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Treffer: Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.

Title:
Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.
Authors:
Pronozin AY; Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Russia.; Kurchatov Center for Genome Research, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Russia., Shmakov NA; Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Russia.; Kurchatov Center for Genome Research, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Russia.; Faculty of Natural Sciences, Novosibirsk State University, 630090, Novosibirsk, Russia., Afonnikov DA; Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Russia. ada@bionet.nsc.ru.; Kurchatov Center for Genome Research, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Russia. ada@bionet.nsc.ru.; Faculty of Natural Sciences, Novosibirsk State University, 630090, Novosibirsk, Russia. ada@bionet.nsc.ru.
Source:
BMC genomics [BMC Genomics] 2026 Jan 03; Vol. 27 (1), pp. 1. Date of Electronic Publication: 2026 Jan 03.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
Imprint Name(s):
Original Publication: London : BioMed Central, [2000-
MeSH Terms:
Zea mays*/genetics , RNA, Long Noncoding*/genetics , Transcriptome* , Genetic Variation*, RNA, Messenger/genetics ; Evolution, Molecular ; Gene Expression Profiling
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Grant Information:
agreement No 075-15-2025-516 Ministry of Science and Higher Education of the Russian Federation
Contributed Indexing:
Keywords: Conservation; Evolution; Long noncoding RNA; MRNA; Maize inbred lines; Pan-transcriptome; SNP
Substance Nomenclature:
0 (RNA, Long Noncoding)
0 (RNA, Messenger)
Entry Date(s):
Date Created: 20260104 Date Completed: 20260104 Latest Revision: 20260107
Update Code:
20260130
PubMed Central ID:
PMC12764133
DOI:
10.1186/s12864-025-12242-0
PMID:
41484696
Database:
MEDLINE

Weitere Informationen

Background: Long non-coding RNAs (lncRNAs) constitute a substantial portion of the plant transcriptomes and performs important functions in numerous molecular, regulatory, growth and developmental processes and stress responses. However, functional characteristics supported by experimental evaluation are known only for a small part of lncRNAs. In this regard, evolutionary and comparative analysis of lncRNA sequences can provide additional information about the functional role of these molecules.
Results: Analysis of RNA-seq libraries from 503 maize inbred lines obtained by Hirsch et al. (2014) enabled the assessment of sequence diversity and evolutionary patterns of maize lncRNAs within the pan-transcriptome framework and their comparison with analogous mRNA characteristics. The lncRNA pan-transcriptome comprises a greater number of representative sequences (595,198), compared to mRNA pan-transcriptome (245,436), smaller fraction of core and shell parts and larger cloud component (52.5% vs 11%). However, both pan-transcriptomes are closed according to estimates of the power-law parameters. Nucleotide diversity of the lncRNAs significantly higher compared to mRNAs. Moreover, nucleotide substitution rates estimates for coding and non-coding sequences demonstrated systematic increase of the gamma distribution shape parameter α in the order α(K<subscript>a</subscript>) < α(K<subscript>s</subscript>) < α(K<subscript>n</subscript>) across all pan-transcriptome components (core, shell, cloud). Comparison of evolutionary characteristics also demonstrated that antisense lncRNAs are the most conserved in terms of both nucleotide substitution rates and their representation in the core; intronic lncRNAs display the highest mutation rate, while intergenic lncRNAs exhibit the greatest sequence repertoire diversity and highest line specificity.
Conclusions: These results allowed to evaluate the diversity of lncRNAS from the pan-transcriptomic point of view and supported their high lineage-specificity and sequence variation across maize inbred lines in comparison to mRNA sequences.
(© 2025. The Author(s).)

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing Interests: The authors declare no competing interests.