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. 2024 Apr 1;31(2):dsae007.
doi: 10.1093/dnares/dsae007.

High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis

Zhichao Huang  1 , Qi Liu  2 , Xiaoqi Zeng  1   3 , Gang Ni  1
Affiliations

High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis

Zhichao Huang et al. DNA Res. .

Abstract

Asterias amurensis, a starfish species that is native to countries such as China and Japan, as well as non-native regions like Australia, has raised serious concerns in terms of its impact on ecology and economy. To gain a better understanding of its population genomics and dynamics, we successfully assembled a high-quality chromosome-level genome of A. amurensis using PacBio and Hi-C sequencing technologies. A total of 87 scaffolds assembly with contig N50 length of 10.85 Mb and scaffold N50 length of 23.34 Mb were obtained, with over 98.80% (0.48 Gb) of them anchored to 22 pseudochromosomes. We predicted 16,673 protein-coding genes, 95.19% of which were functionally annotated. Our phylogenetic analysis revealed that A. amurensis and Asterias rubens formed a clade, and their divergence time was estimated ~ 28 million years ago (Mya). The significantly enriched pathways and Gene Ontology terms related to the amplified gene family were mainly associated with immune response and energy metabolism, suggesting that these factors might have contributed to the adaptability of A. amurensis to its environment. This study provides valuable genomic resources for comprehending the genetics, dynamics, and evolution of A. amurensis, especially when population outbreaks or invasions occur.

Keywords: Asterias amurensis; Hi-C; comparative genomics; genome assembly.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Circular map of A. amurensis genome. a: GC content, b: gene density, c: all repeats density distributions except TRF, d: LTR type repeat density distribution, e: LINE type repeat density distribution, f: DNA-TE type repeat density distribution.
Figure 2.
Figure 2.
Phylogenetic relationship and comparative genomics analyses. (A) Venn diagram showing the orthologous gene families shared among the genomes of A. amurensis, Acanthaster planci, Anneissia japonica, Asterias rubens, Lytechinus pictus, Lytechinus variegatus, Patiria miniata, and Strongylocentrotus purpuratus (B) A phylogenetic tree of A. amurensis and seven other species. The numbers of gene families that expanded or contracted in each lineage after speciation are shown in the circles of the corresponding branch. (C) Gene comparison of homologous chromosomes between A. amurensis and A. rubens. Grey lines indicate collinearity between the genomes.
Figure 3.
Figure 3.
(A) KEGG pathway enrichment analysis of significantly expanded gene families. The horizontal axis represents the number of genes, the vertical axis represents the KEGG Pathway, and the colour indicates the q-value. A smaller q-value indicates a more significant enrichment result. (B) GO enrichment analysis of significantly expanded gene families. The horizontal axis represents the number of genes, the vertical axis represents the Gene Ontology functional categories, and the colour indicates the q-value. A smaller q-value indicates a more significant enrichment result.
See this image and copyright information in PMC

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