PXD008065-3

PXD008065 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Protein ID of ϕXacN1
Description	ϕXacN1 is a novel jumbo myovirus infecting the causative agent of Asian citrus canker, Xanthomonas citri. Its linear 384,670 bp double-stranded DNA genome encodes 592 predicted protein coding genes and shows 65,875 bp direct terminal repeats (DTRs), so far the longest DTRs among sequence phage genomes. The DTRs harbor 56 tRNA genes, corresponding to all 20 amino acids. This is the highest number of tRNA genes reported in a phage genome. Codon usage analyses revealed a propensity that the phage encoded tRNAs target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes, additional seven translation-related genes as well as a chaperonin gene found in the ϕXacN1 genome suggests an increased level of independence of phage replication on host molecular machinery and a wide host range. Consistently, ϕXacN1 showed a wider host range than other X. citri phages in an infection test against a panel of X. citri strains. Phylogenetic analyses revealed a clade of phages composed of ϕXacN1 and ten other jumbo phages showing an evolutionary stability in their large genome sizes.
HostingRepository	jPOST
AnnounceDate	2018-10-30
AnnouncementXML	Submission_2022-09-18_03:41:21.831.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miyako Nakano
SpeciesList	scientific name: cellular organisms; NCBI TaxID: 131567;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; unknown modification
Instrument	LTQ Orbitrap

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-30 01:49:05	ID requested
1	2018-10-29 08:00:10	announced
2	2021-02-04 16:51:55	announced	2021-02-04: Updated FTP location.
⏵ 3	2022-09-18 03:41:22	announced	2022-09-18: Updated FTP location.

Publication List

Yoshikawa G, Askora A, Blanc-Mathieu R, Kawasaki T, Li Y, Nakano M, Ogata H, Yamada T, Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes. Sci Rep, 8(1):4486(2018) [pubmed]

Yoshikawa G, Askora A, Blanc-Mathieu R, Kawasaki T, Li Y, Nakano M, Ogata H, Yamada T, Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes. Sci Rep, 8(1):4486(2018) [pubmed]

Keyword List

submitter keyword: Xanthomonas citri, ϕXacN1, jumbo phage,

submitter keyword: Xanthomonas citri, ϕXacN1, jumbo phage,

Contact List

Takashi Yamada
lab head
Miyako Nakano
contact affiliation	Hiroshima University
dataset submitter

Full Dataset Link List

jPOST dataset URI
Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST000339/

jPOST dataset URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST000339/