A chromosome-level genome assembly of the Chinese herring (Ilisha elongata) uncovered its population dynamics and genes related to lipid metabolism.

Abstract

The Chinese herring (Ilisha elongata) is an economically important clupeiform fish, mostly found along the coast of China and Japan in the western Pacific Ocean. Overfishing and climate change have caused a substantial decline in its annual catch, which may have impacted its population size and structure. Here, we present a chromosome-level genome assembly of the Chinese herring, generated using a combination of Nanopore sequencing, Illumina sequencing, and high-throughput chromatin conformation capture (Hi-C) technologies. The total length of this assembly is802.47 Mbp, anchored to 24 chromosomes, with contig N50 and scaffold N50 values of 13.22 Mbpand 33.10 Mbp, respectively. BUSCO analysis indicated high completeness of this assembly, with 94.9% of universal single-copy orthologs. Analysis of resequencing samples from various coastal regions of China and Japan revealed four distinct genetic populations of Chinese herring along the East Asian coast. The Dandong population (Yellow Sea) diverged earliest, exhibiting unique genetic structures and selective sweep signals, whereas the other three populations expanded from a tropical South China Sea ancestral population to the East China Sea and to Japanese waters. Among 23,366 protein-coding genes, several families related to metabolism of very-long-chain unsaturated fatty acids are particularly contracted compared to the American shad. Additionally, several genes associated with fatty acid synthesis formation have undergone accelerated positive selection. These findings may explain the differential fatty acid ratios in marine versus riverine migratory clupeiforms. This high-quality genome assembly of the Chinese herring may provide valuable resources for comparative study of coastal fishes and benefit the development of a sustainable management strategy for fisheries of the Chinese herring.