Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution.

Authors:
Zhang S; Yang C; Qiu Y; Liao R; Xuan Z and 10 more

Journal:
Virus Evol

Publication Year: 2024

DOI:
10.1093/ve/veae004

PMCID:
PMC10868557

PMID:
38361819

Journal Information

Full Title: Virus Evol

Abbreviation: Virus Evol

Country: Unknown

Publisher: Unknown

Language: N/A

Publication Details

Subject Category: Virology

Available in Europe PMC: Yes

Available in PMC: Yes

PDF Available: No

Transparency Score
5/6
83.3% Transparent
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Evidence found in paper:

"in this study we reanalysed the corresponding sequencing data (accession no: srr11364892) available in the sra database.; tpnrbv-ca1_rna5 is inferred as a new ors omitted previously as an equivalent rna was identified for the tpnrbv by reanalysis of the available original sra dataset (srr6459579).; data availability all data obtained from this study are available in the main text the supporting information and the ncbi databases with genbank accession numbers of ol344024-ol344048 bk061344-bk061350 op807958-op807963 om687521-om687525 mn915109-mn915111 and or532447-or532448 and with bioproject and sra accession numbers recorded in supplementary table s2 . as a result a longer contig of 3243 nt was obtained surpassing the previous3173 nt ( supplementary data s1 table s3 ).; viral genomes of the order martellivirales (taxonomy id: 2732544) were obtained from the ncbi databases and the rdrp sequences were identified using the batch cd-search server ( https://www ncbi nlm nih gov/structure/bwrpsb/bwrpsb cgi ) and extracted by the strawberry perl (5 32 1 1) using a script ( supplementary data s2 ).; all of the rdrps were aligned by mafft v7 471 ( ) using the e-ins-i algorithm and then trimmed by trimal 1 2rev57 ( ) with the automated1 algorithm to remove poorly aligned regions ( supplementary data s3 ). data availability all data obtained from this study are available in the main text the supporting information and the ncbi databases with genbank accession numbers of ol344024"

Evidence found in paper:

"four distinct iblast tools were developed and made available in an online repertory ( https://github com/qq371260/iterative-blast-v 1 0 ) including utr-iblastn ( fig 2 ) iblastx iblastp and iblastn/itblastx."

Evidence found in paper:

"Conflict of interest: The authors declare no competing interests."

Evidence found in paper:

"We would like to express genuine appreciation to the producers of the original data publicly available in NCBI databases and used in this work, who greatly contribute to our secondary analyses. This research was supported by National Natural Science Foundation of China (32370005), Chongqing Science Funds for Distinguished Young Scientists (CSTB2022NSCQ-JQX0027), Innovation Research 2035 Pilot Plan of Southwest University (SWU-XDPY22002, SWU-5331000008), Special Fund for Youth Team of Southwest University (SWU-XJLJ202310), Chongqing Talents of Exceptional Young Talents Project (cstc2022ycjh-bgzxm0143), Earmarked Fund for China Agriculture Research System (CARS-26-05B), Chongqing Postgraduate Research and Innovation Project (CYB21133), and Guangxi Natural Science Foundation for Young Scientists (2023GXNSFBA026285). We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript."

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Last Updated: Aug 05, 2025