( Murad et al, 2004 ; Filloux et al, 2015 ; and reference therein). However, unlike endogenous caulimovirids, geminiviral EVEs have not so far been reported to give rise to episomal viruses.…”

“…However, unlike endogenous caulimovirids, geminiviral EVEs have not so far been reported to give rise to episomal viruses. Interestingly, geminiviral EVEs integrated in the genomes of water yam ( Dioscorea alata ) and other Dioscorea species appear to express the viral replication protein Rep ( Filloux et al, 2015 ). In D. alata , one of the two EVEs possessing uninterrupted ORFs for Rep and replication enhancer (but not coat) proteins spawns siRNAs covering both strands of the integrated sequence, with 21-nt and 24-nt species being the first and the second most abundant ( Filloux et al, 2015 ), indicative of post-transcriptional and transcriptional silencing.…”

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

“…Thus, many water yam species ( Dioscorea spp.) have been found to contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed (Filloux et al, 2015). Correspondingly, multiple copies of geminiviral DNA were found in the genomes of four closely related Nicotiana spp.…”

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

“…In the context of African agriculture, the rapidly evolving field of metagenomics will have a significant impact in revealing the diversity of microorganisms, and in describing the relationship between host-associated microbial communities and host phenotype. The declining cost of sequencing and the associated analytical tools will likely create the opportunity to develop cost-effective and efficient diagnostic kits to address the challenge of multiple infections (pathogenic races and strains) in the major crops such as cassava [110], banana [111], and yams [112]. Survey of the incidence and distribution of viruses infecting these crops makes it one of the important tools for understanding the microbial genetics, physiology, and community ecology.…”

“…Conventional methods of virus diagnostics, using antibodies and PCR, often lack the sensitivity to detect viruses that exist in low abundance and emerging viruses with unknown genomes. Therefore, next-generation deep sequencing approaches and bioinformatics analysis can be used for de novo assembly of virus and viroid genomes, to perform reliable characterization and diagnostics of known and unknown viruses and viroids [112,154,155]. In the wake of NGS technologies, powerful and high-throughput novel approaches, such as metagenomics, have been developed and widely used to analyze nucleotide sequence of microbial populations in plant samples (see section 2.8) [8,105,156].…”