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. 2024 Apr 20;11(1):403.
doi: 10.1038/s41597-024-03238-8.

Chromosome-level genome assembly of marine diatom Skeletonema tropicum

Shuya Liu  1   2   3 , Nansheng Chen  4   5   6   7
Affiliations

Chromosome-level genome assembly of marine diatom Skeletonema tropicum

Shuya Liu et al. Sci Data. .

Abstract

Skeletonema tropicum is a marine diatom of the genus Skeletonema that also includes many well-known species including S. marinoi. S. tropicum is a high temperature preferring species thriving in tropical ocean regions or temperate ocean regions during summer-autumn. However, mechanisms of ecological adaptation of S. tropicum remain poorly understood due partially to the lack of a high-quality whole genome assembly. Here, we report the first high-quality chromosome-scale genome assembly for S. tropicum, using cutting-edge technologies including PacBio single molecular sequencing and high-throughput chromatin conformation capture. The assembled genome has a size of 78.78 Mb with a scaffold N50 of 3.17 Mb, anchored to 23 pseudo-chromosomes. In total, 20,613 protein-coding genes were predicted, of which 17,757 (86.14%) genes were functionally annotated. Collinearity analysis of the genomes of S. tropicum and S. marinoi revealed that these two genomes were highly homologous. This chromosome-level genome assembly of S. tropicum provides a valuable genomic platform for comparative analysis of mechanisms of ecological adaption.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Construction of the first chromosome-level genome assembly of S. tropicum. (A). Circos plot of the S. tropicum genome assembly. From outer to inner layers were chromosomes (a), repetitive elements (b), gene densities (c), GC contents (d), respectively. The inner most part layer was the collinear gene pair blocks. (B). Hi-C intra-chromosomal contact map of the genome assembly in S. tropicum.
Fig. 2
Fig. 2
The composition of gene elements in the S. tropicum and other closely related species. (A) Distribution of gene length. (B) Distribution of exon number. (C) Distribution of intron length. (D) Distribution of exon length.
Fig. 3
Fig. 3
The venn diagram of PCG annotation of S. tropicum to five databases: NR, InterPro, KEGG, SwissProt and KOG.
Fig. 4
Fig. 4
The distribution of GC ratio and sequencing depth. Histograms on the top and right show the frequency distribution of GC ratio and sequencing depth, respectively.
Fig. 5
Fig. 5
Collinearity analysis between S. tropicum and S. marinoi in the view of amino acid sequences (A) and DNA sequences (B).
See this image and copyright information in PMC

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