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)..., Sample preparation and genome sequencing
We isolated one Berghia juvenile from the Lyons lab culture prior to mating to minimize genomic contamination. While isolated, we fed the animal ~½ of a medium Exaiptasia diaphana (defined by Taraporevala et al. 2022) each day for 34 days. We then starved the animal for 44 days prior to shipping. To minimize residual food in the gut diverticula, cerata were removed with forceps and the remaining body was blotted on a kimwipe to remove excess water, then the animal was placed in a cryotube and flash frozen in liquid nitrogen and stored at -80 until shipping to Dovetail Genomics (now Catana Bio, Scotts Valley, CA). Technicians at Dovetail Genomics used an input of ~101mg into a slow CTAB protocol, which yielded 12.1µg using the Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) High Sensitivity Kit. They then used a Mini Column for clean up and resuspended the pellet in 75 µl TE. They then quantified DNA samples using the Qubit. They cons..., , This README.txt file was generated on 2023-08-01 by Jessica Goodheart

GENERAL INFORMATION

1. Title of Dataset: Data from: Phylogenomics suggests that larvae are ancestral in polyclads, but not homologous to the trochophore.
2. Author Information
Corresponding Investigator
Name: Dr Jessica A Goodheart
Institution: Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
Email: [e-mail]

Co-investigator 1
Name: Robin A. Rio
Institution: Bioengineering Department, Stanford University, Stanford, CA, USA

Co-investigator 2
Name: Neville F. Taraporevala
Institution: Quinney College of Natural Resources, Utah State University, Logan, UT, USA

Co-investigator 3
Name: Rose A. Fiorenza
Institution: Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA

Co-investigator 4
Name: Seth R. Barnes
Institution: Scripps Institution of Oceanography, Univers...