# Long-read sequencing reveals increased isoform diversity in key transcription factor effectors of intercellular signalling at the invertebrate-vertebrate transition

## TL;DR

Long-read sequencing shows that vertebrates have more diverse isoforms of key signaling transcription factors compared to invertebrates, possibly aiding vertebrate evolution.

## Contribution

Quantifies increased isoform diversity in transcription factors of key signaling pathways at the invertebrate-vertebrate transition.

## Key findings

- Transcript isoform diversity increases significantly in TCF/LEF, GLI, and SMAD proteins during vertebrate evolution.
- The increase is specific to main transcription factor effectors of Wnt/β-catenin, Hh, and BMP pathways.
- This diversity may have contributed to vertebrate evolutionary complexity.

## Abstract

Several intercellular signalling pathways (including wingless (Wnt), hedgehog (Hh), and bone morphogenetic protein (BMP)) are used repeatedly in animals throughout development and evolution and are also frequent targets for disease-associated disruptions. We have previously shown that the major transcriptional effectors of β-catenin-dependent Wnt signalling, the TCF/LEF proteins, in contrast to other pathway components, have a higher gene number and isoform diversity in vertebrates versus invertebrates, but this increased diversity has only been poorly quantified. Considering that isoform diversity correlates with organism complexity, any increase in major signalling effectors is likely to have made a significant contribution to vertebrate evolution.

Using de novo long-read transcriptomes, we compared isoform number per gene for the chordates Ciona intestinalis, Lampetra planeri and Xenopus tropicalis, thus encompassing the invertebrate sister group to vertebrates, as well as a cyclostome and a gnathostome vertebrate. We find a significant increase in the number of transcript isoforms per gene expressed during embryo development and organogenesis at the invertebrate-to-vertebrate transition, specifically for the main transcription factor effectors of the Wnt/β-catenin, Hh and BMP pathways, i.e. TCF/LEF, GLI and SMAD.

Our results implicate an increase in isoform diversity of the transcription factors of major intercellular signalling pathways as having a disproportionate role in the evolutionary origin and diversification of vertebrates.

The online version contains supplementary material available at 10.1186/s12915-026-02522-w.