Krüppel-like factor/specificity protein evolution in the Spiralia and the implications for cephalopod visual system novelties

Kyle J Mcculloch,Kristen M Koenig

doi:10.1098/rspb.2020.2055

Abstract

The cephalopod visual system is an exquisite example of convergence in biological complexity. However, we have little understanding of the genetic and molecular mechanisms underpinning its elaboration. The generation of new genetic material is considered a significant contributor to the evolution of biological novelty. We sought to understand if this mechanism may be contributing to cephalopod-specific visual system novelties. Specifically, we identified duplications in the Krüppel-like factor/specificity protein (KLF/SP) sub-family of C2H2 zinc-finger transcription factors in the squid Doryteuthis pealeii. We cloned and analysed gene expression of the KLF/SP family, including two paralogs of the DpSP6-9 gene. These duplicates showed overlapping expression domains but one paralog showed unique expression in the developing squid lens, suggesting a neofunctionalization of DpSP6-9a. To better understand this neofunctionalization, we performed a thorough phylogenetic analysis of SP6-9 orthologues in the Spiralia. We find multiple duplications and losses of the SP6-9 gene throughout spiralian lineages and at least one cephalopod-specific duplication. This work supports the hypothesis that gene duplication and neofunctionalization contribute to novel traits like the cephalopod image-forming eye and to the diversity found within Spiralia.

Highlights

The generation of new genetic material subject to mutation is considered a significant contributor to the evolution of biological novelty [1]
To better understand the evolutionary history of one of these cephalopod duplications we focused on the SP6-9 homologues, which are enriched in the RNA-seq time course of the eye and optic lobe development
Our results show that the SP6-9 gene has undergone multiple duplications and losses within Spiralia including a cephalopod-specific duplication

Summary

Introduction

The generation of new genetic material subject to mutation is considered a significant contributor to the evolution of biological novelty [1]. To confirm orthology of our cephalopod sequences, we generated spiralian-specific SP6-9 trees This sub-family shares much more sequence identity within Spiralia, when possible, alignments of full-length amino acid sequences were made to construct ML and Bayesian trees (electronic supplementary material, figure S3). The second member of the SP gene family assessed, SP5, has dynamic expression in D. pealeii including high expression in the optic lobe at stage 23 (electronic supplementary material, figure S6). Our spiralian SP6-9 trees did not give strong support for deeper nodes, so we assembled additional transcriptomes with a particular focus on basal branching annelid and molluscan lineages, and generated Bayesian SP6-9 trees specific to each group (electronic supplementary material, figures S7 and S8). Further research in this major branch of the animal tree will shed light on whether these patterns are in part responsible for the vast morphological diversity found in this group

Conclusion

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