RT Journal Article
SR Electronic
T1 Discovery of several thousand highly diverse circular DNA viruses
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 555375
DO 10.1101/555375
A1 Michael J. Tisza
A1 Diana V. Pastrana
A1 Nicole L. Welch
A1 Brittany Stewart
A1 Alberto Peretti
A1 Gabriel J. Starrett
A1 Yuk-Ying S. Pang
A1 Siddharth R. Krishnamurthy
A1 Patricia A. Pesavento
A1 David H. McDermott
A1 Philip M. Murphy
A1 Jessica L. Whited
A1 Bess Miller
A1 Jason M. Brenchley
A1 Stephan P. Rosshart
A1 Barbara Rehermann
A1 John Doorbar
A1 Blake A. Ta’ala
A1 Olga Pletnikova
A1 Juan Troncoso
A1 Susan M. Resnick
A1 Ben Bolduc
A1 Matthew B. Sullivan
A1 Arvind Varsani
A1 Anca M. Segall
A1 Christopher B. Buck
YR 2019
UL http://biorxiv.org/content/early/2019/09/17/555375.abstract
AB Although it is suspected that there are millions of distinct viral species, fewer than 9,000 are catalogued in GenBank’s RefSeq database. We selectively enriched for and amplified the genomes of circular DNA viruses in over 70 animal samples, ranging from cultured soil nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2,500 circular genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA viruses and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these “dark matter” sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.