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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #411351
Research Project: Genomes to Phenomes in Beef Cattle Research

Location: Genetics and Animal Breeding

Title: Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis

Author
item DE JODE, AURELIEN - University Of Gothenburg
item FARIA, RUI - Universidade Do Porto
item FORMENTI, GIULIO - Rockefeller University
item SIMS, YING - Wellcome Trust Sanger Institute
item Smith, Timothy
item TRACEY, ALAN - Wellcome Trust Sanger Institute
item WOOD, JOHNATHAN - Wellcome Trust Sanger Institute
item ZAGRODZKA, ZUZANNA - University Of Sheffield
item JOHANNESSON, KERSTIN - University Of Gothenburg
item BUTLIN, ROGER - University Of Gothenburg
item LEDER, ERICA - University Of Gothenburg

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/29/2024
Publication Date: 4/2/2024
Citation: De Jode, A., Faria, R., Formenti, G., Sims, Y., Smith, T.P., Tracey, A., Wood, J.M.D., Zagrodzka, Z.B., Johannesson, K., Butlin, R.K., Leder, E.H. 2024. Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis. Genome Biology and Evolution. 16(4). Article evae076. https://doi.org/10.1093/gbe/evae076.
DOI: https://doi.org/10.1093/gbe/evae076

Interpretive Summary: A genome assembly of a sea snail called the "rough periwinkle", scientific name Littorina Saxatilis, was constructed and analyzed. This snail inhabits the intertidal region of coastlines, and is an interesting model system for studying how species arise because of the numerous different types that have evolved in different microenvironments. Changes in the genome among these "ecotypes" were identified in the study. The new reference genome will support more in-depth analysis and comparison of the genomes among the ecotypes and provide new information about how evolution at the level of genome arrangement occurs in marine organisms.

Technical Abstract: The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35 Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44 kb), and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here, we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1% of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation.