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. 2021 Feb 11;8(1):60.
doi: 10.1038/s41597-021-00842-w.

Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis

Cristian Gallardo-Escárate  1   2 , Valentina Valenzuela-Muñoz  3   4 , Gustavo Nuñez-Acuña  3   4 , Diego Valenzuela-Miranda  3   4 , Ana Teresa Gonçalves  3   4 , Hugo Escobar-Sepulveda  3   4 , Ivan Liachko  5 , Bradley Nelson  5 , Steven Roberts  6 , Wesley Warren  7
Affiliations

Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis

Cristian Gallardo-Escárate et al. Sci Data. .

Abstract

Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.

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Conflict of interest statement

IL and BN are employees and shareholders of Phase Genomics, Inc, a company commercializing Hi-C technology.

Figures

Fig. 1
Fig. 1
The sea louse Caligus rogercresseyi. Adult female (right) and adult male (left). Magnification 10x.
Fig. 2
Fig. 2
The sea louse Caligus rogercresseyi genome contig contact matrix using Hi-C data. The blue squares represent the draft scaffold. The color bar illuminates the Hi-C contact density in the plot.
Fig. 3
Fig. 3
The sea louse Caligus rogercresseyi genome. The circos plot shows the genomic features for the 21 pseudo-chromosomes. A) GC content, B) Gene density, C) lncRNA density, D) miRNA density and E) Repetitive elements. The chromosome size is shown in Mb scale.
Fig. 4
Fig. 4
Stage-specific transcriptome analysis in the sea louse Caligus rogercresseyi. (A) Transcriptome patterns of coding genes during the lifecycle. The heatmap was based on Transcripts Per Million (TPM) calculation and hierarchical clustering on Manhattan distances with average linkage. White colors mean upregulated coding genes, blue colors downregulated genes. (B) Venn diagram showing shared and unique genes expressed among the six developmental stages. (C) GO enrichment of stage-specific genes (P-value ≤ 10–16;|fold-change| > 5) annotated for key biological processes differentially expressed. The radar plot represents the comparison between two developmental stages according the C. rogercresseyi lifecycle.
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References

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