Viral-derived DNA invasion and individual variation in an Indonesian population of large flying fox Pteropus vampyrus

Abstract

Here, we performed next-generation sequencing (NGS) on six large flying foxes (Pteropus vampyrus) collected in Indonesia. Seventy-five virus species in the liver tissue of each specimen were listed. Viral homologous sequences in the bat genome were identified from the listed viruses. This finding provides collateral evidence of viral endogenization into the host genome. We found that two of the six specimens bore partial sequences that were homologous to the plant pathogens Geminiviridae and Luteoviridae. These sequences were absent in the P. vampyrus chromosomal sequences. Hence, plant viral homologous sequences were localized to the hepatocytes as extrachromosomal DNA fragments. Therefore, this suggests that the bat is a potential carrier or vector of plant viruses. The present investigation on wild animals offered novel perspectives on viral invasion, variation, and host interaction.

Keywords: Indonesia; Pteropus vampyrus; endogenization; plant virus; virus.

Fig. 1.

Distribution of viral sequences in Pteropus vampyrus specimens. A. Graph indicating the distribution of viral species classifications in each specimen. B. Graph indicating the distribution of heritable factors for the viral species in each specimen. C. Graph indicating the distribution of the general viral species hosts of in each specimen. D. Filled columns indicate the viral homologous sequences identified in the specimen. Original data including all candidate virus names are listed in Supplementary Table 1. Five viruses were subjected to analysis to determine whether they were endogenous viral elements (Figs. 2, 3, 4).

Fig. 2.

Comparison of Bracovirus and U6 spliceosomal small RNAs. A. Sequence comparison of Bracovirus and U6 spliceosomal small RNAs from Pteropus vampyrus and other animals. Gray boxes indicate sequences identical to Bracovirus. Lined squares indicate functional motif forming spliceosome complex. B. Phylogenetic tree indicating the relationship between Bracovirus and U6 spliceosomal small RNA sequences in animal genomes. The viral sequence was predicted to be distant from other animal sequences.

Fig. 3.

Comparison of Bovine viral diarrhea virus (BVDV) and dnajc14. A. Sequence comparison of BVDV and dnajc14 in Pteropus vampyrus and other animals. Gray boxes indicate sequences identical to BVDV. B. Illustration indicates vertebrate dnajc14 structure. In all species except elephant shark (Callorhinchus milii), the 161-bp conserved sequence was found as a single exon. C. Phylogenetic tree indicating the relationship between the conserved BVDV sequences and dnajc14 in vertebrate genomes. Viral sequence was predicted to be the closest to bovine Bos taurus sequence.

Fig. 4.

Plant virus homologous sequences identified from Pteropus vampyrus. A. Black line indicates whole Tomato yellow leaf curl virus (TYLCV) genome. Gray boxes under line indicate viral protein coding region. Short lines above viral genome indicate Next generation sequencing (NGS) reads identified in Institut Pertanian Bogor_4 (IPB_4) specimen. B. Black line indicates whole Beet mild yellowing virus (BMYV) genome. Gray boxes under line indicate viral protein coding region. Short lines above viral genome indicate overlap region of the NGS reads identified in IPB_41 specimen.