The smallscale yellowfin, Plagiognathops microlepis is the only one species in the genus Plagiognathops. In this study, we sequenced the complete mitochondrial genome of the P. microlepis. The complete mitogenome was 16,623 bp in size, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 control region. It has the typical circular molecule structure of vertebrate's mitochondrial genome. The whole base composition was estimated to be 30.60% A, 25.19% T, 27.32% C and 16.89% G with AT bias of 55.79%. The complete mitogenome of P. microlepis provides the basis for preservation of genetic resources and genetic breeding studies on this species.

The Pseudobrama simoni (Bleeker) is the only one species within the genus Pseudobrama of the subfamily Xenocyprinae. In this study, we first determined the complete mitochondrial genome sequence of the P. simoni. The whole mitogenome is 16,618 bp in size, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. The gene order and molecule structure are similar to most vertebrates. The complete mitogenome of P. simoni provides the valuable information for the biogeographic and phylogenetic studies on the subfamily Xenocyprinae.

To investigate the effects of different raising environments on the flesh quality, the study set up three groups of silver carp (Hypophthalmichthys molitrix), that is, pond-farmed; short-term stocked; and ranched, grown in a natural water ranch. This study compared the differences in muscle proximate composition and amino acid composition among three groups. The results showed that there was no difference between the ranched and the stocked groups in content of crude protein, ash, total amino acids (TAA), essential amino acids (EAA), and umami-flavored amino acids (UAA), with both groups being significantly higher than the farmed group. This shows that, in terms of flesh quality, the stocked group was closer to the ranched group and better than the farmed group after being stocked in natural water for 30 days. The results suggest that the flesh quality of farmed fish was improved by short-term stocking in natural water. To elucidate the reasons of flesh quality change in the stocked group, this study compared the food composition and intestinal digestive enzyme activity in three groups, demonstrating that the ranched and stocked groups had similar food composition, with their detritus proportion lower than that of the farmed group, consuming easily digestible phytoplankton diatoms rich in amino acids and fatty acids. No significant difference was seen between the ranched group and the stocked group, for which amylase, lipase, and trypsin activities were lower than that of the farmed group. It is hypothesized that differences in environmental and food composition resulted in lower digestive enzyme activity in the ranched group and the stocked group. In summary, the short-term stocking of farmed fish in a natural water ranch can effectively improve the nutrient content, quality and flavor, and promote value of fish products.

In the last decade, the phylogenetic relationships within the genus Triplophysa have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. Herein, we obtained the complete mitogenome of Triplophysa bombifrons via HiFi reads of the Pacbio Sequel II system and DNBSEQ short-reads. We compared all available mitogenomes of the Triplophysa genus and reconstructed the phylogeny of Nemacheilidae, based on the mitogenomes, using maximum likelihood (ML) methods. The results show that the complete mitogenome sequence of T. bombifrons was circular and 16,568 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and a typical control region (D-loop). The most common start codons were ATG, except for cox1, and TAA/TAG were the stop codons for all PCGs. In total, 677 SNPs and 9 INDELs have been found by comparing the sequence divergence between this study and previous reports. Purity selection was found in all PCGs. Phylogeny was inferred by analyzing the 13 PCGs and the concatenated nucleotide sequences of 30 mitogenomes. The phylogenetic analyses based on the nucleotides of the 13 PCGs supported the assumption that the Triplophysa genus can be divided into 4 main clades and demonstrated that T. bombifrons and T. tenuis are closely related species for the first time. This study laid the foundation for further study on the mitogenome and phylogeny of Nemacheilidae fishes.

Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the traditional sequence alignment method is considerably complicated in proportion to the sequences' length, and it is significantly challenging to align long sequences such as a human genome. Currently, several multiple sequence alignment algorithms are available that can reduce the complexity and improve the alignment performance of various genomes. However, there have been relatively fewer attempts to improve the alignment performance of the pairwise alignment algorithm. After grasping these problems, we intend to propose a new sequence alignment method using deep reinforcement learning. This research shows the application method of the deep reinforcement learning to the sequence alignment system and the way how the deep reinforcement learning can improve the conventional sequence alignment method.