Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus.
Journal
The plant genome
ISSN: 1940-3372
Titre abrégé: Plant Genome
Pays: United States
ID NLM: 101273919
Informations de publication
Date de publication:
Mar 2024
Mar 2024
Historique:
revised:
21
12
2023
received:
26
10
2023
accepted:
27
12
2023
pubmed:
20
1
2024
medline:
20
1
2024
entrez:
20
1
2024
Statut:
ppublish
Résumé
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5' site to an upstream 3' end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e20429Subventions
Organisme : Directorate for Biological Sciences
ID : DGE-1828820
Organisme : North Carolina State University
Organisme : U.S. Department of Education
ID : P200A210002
Organisme : Novo Nordisk Fonden
ID : NNF19SA0059362
Organisme : Biological and Environmental Research
ID : DE-SC0018269
Organisme : Southern Regional Educational Board Fellowship
Organisme : National Institute of Health
ID : 1T32GM133366-01
Informations de copyright
© 2024 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.
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