The elongate ilisha (Ilisha elongata) is a significant commercial species found along the Northwestern Pacific Coast. A sharp decline in the annual catch of I. elongata over recent decades implies a concerning situation regarding its fishery stocks. Nonetheless, inadequate knowledge of the genetic diversity, population structure, and historical demography of this species has hindered the establishment of sustainable fishery policies and appropriate conservation measures. In this study, the genetic structure and population demography of I. elongata stocks along the Northwestern Pacific Coast were examined using target-gene enrichment data from 144 I. elongata individuals collected from 18 locations. The findings reveal that with an average value of 0.2173, I. elongata maintains a notable level of nucleotide diversity despite facing considerable fishing pressure. Furthermore, inter-population differentiation is relatively low, with most geographical populations displaying minimal genetic distinctions or none from one another. Population clustering analysis identified four lineages of I. elongata stocks. Through historical demography simulations, it was proposed that the Yalu River Estuary population diverged initially around 19500 generations before present, while the remaining lineage split into two about 18800 generations ago. One lineage represents the southern population, while the other further separated into the northern population and the Japanese population approximately 3000 generations ago. These results underscore that the current phylogeographic patterns of I. elongata may result from directional selection due to low temperatures and geographic barriers during glacial periods, followed by recent expansions.

A combination of short-read paired-end and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libraries require high-molecular-weight DNA, making the use of these libraries inappropriate for samples with only degraded DNA. An in silico method that generates mate-pair libraries using a reference genome was devised for the task of assembling target genomes. Although the contiguity and completeness of assembled genomes were significantly improved by this method, a high level of errors manifested in the assembly, further to which the methods for using reference genomes were not optimized. Here, we tested different strategies for using reference genomes to generate in silico mate-pairs. The results showed that using a closely related reference genome from the same genus was more effective than using divergent references. Conservation of in silico mate-pairs by comparing two references and using those to guide genome assembly reduced the number of misassemblies (18.6% – 46.1%) and increased the contiguity of assembled genomes (9.7% – 70.7%), while maintaining gene completeness at a level that was either similar or marginally lower than that obtained via the current method. Finally, we developed a pipeline of optimized method and compared it with another reference-guided assembler, Ragtag. We found that Ragtag produced longer scaffolds (17.8 Mbp vs. 3.0 Mbp), but resulted in a much higher misassembly rate (85.68%) than our optimized in silico mate-pair method. This optimized in silico pipeline developed in this study should facilitate further studies on genomics, population genetics and conservation of endangered species.

A combination of next-generation sequencing technologies and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libraries require high-molecular-weight DNA, making the use of these libraries inappropriate for samples with only degraded DNA. An in silico method that generates mate-pair libraries using a reference genome was devised for the task of assembling target genomes. Although the contiguity and completeness of assembled genomes were significantly improved by this method, a high level of errors manifested in the assembly, further to which the methods for using reference genomes were not optimized. Here, we tested different strategies for using reference genomes to generate in silico mate-pairs. The results showed that using a closely related reference genome from the same genus was more effective than using divergent references. Conservation of in silico mate-pairs by comparing two references and using those to guide genome assembly reduced the number of misassemblies (18.6% – 46.1%) and increased the contiguity of assembled genomes (9.7% – 70.7%), while maintaining gene completeness at a level that was either similar or marginally lower than that obtained via the current method. Finally, we compared the optimized method with another reference-guided assembler, RaGOO. We found that RaGOO produced longer scaffolds (17.8 Mbp vs 3.0 Mbp), but resulted in a much higher misassembly rate (85.68%) than our optimized in silico mate-pair method.