Discovery of a new konkovirus species in Lachenalia plants reveals possible co-evolution between 5' and 3' RNA sequence motifs

Abstract

This study reports the discovery of a new konkovirus species, named Lachenalia konkovirus 1 (LaKoV1), from Lachenalia plants in an urban botanic garden in Amsterdam. Using a combination of RNA sequencing (RNA-seq), small RNA-seq and advanced bioinformatics, we identified a segmented, negative-strand RNA virus belonging to the family Konkoviridae. Our findings show significant divergence between this novel virus and known members of the family Konkoviridae, such as tulip streak virus (TuSV) and Lactuca big vein-associated Phlebovirus (LBVaPV), supporting its classification as a distinct species. Notably, the sequence differences found in the conserved 5' and 3' ends of these segments suggest potential co-evolution. Despite the observed genomic distances, there is significant conservation in the RNA-dependent RNA polymerase subdomain, underscoring evolutionary relationships among LaKoV1, TuSV and LBVaPV. Our findings expand the known global virome and highlight the importance of exploring plant viromes in diverse ecological settings to better understand virus evolution and diversity.

Keywords: Konkoviridae; Lachenalia; RNA viruses; RNA-dependent RNA polymerase (RdRp); plant viruses; virus discovery.

Fig. 1.. Genomic organization, sequence similarity and terminal motif features of LaKoV1. (a) Schematic illustration of the discovered LaKoV1 genome and its associated proteins. Indicated on the +strand are the proposed open reading frames (grey arrow box) and corresponding protein sizes (blue). (b)The aa similarity between (LaKoV1-NL1-26) and the three most similar konkovirus genome sequences: FreKV1, TuSV and LBVaPV. (c) Similarities between the 5′ and 3′ terminus motifs of the four genomic RNA segments of each virus. To facilitate interpretation of the sequence complementarity, the reverse complement of the 3′ terminal sequences (3′RC) is shown. Nucleotides identical to the consensus nucleotide are highlighted in green. The hallmark non-complementary, protruding CC at positions 10 and 11 in the 5′ motif is indicated in pink [22]. Nucleotides at positions 11 (3′) and 12 (5′) that are identical in the same RNA molecule are indicated by a black box. The AUG translation start sites for the RdRp proteins are highlighted in blue.

Fig. 2.. RdRp protein sequence similarity tree of LaKoV1 and representative viruses from related families. A neighbour-joining tree was constructed based on the RdRp aa sequences from LaKoV1 and representative members of related bunyavirus families. Multiple sequence alignment was performed using muscle v3.8.31 with 32 iterations. The tree was generated using the Kimura protein distance measure with 1,000 bootstrap replicates. LaKoV1 clusters within the Konkoviridae family (yellow shading), along with TuSV, LBVaPV and other known konkoviruses. Related viral families are colour-coded: Phenuiviridae (green), Leishbuviridae (blue), Discoviridae (purple), Arenaviridae (red) and Wupedeviridae (grey). The scale bar represents the estimated number of aa substitutions per site based on the Kimura protein distance model.

Fig. 3.. Sequence comparison of the conserved RdRp palm subdomains with the characteristic motifs. Alignment of the LaKoV1 conserved RdRp palm subdomain protein sequences with the three most similar RdRp subdomain sequences in GenBank. The aa sequences of the RdRp subdomain motifs A, B and C are shaded in grey. The aa sequences that diverge from the LaKoV1 RdRp subdomain motifs are highlighted in red.