Evolution | Thomas Blein

Conservation and evolution of lncRNAs

Tue, 03 Aug 2021 18:20:46 +0200

Unlike protein-coding genes, lncRNAs show limited sequence conservation, which makes orthology assignment and functional transfer difficult. We investigate alternative levels of conservation—expression, genomic position, secondary structure and function—to understand how lncRNAs evolve and contribute to plant adaptation. Comparing two Arabidopsis accessions under phosphate starvation, we found that lncRNAs are far more variable between accessions than coding genes, even when their DNA sequence is conserved, and identified ecotype-specific lncRNAs linked to root responses. At the genome-wide level, we analysed the evolutionary age, sequence conservation and transcriptional regulation of Arabidopsis lincRNAs, revealing a root-specific transcription-factor network and distinct selective pressures across lincRNA age classes.

Related publications

— Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation
— Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots

Conservation can also be functional rather than sequence-based. APOLO and the human UPAT lncRNA share neither sequence nor structure, yet both are recognised by the conserved VIM1/LHP1 machinery in plants, illustrating how lncRNA function can be preserved through conserved protein interactions. We have synthesised these findings in reviews on lncRNA conservation and on their contribution to environmental adaptation.

Related publications

— The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants
— From environmental responses to adaptation: the roles of plant lncRNAs

More broadly, the same evolutionary question applies to other multigenic and regulatory loci. In apple, we contributed to a haplotype-resolved analysis of the S-locus showing that long-term balancing selection preserves multigenic S-haplotype architectures despite extensive structural divergence and transposable-element accumulation. This broader perspective will help us connect lncRNA evolution to the evolution of plant genomes, regulatory sequences and adaptive traits.

Related publications

— Innovation within stability: balancing selection preserves multigenic S-haplotype architecture in apple

Leaf development and morphogenesis

Thu, 01 Oct 2026 00:00:00 +0000

Leaves are a powerful system to understand how organs acquire their shape. We study the genetic and hormonal control of leaf margin dissection, boundary formation and leaflet individualisation, with a focus on the NAM/CUC transcription factors, miR164 and auxin. We showed that the balance between MIR164A and CUC2 controls leaf margin serration, that miR164, CUC genes and LATERAL SUPPRESSOR interact to control axillary meristem formation, and that NAM/CUC boundary genes promote leaflet formation in distantly related eudicots.

Related publications

— The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis
— Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana
— A conserved molecular framework for compound leaf development

These findings led us to propose that leaf dissection relies on the interplay between boundary domains, KNOX gene activity and auxin gradients. We further reviewed the genetic and molecular networks controlling leaf polarity and the comparison between simple and compound leaves, and analysed the evolution and specific roles of CUC1–CUC3 during Arabidopsis leaf serration.

Related publications

— Leaf development: what it needs to be complex
— A conserved mechanism at the base of leaf dissection
— Leaving the meristem behind: the genetic and molecular control of leaf patterning and morphogenesis
— Evolution and diverse roles of the CUP-SHAPED COTYLEDON genes in Arabidopsis leaf development

More recently, we combined genetics and morphometrics to show that mutations in different pathways can act synergistically to alter leaf dissection, and that GDP-L-fucose is required for boundary definition and differential growth at the leaf margin. Together, this work connects molecular boundary formation to the evolution and diversification of leaf shape.

Related publications

— Combinations of Mutations Sufficient to Alter Arabidopsis Leaf Dissection
— GDP-L-fucose is required for boundary definition in plants

Evolution and diverse roles of the CUP-SHAPED COTYLEDON genes in Arabidopsis leaf development

Sat, 01 Jan 2011 00:00:00 +0000

[A conserved mechanism at the base of leaf dissection]

Sun, 01 Nov 2009 00:00:00 +0000