TY - JOUR

T1 - Diversity of lncRNAs in the pan-transcriptome of maize inbred lines

AU - Pronozin, Artem Yu

AU - Shmakov, Nikolai A.

AU - Afonnikov, Dmitry A.

N1 - Pronozin, A.Y., Shmakov, N.A. & Afonnikov, D.A. Diversity of lncRNAs in the pan-transcriptome of maize inbred lines. BMC Genomics 27, 1 (2026). https://doi.org/10.1186/s12864-025-12242-0 This work was supported by the Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical programme for genetic technologies development for 2019–2030, agreement № 075–15-2025–516).

PY - 2026/1/3

Y1 - 2026/1/3

N2 - 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(Ka) < α(Ks) < α(Kn) 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.

AB - 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(Ka) < α(Ks) < α(Kn) 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.

KW - Conservation

KW - Evolution

KW - Long noncoding RNA

KW - MRNA

KW - Maize inbred lines

KW - Pan-transcriptome

KW - SNP

UR - https://www.scopus.com/pages/publications/105026354207

UR - https://www.mendeley.com/catalogue/d8e3704c-6d22-3605-b249-9061aef6f7e1/

U2 - 10.1186/s12864-025-12242-0

DO - 10.1186/s12864-025-12242-0

M3 - Article

C2 - 41484696

VL - 27

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

ER -