A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

How novel phenotypes originate from conserved genes, processes, and
tissues remains a major question in biology. Research that sets out to
answer this question often focuses on the conserved genes and processes
involved, an approach that explicitly excludes the impact of genetic
elements that may be classified as clade-specific, even though many of
these genes are known to be important for novel, or clade-restricted,
phenotypes. This is especially true for understudied phyla such as
mollusks, where limited genomic and functional biology resources for
members of this phylum has long hindered assessments of genetic homology
and function. To address this gap, we constructed a chromosome-level
genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate
the expression of clade-specific genes across both novel and conserved
tissue types in this species. The final assembled and filtered Berghia
genome is comparable to other high quality mollusk genomes in terms of
size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly
contiguous. The proportion of upregulated, clade-specific genes varied
across tissues, but with no clear trend between the proportion of
clade-specific genes and the novelty of the tissue. However, more complex
tissue like the brain had the highest total number of upregulated,
clade-specific genes, though the ratio of upregulated clade-specific genes
to the total number of upregulated genes was low. Our results, when
combined with previous research on the impact of novel genes on phenotypic
evolution, highlight the fact that the complexity of the novel tissue or
behavior, the type of novelty, and the developmental timing of
evolutionary modifications will all influence how novel and conserved
genes interact to generate diversity.