The role of heterochronic gene expression and regulatory architecture in early developmental divergence

Abstract

New developmental programs can evolve through adaptive changes to gene expression. The annelidS. benedictihas a developmental dimorphism, which provides a unique intraspecific framework for understanding the earliest genetic changes that take place during developmental divergence. Using comparative RNAseq through ontogeny, we find that only a small proportion of genes are differentially expressed at any time, despite major differences in larval development and life-history. These genes shift expression profiles across morphs by either turning off any expression in one morph or changing the timing or amount of gene expression. We directly connect the contributions of these mechanisms to differences in developmental processes. We examine F1offspring —using reciprocal crosses— to determine maternal mRNA inheritance and the regulatory architecture of gene expression. These results highlight the importance of both novel gene expression and heterochronic shifts in developmental evolution, as well as thetrans-acting regulatory factors in initiating divergence.

Comparative Hox genes expression within the dimorphic annelidStreblospio benedictireveals patterning variation during development

“…Most significant differences in expression are at the blastula stage, with later stages having largely conserved Hox gene expression. This is consistent with other spiralian patterns of gene expression, where typically there is more divergence (across species) or variation (within species) in gene expression in early embryogenesis that converge around gastrulation (Martín-Zamora et al 2023;Harry and Zakas, 2023).…”

“…Our Hox gene analysis clearly demonstrates that in terms of body plan formation, the former stages ('early-planktotrophic' larvae and 'swimming lecithotrophic' larvae) are the most equivalent despite the size and morphological differences. We have also recently completed an extensive gene expression analysis over larval development of the two morphs (Harry and Zakas, 2023), which confirms that these are equivalent stages. Because the planktotrophic larvae have a longer and more differentiated larval phase covering two time points, where the lecithotrophic larvae have one, it leads to destinations of minor heterochronies.…”

“…RNAseq reads from six developmental stages (Harry and Zakas, 2023) of both planktotrophic and lecithotrophic offspring were assembled with long-read (iso-seq CCS reads) guidance using the Trinity assembler (Grabherr et al, 2011). Hox gene transcripts were identified from the resulting contigs using tblastn (e-value cutoff 1*10^-30) from the BLAST command line tools (Altschul et al, 1990) and a set of Hox gene queries taken from other related taxa/species (Supplementary DataSheet).…”

“…While we can visualize the onset and expression levels of the Hox genes using HCR in situ hybridization, we also wanted to compare Hox gene expression using a RNAseq approach. We sequenced RNA from three developmental stages across both types: 16-cell, blastula, gastrula, 2-eye larvae, swimming larvae which are ~5-7 dpf (early-planktotrophic larvae and early swimming lecithotrophic larvae that we manually removed from the mother's brood pouch), and 1-week old larvae which are seven dpf ('late-planktotrophic' larvae and 'swimming lecithotrophic' larvae; Harry and Zakas, 2023;Figs. 1, 7).…”

“…Hox gene expression data was generated using RNAseq (Harry and Zakas, 2023). Each developmental stage consisted of three to five biological replicates.…”