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Post a Comment Rna-seq contamination as a metatranscriptomic data for screening of plant pests and symbionts
- Authors: Zykin P.A.1, Andreeva E.A.1,2, Tsvetkova N.V.1, Bulanov A.N.2, Voylokov A.V.2
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Affiliations:
- Saint Petersburg State University
- Institute of General Genetics
- Issue: Vol 23, No 3 (2025)
- Pages: 235-247
- Section: Ecosystems metagenomics
- URL: https://journal-vniispk.ru/ecolgenet/article/view/361849
- DOI: https://doi.org/10.17816/ecogen642484
- EDN: https://elibrary.ru/RMHFWD
- ID: 361849
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Abstract
Background: Transcriptome sequencing data can contain up to 30 % contaminating reads. These may originate from laboratory contamination or biologically relevant sources, amenable to metatranscriptomics analysis.
Aim: To evaluate the utility of contaminating reads for large-scale screening of plant pests and symbionts.
Methods: We analyzed the data of RNA-seq experiments of rye (Secale cereale L.) including five in-house accessions and 50 public datasets from NCBI SRA archive. Reads with good mapping to the rye genome were filtered out, retaining putative contaminats for downstream analysis.
Results: After removing laboratory contaminants, we compared aphids, symbiotic fungi, bacteria and viruses across accessions. Symbiome-derived reads were reproducible in biological replicates and varied by location, condition, and plant species, enabling post-hoc metatranscriptomic analysis.
Conclusions: Contaminating reads correlated with field-observed species or expected symbionts. Distribution patterns across accessions support repurposing existing and future sequencing data to screen for plant pests, monitor symbiotic organisms, and plan eradication strategies amid global climate change.
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##article.viewOnOriginalSite##About the authors
Pavel A. Zykin
Saint Petersburg State University
Email: pavel.zykin@spbu.ru
ORCID iD: 0000-0003-1624-6163
SPIN-code: 2730-5890
Cand. Sci. (Biology)
Russian Federation, 7–9 Universitetskaya emb., Saint Petersburg, 199034Elena A. Andreeva
Saint Petersburg State University; Institute of General Genetics
Email: e.a.andreeva@spbu.ru
ORCID iD: 0000-0002-9326-3170
SPIN-code: 7269-8240
Cand. Sci. (Biology)
Russian Federation, 7–9 Universitetskaya emb., Saint Petersburg, 199034; 3 Gubkina st, Moscow, 117971Natalia V. Tsvetkova
Saint Petersburg State University
Email: n.tswetkowa@spbu.ru
ORCID iD: 0000-0002-7353-1107
SPIN-code: 1687-5757
Cand. Sci. (Biology)
Russian Federation, 7–9 Universitetskaya emb., Saint Petersburg, 199034Andrey N. Bulanov
Institute of General Genetics
Email: an.bulanov20002014@gmail.com
ORCID iD: 0009-0003-8092-9978
SPIN-code: 3791-9700
Russian Federation, 3 Gubkina st, Moscow, 117971
Anatoly V. Voylokov
Institute of General Genetics
Author for correspondence.
Email: av_voylokov@mail.ru
ORCID iD: 0000-0003-3423-8511
Dr. Sci. (Biology)
Russian Federation, 3 Gubkina st, Moscow, 117971References
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