TOmicsVis: An all-in-one transcriptomic analysis and visualization R package with Shinyapp interface.

Transcriptomic analysis has been widely used in comparative experiments to uncover biological mechanisms in various species. However, a simple tool is still lacking to optimize and integrate the features from multiple R packages. In this study, we developed TOmicsVis (Transcriptomics Visualization) (CRAN: https://cran.

Liver transcriptome analysis reveal the metabolic and apoptotic responses of Trachinotus ovatus under acute cold stress.

Trachinotus ovatus is an economically important fish and has been recommended as a high-quality aquaculture fish breed for the high-quality development of sea ranches in the South China Sea. However, T. ovatus shows intolerance to low temperature, greatly limiting the extension of farming scale, reducing production efficiency in winter, and increasing farming risks.

Integrated Transcriptomics and Metabolomics Reveal Changes in Cell Homeostasis and Energy Metabolism in in Response to Acute Hypoxic Stress.

is an economically important mariculture fish, and hypoxia has become a critical threat to this hypoxia-sensitive species. However, the molecular adaptation mechanism of liver to hypoxia remains unclear. In this study, we investigated the effects of acute hypoxic stress (1.

OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data.

With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems; however, it is challenging for most experimental biologists to analyse data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization.

Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of .

Savalani hairtail is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled genome was 790.

The second complete mitogenome of (Perciformes, Nemipteridae) to analyze control region structure and intraspecific variation.

In this study, we reported the complete mitogenome of sampled from the Beibu Gulf, South China Sea. It was 16,734 bp in length and contained 37 canonical mitochondrial genes and 2 non-coding regions. Fifty-one single nucleotide polymorphisms and five insertion and deletions were detected between two mitogenomes, suggesting a high level of intraspecific genetic variation in the species.

The second complete mitogenome of to dissect control region structure and phylogenetic problem of the superfamily Sparoidea (Teleostei, Perciformes).

In this study, we determined the complete mitogenome of of which the length was 17,073 bp, including 37 canonical mitochondrial genes and 2 non-coding regions. The control region contained termination associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), conserved sequence block domain (CSB-1, CSB-2, and CSB-3), and tandem repeat sequence domain (TTD). Nine single nucleotide polymorphisms and three insertion of tandem repeat sequence (each length in 28 bp) were detected between two mitogenomes.

Complete mitochondrial genome and phylogenetic relationship of ornate threadfin bream, (Perciformes, Nemipteridae).

The complete mitochondrial genome of the ornate threadfin bream, , was first determined by the pairs-walking sequencing in this study. The circular mtDNA molecule was 17,115 bp in size and the overall nucleotide composition of H-stand was A (29.55%), T (27.

Complete mitochondrial genome of yellowback seabream, and phylogenetic analysis of the family Sparidae.

The complete mitogenome sequence of was amplified by designing 15 primer pairs. The circle genome was 16,618 bp in size and the overall base composition was 27.04% of A, 26.