Genetic diversity and population structure of the roughskin sculpin (Trachidermus fasciatus Heckel) inferred from microsatellite analyses: implications for its conservation and management

Genetic Diversity and Signatures of Selection in the Roughskin Sculpin (Trachidermus fasciatus) Revealed by Whole Genome Sequencing

The roughskin sculpin (Trachidermus fasciatus) is an endangered fish species in China. In recent years, artificial breeding technology has made significant progress, and the population of roughskin sculpin has recovered in the natural environment through enhancement programs and the release of juveniles. However, the effects of released roughskin sculpin on the genetic structure and diversity of wild populations remain unclear. Studies on genetic diversity analysis based on different types and numbers of molecular markers have yielded inconsistent results. In this study, we obtained 2,610,157 high-quality SNPs and 494,698 InDels through whole-genome resequencing of two farmed populations and one wild population. Both farmed populations showed consistent levels of genomic polymorphism and a slight increase in linkage compared with wild populations. The population structure of the two farmed populations was distinct from that of the wild population, but the degree of genetic differentiation was low (overall average Fst = 0.015). Selective sweep analysis showed that 523,529 genes were selected in the two farmed populations, and KEGG enrichment analysis showed that the selected genes were related to amino acid metabolism, which might be caused by artificial feeding. The findings of this study provide valuable additions to the existing genomic resources to help conserve roughskin sculpin populations.

Population structure and genetic diversity of the endangered fish black shinner Pseudopungtungia nigra (Cyprinidae) in Korea: a wild and restoration population

The black shinner Pseudopungtungia nigra Mori, 1935 is an endangered fish endemic to Korea. It lives in the narrow basin of the Geumgang River, Mangyeonggang River, and Ungcheoncheon Stream, which flow into the West Sea of Korea. One population of P. nigra in Ungcheoncheon Stream has been locally exterminated once; it is now inhabiting the upper reaches of the dam through a restoration program. Efforts to identify and understand the genetic structure of these populations are important for conservation planning. Here, we analyzed genetic diversity using 21 microsatellite markers for 9 populations. The mean number of alleles ranged from 4.4 to 8.1, mean allelic richness ranged from 4.6 to 7.8, mean observed heterozygosity ranged from 0.519 to 0.702, and mean expected heterozygosity ranged from 0.540 to 0.763. All groups had recent and historical bottlenecks (P < 0.05, M-ratio < 0.68). Three groups [YD (2019), OC and UC] had significant inbreeding index values, suggesting that they were engaged in inbreeding. We observed a moderate level of genetic differentiation between MG and the rest of the population (FST = 0.135 to 0.168, P < 0.05). The genetic structure exhibited a fitting constant K = 2, along with separation between MG and the remaining populations. With respect to genetic flow, YD (2019), OC, CG, and ND shifted to the UC population (0.263 to 0.278). The genetic flow of each population was transferred only within the population; there was no gene flow among populations, except for the Ungcheoncheon Stream population. This study shows that the Ungcheoncheon Stream population needs conservation efforts to increase its genetic diversity, and the Geumgang River populations needs a conservation plan that considers the possibility of conservation and evolution through gene exchange among the populations.

Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus fasciatus Genome

Trachidermus fasciatus is a roughskin sculpin fish widespread across the coastal areas of East Asia. Due to environmental destruction and overfishing, the population of this species is under threat. In order to protect this endangered species, it is important to have the genome sequenced. Reference genomes are essential for studying population genetics, domestic farming, and genetic resource protection. However, currently, no reference genome is available for Trachidermus fasciatus, and this has greatly hindered the research on this species. In this study, we integrated nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to thoroughly assemble the Trachidermus fasciatus genome. Our results provided a chromosome-level high-quality genome assembly with a predicted genome size of 542.6 Mbp (2n = 40) and a scaffold N50 of 24.9 Mbp. The BUSCO value for genome assembly completeness was higher than 96%, and the single-base accuracy was 99.997%. Based on EVM-StringTie genome annotation, a total of 19,147 protein-coding genes were identified, including 35,093 mRNA transcripts. In addition, a novel gene-finding strategy named RNR was introduced, and in total, 51 (82) novel genes (transcripts) were identified. Lastly, we present here the first reference genome for Trachidermus fasciatus; this sequence is expected to greatly facilitate future research on this species.

Phylogenetic analysis of the complete mitochondrial genome of Orestias ascotanensis (Cyprinodontiformes, Cyprinodontidae)

The complete mitochondrial genome of this species was first determined in this study, which is 16,617 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region, and 1 origin of replication on the light-strand. The overall base composition includes C(27.11%), A(26.68%), T(29.15%), G(17.04%) and three degenerate bases are R, R and S. Moreover, the 13 PCGs encode 3800 amino acids in total, 12 of which use the initiation codon ATG except COI that uses GTG. Most of them have TAA as the stop codon, whereas ND5 ends with AGA, four protein-coding genes (ND1, ND2, ND3 and Cytb) ended with TAG, and two protein-coding genes (COII and ND4) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the Neighbor Joining method was constructed to provide relationship within Cyprinodontidae, which could be a useful basis for management of this species.

The complete mitochondrial genome of Paracheirodon axelrodi (Characiformes: Characidae) and phylogenetic studies of Characiformes

The Paracheirodon axelrodi is an important freshwater fish in the Amazon basin of South America, more expensive than Paracheirodon innesi. Here, we describe the complete 17,100 base pair (bp) mitochondrial genome of Paracheirodon axelrodi mohavensis. The mitogenome has a nucleotide base composition of A (29.62%), T (29.41%), G (15.39%), and C (25.62%), and encodes 13 protein subunits, 22 tRNAs, a 12S rRNA of 952 bp and 16S rRNA of 1665 bp, and a 1433 bp D-loop control region, each located in the conserved mtDNA structure typical for Characidae fishes. All protein-coding genes have initiation codons of ATG, ND1, ND2, CO2, ND3, ND4L, ND5, ND6 and Cytb ended by TAA as a stop codon, ND4 ended by AGA as a stop codon, CO1 ended by AGG as a stop codon, ATP8 and CO3 ended by TAG as a stop codon, ATP6 ended by ATT as a stop codon. This characterised mitogenome may help inform management practices for Paracheirodon axelrodi mohavensis by facilitating future studies on how allopatric populations of this imperilled species are evolving across refuge habitats.

Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus

Understanding the patterns of genetic diversity and adaptation across species' range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small catadromous fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.

The complete mitochondrial genome of Trachidermus fasciatus (Scorpaeniformes: Cottidae) and phylogenetic studies of Cottidae

Trachidermus fasciatus is a small catadromous fish and has been listed as a second class state protected aquatic animal since 1988 in China due to the declines in its abundance. We describe the complete mitogenome of T. fasciatus in this study. The mitogenome is 16,536 nucleotides long and contains 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two main non-coding regions. The overall base composition includes C (30%), A (26.3%), T (25.5%), and G (18.2%). Moreover, the 13 PCGs encode 3800 amino acids in total, all the PCGs use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, except COII, ND4 and Cytb use an incomplete stop codon T. The phylogenetic tree based on the neighbour joining method was constructed to provide relationship within Cottidae, which could be a useful basis for management of this species.

A rapid and cost-effective approach for the development of polymorphic microsatellites in non-model species using paired-end RAD sequencing

As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective "RAD-seq-Assembly-Microsatellite" approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design. A total of 121,750 RAD contigs were generated with a mean length of 522 bp, and 19,782 contigs contained microsatellite motifs. A total of 156,150 primer pairs were successfully designed based on 16,497 contigs containing priming sites. Experimental validation of 52 randomly selected microsatellite loci demonstrated that 45 (86.54%) loci were successfully amplified and polymorphic in two geographically isolated populations of T. fasciatus. Compared with traditional approaches based on DNA cloning and other approaches based on next-generation sequencing, our newly developed approach could yield thousands of microsatellite loci with much higher successful amplification rate and lower costs, especially for non-model species with shallow background of genomic information. The "RAD-seq-Assembly-Microsatellite" approach holds great promise for microsatellite development in future ecological and evolutionary studies of non-model species.