Communications in Information and Systems

Volume 20 (2020)

Number 1

Whole-genome phylogeny of giant viruses by Fourier transform

Pages: 61 – 76



Changchuan Yin (Department of Mathematics, Statistics, and Computer Science, University of Illinois, Chicago, Il., U.S.A.)

Stephen S.-T. Yau (Department of Mathematical Sciences, Tsinghua University, Beijing, China)


Dozens of giant viruses have been surprisingly discovered since 2003. Giant viruses are notably larger than typical bacteria and have extremely large genomes that encode thousands of genes. Because the giant viruses have super-sized shapes and genome sizes, they are distinguished from classical viruses and bacteria. The evolutionary origin of the giant virus is still an open question. The current phylogenetic studies on giant virus use specific genes or proteins, and can not elucidate the origins of the giant viruses from the global genome perspective. In this study, we perform the wholegenome phylogenetic analysis of the giant viruses using the Fourier transform-based alignment-free method. The phylogenetic analysis shows that the typical giant virus Pandoravirus and tailed giant virus Tupanvirus are closely related to archaea. This new finding suggests that giant viruses may origin from archaea and supports the reductive model on the giant virus evolution.

This research was partially supported by the National Natural Sciences Foundation of China (31271408), by the Tsinghua University Education Foundation Fund (042202008), and by the Tsinghua University Start-up Research Fund (to S.S.‑T. Yau).

Received 20 October 2019

Published 17 April 2020