Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Parameters
• Project Information
• Funding

Nucella lapillus is an important player in rocky shore food chains and has been a focal organism of ecological and evolutionary studies for decades. Despite poor dispersal, they have a broad geographic range, which makes them an ideal species to examine isolation by distance and selection across environmental gradients.  A fully annotated genome of N. lapillus generated with Oxford Nanopore Techonology (ONT) sequencing at ∼37× coverage was described in detail in the following publication:

Ford, M. R., Vollmer, S. V., & Trussell, G. C. (2025). Annotated genome of the Atlantic dog whelk, Nucella lapillus. G3: Genes, Genomes, Genetics, 15(10). https://doi.org/10.1093/g3journal/jkaf182

This dataset provides information on the study and includes links to the genetic dataset at the National Center for Biotechnology Information (NCBI).

Sample collection and DNA extraction
An adult Nucella lapillus individual was collected in May 2024 from Nahant, MA (42.419732, −70.902171). The foot tissue was used for DNA extraction and isolation. 

High molecular weight (HMW) DNA was extracted from the foot via the CTAB method (1.4 M NaCL and 2% CTAB), followed by 3 chloroform reactions. The full extraction protocol is available on the project GitHub repository (https:// github.com/meghanclownfish/Nucella-lapillus-genome/tree/main/ 1_extraction). The HMW DNA was precipitated in ethanol (EtOH) and resuspended in Tris-EDTA buffer. The sample was further purified using a Genomic DNA Clean and Concentrator kit (gDCC-10, ZYMO Research, Irvine, CA, USA) per manufacturer’s instructions. Sample quality and concentration were assessed by running 2 μL of the sample on Nanodrop (Thermo Fisher Scientific, Singapore). A sample was deemed ready for sequencing if the 260/280 ratio was ∼1.9 and the 260/230 ratio fell between 2.0 and 2.2, following Sun et al. 2020.

Library prep and sequencing
N. lapillus long reads were sequenced using ONT platforms and libraries were prepared with the ONT Ligation sequencing kit (SQK-LSK114, ONT, Oxford, UK) and NEBNext Companion Module (E7180S NEB). Standard manufacturer's protocol was implemented with a few exceptions (see Ford et al., 2025 for details). Sequencing was done on a PromithION. Six flow cells in total were used to generate 103,553,219,099 bp raw data. PromethION flow cells (FLO-PRO114M) were primed and loaded per the standard manufacturer's protocol. To increase the yield of each flow cell, runs were paused and flushed using the EXP-WSH004 (ONT) kit and reloaded. High quality base calling was performed with Dorado 0.7.1 (ONT).

Genome size and heterozygosity
Genome size was estimated using JELLYFISH v2.2.10 to count canonical 41-mers from high quality ONT reads (min quality: 5) and computed a histogram of k-mer occurrence (Marcais and Kingsford 2011). The histogram was used to estimate heterozygosity with GenomeScope (Ranallo-Benavidez et al. 2020).

Assembly and annotation
Briefly, we assembled the genome using all reads of 2kb in length or greater with  Hifiasm (0.25.0-r726).  BlobTools2 (v4.4.0, Challis et al. 2020) was used to visually assess the assembly and filter contigs. RepeatModeler (v2.0.6, Flynn et al. 2020) and RepeatMasker (Smit et al.)  identified and soft-masked repetitive regions in the genome. RNASeq data was mapped to the soft-masked genome with HISAT2. This information, along with a custom protein database, was supplied as evidence for Braker3 . TSEBRA was used to merge Braker outputs. Functional annotation was carried out with InterProScan and Funannotate. For full details, please see Ford et al. (2025) paper.

NSF Award Abstract:
Over the past two decades, the Gulf of Maine has experienced unprecedented warming that, among other things, has further enabled the invasive green crab to expand its range in rocky shore habitats. The adverse ecological impacts of this invasive predator have been documented worldwide. This study examines how geographic variation in the capacity of two common prey species to respond to the combination of this predator and warming ocean temperatures can shape prey feeding and performance and impact community structure and dynamics. Hence, this research enhances understanding of the evolution of phenotypes, their plasticity, and the nature of adaptation and its role in eco-evolutionary dynamics. More broadly, it informs understanding of how organisms and marine communities may respond to future environmental change. In addition, this project makes contributions to the STEM pipeline by providing middle and high school, undergraduate, and graduate students with cross-disciplinary training in evolutionary and community ecology. In collaboration with an institutional outreach program, the investigator is also developing web-based multimedia projects and teacher resource materials based on this research.

A central principle in ecology is that species residing in the middle of food chains must balance the benefits of eating with the risk of being eaten by their predators. Solving this foraging-predation risk trade-off often involves plasticity in prey traits with consequences for the evolution of adaptation and species interactions that drive community-level processes. Hence, the foraging-predation risk trade-off provides a powerful conceptual framework that links evolutionary and community ecology. Yet at the same time, other environmental stressors like temperature can shape this trade-off, adding complexity that makes it difficult to predict the capacity of organisms to adapt to environmental change and the consequences for communities. The investigator is conducting this study in rocky shore habitats of the Gulf of Maine (GOM) which have long been influenced by strong latitudinal temperature gradients and non-native species invasions. The overarching hypothesis is that predation risk and temperature are factors shaping geographic variation in plasticity and adaptation, with consequences for individuals, populations, and communities. First, the investigator is conducting field experiments to document geographic variation in the trait plasticity of two common prey species in the green crab's diet. Second, he is using reciprocal transplant experiments to examine trait plasticity in response to risk and water temperature, generating data to compare with similar experiments conducted in the late 90s prior to recent ocean warming and expansion in range of green crabs. Third, he is conducting a laboratory common garden experiment to evaluate the effects of risk and water temperature on trait plasticity. Finally, he is using reciprocal transplant experiments in the field to understand the interactive effects of risk and water temperature on prey foraging rates and the abundance of a species that plays an important role in intertidal community structure and dynamics.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.