Chromosome-level genome assembly of the cosmopolitan diatom Skeletonema costatum provides insights into ecological adaptation

Abstract

The cosmopolitan diatom species Skeletonema costatum is an ecologically important dominant phytoplankton frequently found in the coastal estuarine and marine waters, and often causes harmful algae blooms. Despite of its critical ecological importance, chromosome-level genome assemble is still unavailable, hindering in-depth understanding of their evolution and environmental adaption. Here, we report a chromosome-level genome assembly for the marine diatom species S. costatum. The assembled genome size was 136.49 Mb, with a contig N50 of 302 Kb and 95.30 % of the reads anchored into 23 pseudo-chromosomes with a scaffold N50 of 6.19 Mb. A total of 28,321 protein-coding genes were predicted, with 86.03 % being functional annotated. The BUSCO assessment of genome assembly and genome annotation were both above 90 %. Phylogenetic analysis showed the expected topology, with S. costatum and its closely related species S. marinoi diverged from their common ancestor around 22.6 million years ago. The genome size of S. costatum is comparatively larger than those of its closely related diatoms, due mostly to its higher transposable element contents and larger number of proteincoding genes. Collinearity analysis revealed strong collinearity between S. costatum and other Skeletonema with most chromosomes showing clear one-to-one correspondences. A larger family of nine copies of the cryptochrome genes that function as blue light photoreceptors were identified in S. costatum, which could contribute its ecological success. The availability of the high-quality chromosome-level genome assembly for S. costatum represents a valuable resource that may facilitate comparative genomics for revealing important ecological clues and gene families, and future genetics and environmental studies among Skeletonema species.