Identification of novel Bromus- and Trifolium-associated circular DNA viruses

Abstract

The genomes of a large number of highly diverse novel circular DNA viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) viruses that share similarities with plant-infecting ssDNA viruses of the family Geminiviridae. Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiviruses or gemycircularviruses (a new group of ssDNA viruses that are closely related to geminiviruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share >99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these viruses, this is the first report of circular DNA viruses associated with grasses in New Zealand.

Viral nucleic acids in human plasma pools

“…Beside known human viruses, we also detected two gemycircularvirus genomes in the same plasma pool. Gemycircularviruses are genetically highly diverse and have been found in a wide variety of sources but their tropism remain largely unknown except for one virus replicating in fungi (SsHADV‐1 or sclerotinia sclerotiorum hypovirulence‐associated DNA virus 1) …”

A comprehensive genealogy of the replication associated protein of CRESS DNA viruses reveals a single origin of intron-containing Rep

“…Likelihood scores were calculated for each matrix of interest (LG, RtREV, VT, fitLG1-10, fitVT1-10, fmgLG1-10, and fmgVT1-10) describing the ten test datasets (half alignment and tree) in PAML: codeml using model 3, Empirical+F (Yang, 1997). We included the LG and VT matrices that the estimated matrices were based on, and included rtREV because it is a specific matrix that has been previously used to describe CRESS DNA virus Rep evolution (Dayaram et al, 2016;Dayaram et al, 2015a;Dayaram et al, 2015b;Kraberger et al, 2015b;Rosario et al, 2015). To examine how similar the estimated matrices are to each other (and to the three established matrices), we calculated Pearson correlations in Excel (Redmond, WA) for the matrices.…”

“…Unsurprisingly, these specific matrices repeatedly outperform the general matrices in describing their designated sequences. The rtREV matrix has even been selected as the best-fitting matrix by ProtTest for CRESS DNA viral sequences on occasion (Dayaram et al, 2016;Dayaram et al, 2015a;Dayaram et al, 2015b;Kraberger et al, 2015b;Rosario et al, 2015). This result highlights the shortfalls of the general substitution matrices to describe CRESS DNA viral evolution rather than suggesting that CRESS DNA viruses evolve in an identical manner to retro-transcribing viruses.…”

Genomoviridae: a new family of widespread single-stranded DNA viruses

“…It shares with geminiviral proteins two conserved domains, namely geminivirus Rep catalytic domain (Gemini_AL1; PF00799) and geminivirus Rep protein central domain (Gemini_AL1_M; PF08283), with conserved motifs for rolling-circle replication. Notably, similar to some geminiviruses [31], certain SsHADV-1-like viruses also contain introns within their Rep-encoding genes [6,7,12,13,18,19,[26][27][28]30]. However, Rep-based phylogenetic analysis shows that SsHADV-1 and other related putative viruses form a well-supported, monophyletic clade, which branches as a sister group to geminiviruses (Fig.…”