1
Scientific RepoRts | (2018) 8:4486 | DOI:10.1038/s41598-018-22239-3
www.nature.com/scientificreports
Xanthomonas citri jumbo phage
XacN1 exhibits a wide host range
and high complement of tRNA
genes
Genki Yoshikawa
1
, Ahmed Askora
2,3
, Romain Blanc-Mathieu
1
, Takeru Kawasaki
2
, Yanze Li
1
,
Miyako Nakano
2
, Hiroyuki Ogata
1
& Takashi Yamada
2,4
Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative
agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins
and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The
DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number
of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage
encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The
existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin
gene found in the XacN1 genome suggests a relative independence of phage replication on host
molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We conrmed
the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test
against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1
and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of
phages.
Tailed bacteriophages (phages) with genomes larger than 200 kbp are commonly named “jumbo phages”
1
. ey
usually show large virions, being capable of enclosing a larger genome than those of other smaller phages
2
.
Jumbo phages are classied into several evolutionarily unrelated clades
3,4
. e largest reported phage is Bacillus
phage G with a 160 nm capsid and a 453 nm tail. Phage G genome assembly is 497,513 bp long (accession num-
ber: NC_023719). Recently, a new group of jumbo phages has been recognized
5
. is group, named Rak2-like
phages, is composed of phages with a genome longer than 300 kbp including Klebsiella phage vB_KleM-RaK2
6
,
Escherichia phage PBECO 4
7
, Cronobacter phage vB_CsaM_GAP32
5
, Escherichia phage 121Q (accession number:
NC_025447), Klebsiella phage K64-1
8
, Enterobacteria phage vB_PcaM_CBB
9
, and Serratia phage BF
10
. Rak2-like
phages encode genes homologous to the “core genes” that are conserved among T4-related phages
6,11
. However,
given the level of sequence divergence, the lack of many of the core genes of T4-related phages, and a large num-
ber of genes that are shared within Rak2-like phages but not with T4-like phages, Rak2-like phages were proposed
to be only distantly related to T4-like phages
9
.
Xanthomonas citri (Gammaproteobacteria) is the causative agent of Asian citrus canker, one of the most
serious plant diseases, which can lead to significant economic losses worldwide
12,13
. X citri is a rod-shaped
Gram-negative bacterium with polar agella. e rst X. citri genome was determined for the strain 306, and
consists of a 5.18 Mbp chromosome (64.8% G + C) and two plasmids, pXAC33 (33.7 kbp, 60.8% G + C) and
pXAC64 (64.9 kbp, 61.4% G + C)
14
. In total, 4,429 protein-encoding genes and 62 RNA genes were identied in
the genome. Currently genome sequences are available for 40X. citri strains. Many X. citri genes were suggested
to be involved in the pathogenicity and virulence
15
. X. citri forms a biolm to attach its host. e biolm results
from the production of extracellular polysaccharide (xanthan) and ensures the virulence and epiphytic survival
1
Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan.
2
Department of Molecular
Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, 739-8530,
Japan.
3
Department of Microbiology, Faculty of Science, Zagazig University, 44519, Zagazig, Egypt.
4
Hiroshima Study
Center, The Open University of Japan, Hiroshima, 730-0053, Japan. Correspondence and requests for materials should
be addressed to H.O. (email: ogata@kuicr.kyoto-u.ac.jp) or T.Y. (email: tayamad@hiroshima-u.ac.jp)
Received: 28 November 2017
Accepted: 19 February 2018
Published: xx xx xxxx
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