Abstract
BackgroundSeasonal 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).ResultsIn 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.ConclusionsWe 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.
Highlights
Migration is one of the most spectacular events in nature
Our genome assembly spanned ∼870.0 Mb, which is consistent with the predicted genome size of 857.5 Mb based on a k-mer analysis (Supplementary Fig. 1 and Supplementary Table 2) [10]
The Benchmarking Universal Single-Copy Orthologs (BUSCO) (University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland; version 3.03, RRID:SCR 015008) [11] with actinopterygii odb9 orthologues was used to evaluate the completeness of our assembly
Summary
Migration is one of the most spectacular events in nature. Every year, billions of animals take part in a seasonal movement to find food or mates, avoid predators, or escape from a severe living environment. This represents a distance of thousands of kilometers between the open ocean (for growth) and the natal stream (for reproduction) [4].
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