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Title:Combining short- and long-read transcriptomes for targeted enzyme discovery
Authors:ID Juteršek, Mojca (Author)
ID Petek, Marko (Author)
ID Baebler, Špela (Author)
Files:URL URL - Source URL, visit https://link.springer.com/protocol/10.1007/978-1-0716-4276-4_4
 
.pdf PDF - Presentation file, download (1,00 MB)
MD5: A57AE1B9B964888442866FFDB826A5C6
 
Language:English
Typology:1.16 - Independent Scientific Component Part or a Chapter in a Monograph
Organization:Logo NIB - National Institute of Biology
Abstract:The discovery of genes that code for a specific enzymatic activity is important in various fields of life science and provides valuable biotechnological tools. Many genes that contribute to the production of secondary metabolites and specialized metabolic pathways are still not identified. Due to the great diversity of metabolic functions found in nature and their rapid evolutionary adaptation, we need precise but high-throughput approaches for a targeted search based on minimal prior knowledge. In this chapter, we describe a transcriptomics pipeline that was used to search for candidate genes coding for a specific enzymatic activity in a nonmodel species. We generated and combined short- and long-read transcriptomic data to obtain reliable full-length transcript sequences along with information on allelic variation, isoform expression, and condition-specific expression. Based on protein domain annotations of coding sequences and transcriptomic data, we selected candidate genes for activity assays. We provide detailed instructions for analysis and quality control steps in our pipeline that can be applied to other biological questions.
Keywords:genes, enzymatic activity, transcriptomics, metabolic pathways, allelic variation, isoform expression, biotechnological tools
Publication status:Submitted to the publisher
Publication version:Submitted Version
Publication date:04.02.2025
Year of publishing:2025
Number of pages:str. 69-99
PID:20.500.12556/DiRROS-21960 New window
UDC:577
DOI:10.1007/978-1-0716-4276-4_4 New window
COBISS.SI-ID:231281411 New window
Publication date in DiRROS:14.04.2025
Views:92
Downloads:32
Metadata:XML DC-XML DC-RDF
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JUTERŠEK, Mojca, PETEK, Marko and BAEBLER, Špela, 2025, Combining short- and long-read transcriptomes for targeted enzyme discovery. In : Gene expression analysis [online]. New York. p. 69–99. P. 69–99. [Accessed 20 April 2025]. Retrieved from: https://dirros.openscience.si/IzpisGradiva.php?lang=eng&id=21960
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Record is a part of a monograph

Title:Gene expression analysis : methods and protocols
Editors:Nalini Raghavachari, Natàlia Garcia-Reyero
Place of publishing:New York
Publisher:Humana Press
ISBN:978-1-0716-4275-7
COBISS.SI-ID:231270147 New window
Collection title:Methods in molecular biology
Collection numbering:2990
Collection ISSN:1064-3745

Document is financed by a project

Funder:RCUK - Research Council UK
Project number:BB/R021554/1
Name:17-ERACoBioTech - SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
Funder:ARIS - Slovenian Research and Innovation Agency
Project number:P4-0165-2022
Name:Biotehnologija in sistemska biologija rastlin

Licences

License:CC BY-NC-SA 4.0, Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
Link:http://creativecommons.org/licenses/by-nc-sa/4.0/
Description:A Creative Commons license that bans commercial use and requires the user to release any modified works under this license.

Secondary language

Language:Slovenian
Keywords:geni, encimska aktivnost, transkriptomika, presnovne poti, alelna variacija, izražanje izoforme, biotehnološka orodja, molekularna biologija, molekularna genetika


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