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.2020 Jan 1;9(1):giz157.
doi: 10.1093/gigascience/giz157.

Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation

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Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation

Gangchun Xu et al. Gigascience..

Abstract

Background: Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents).

Results: In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents.

Conclusions: We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.

Keywords: Chinese tapertail anchovy (Coilia nasus); genome and population sequencing; genome assembly; migratory dimorphism and adaptation.

© The Author(s) 2020. Published by Oxford University Press.

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Figures

Figure 1:
Figure 1:
Seasonal migration and migratory dimorphism of the Chinese tapertail anchovy. (A) A representative image of this economically important fish and geographic distribution of the collected samples along the putative migration route. The red stars represent the sample collection sites (see details in Table   1) and the green arrows indicate the direction of reproductive migration. (B) Neighbor-joining phylogenetic tree constructed with genome-wide SNPs. The scale bar represents the similarity level. (C) Representative X-ray intensity maps of the Sr content in the otoliths ofC. nasus. The constant blue color represents the freshwater residential pattern, while the alternative blue and green colors indicate the migratory pattern.
Figure 2:
Figure 2:
Circos plot of the genome assembly. The rings from outside to inside indicate (A) pseudo-chromosomes, (B) a genetic map, (C) a heat map of gene density (in orange) in 100 kb of non-overlapping windows, (D) line chart of the genome GC content in 100 kb of non-overlapping windows, and (E) a heat map of repeat density (in violet) in 100 kb of non-overlapping windows. Syntenic blocks are connected with navy lines, and each line indicates 1 paralog gene pair in the assembled genome.
Figure 3:
Figure 3:
Comparison of selection sweep regions in the freshwater residential and migratory groups. (A) Distributions of ROD and Fst values in 5-kb non-overlapping windows. Red dots denote windows with the top 5% ROD and Fst values. (B) Migratory adaptation–related genes distributed on 11 chromosomes. Examples of genes (C, D) with selection sweep signals identified by πmigration/πfreshwater, Fst, and ROD values using a 5-kb sliding window. Blue and red lines represent πmigration and πfreshwater, respectively. Dashed lines denote the threshold of top 5%.
Figure 4:
Figure 4:
Three enriched Ca2+-related pathways. The genes highlighted in red were positively selected for the migratory adaptation. Green lines and arrows indicate positive regulation, and red lines, negative regulation. Interestingly, 14 of the selected genes (highlighted in red) potentially participate in the 3 critical Ca2+-related pathways, including calcium signaling pathway, MAKP signaling pathway, and Wnt signaling pathway.
Figure 5
Figure 5
Representative mRNA transcription and protein structural changes in the selected genes with the 3 Ca2+-related pathways. (A-F) Quantitative RT-PCR validation of the mRNA transcription differences in 6 representative genes. (G) A heat map of the DEGs in the 3 Ca2+-related pathways based on the brain transcriptome. (I) Changes in the tertiary protein structure of Tgfr2.
See this image and copyright information in PMC

References

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