Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis

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.

Keywords: Littorina; chromosomal inversion; chromosome-level assembly; ecotype formation; gastropod; speciation.

Fig. 1.

Littorina saxatilis “crab” ecotype photograph and Hi-C map. A) Photograph of Littorina saxatilis “crab” ecotype on Swedish shore (Photo: Patrik Larsson). B) Hi-C contact map of the new Littorina saxatilis assembly after manual curation, visualized in HiGlass. Chromosomes are arranged in size order from left to right and top to bottom.

Fig. 2.

Genome assembly of Littorina saxatilis: metrics. A) BlobToolKit Snailplot shows N50 metrics. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 1,256,336,603 bp assembly. The distribution of scaffold lengths is shown in dark gray with the plot radius scaled to the longest scaffold present in the assembly (111,777,080 bp, the smallest of the three arcs, also shown in red). Next two sectors in size (orange and pale-orange arcs) show the N50 and N90 scaffold lengths (67,515,031 and 44,900,717 bp), respectively. The pale gray spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The dark-blue and pale-blue area around the outside of the plot shows the distribution of GC, AT, and N percentages in the same bins as the inner plot. B) BUSCO scores for the genome and predicted proteins for the Eukaryota, Metazoa, and Mollusca datasets.