Unraveling the stereoscopic gene transcriptional landscape of zebrafish using Fish SED,a fish spatial expression database with multispecies scalability

Dear Editor,The expression profile demonstrates how each gene was expressed in the target tissue or cell at a given time.Cell heterogeneity is a biological concept characterized by the presence of numerous cells with varying functions and expression profiles within organ/tissue samples.There is also cell-to-cell signaling,which implies that the extracellular environment and spatial location influence intracellular transcription,resulting in spatial heterogeneity of gene expression within the same cell type.

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

Fishes are the largest group of vertebrates,representing more than half of all vertebrate species on Earth.Important aquaculture species,such as Atlantic salmon,cod,and large yellow croaker,contribute to over 16%of the global seafood supply for human consumption(Food and Agriculture Organization of the United Nations,2020).Zebrafish(Danio rerio),medaka(Oryzias latipes),threespined stickleback(Gasterosteus aculeatus),and other fish species are important model organisms in life science research.

A method for custom measurement of fish dimensions using the improved YOLOv5-keypoint framework with multi-attention mechanisms

Dimensional data directly reflects the growth rate of individual fish,an important economic trait of interest to fish researchers.Efficiently obtaining large-scale fish dimension data would be valuable for both selective breeding and production.To address this,our study proposes a custom dimension measurement method for fish using the YOLOv5-keypoint framework with multi-attention mechanisms.We optimized the YOLOv5 framework,incorporated the SimAM attention mechanism to achieve more accurate and faster fish detection,and added customizable landmarks to the network structure,enabling flexible configuration of the number and location of feature points in the training dataset.This method is applicable to various aquacultural species and other objects.We tested the effectiveness of the method using the economically important grass carp(Ctenopharyngodon idella).The proposed method outperforms pure YOLOv5,Faster R-CNN,and SSD in terms of precision and recall rates,achieving an impressive average precision of 0.9781.Notably,field trials confirmed the method's exceptional measurement accuracy,exceeding 97%compatibility with manual measurements,while demonstrating a realtime speed of 38 frames per second on the NVIDIA RTX A4000.This enables efficient and accurate large-scale surface dimension measurements of economic fish.To facilitate massive measurements in agricultural research,we have implemented this method as an online platform,called Mode-recognition Ruler(MrRuler,http://bioinf o.ihb.ac.cn/mrruler).The platform identifies objects in a single image at an average speed of 0.486±0.005 s,based on a dataset of 10,000 images.MrRuler includes two preset carp models and allows users to upload training datasets for custom models of their targets of interest.

Fish SCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome

Dear Editor,Using sc RNA-seq technology, researchers may distinguish between different cell types and tissue heterogeneity as well as perform transcriptome investigations at the single-cell level (Regev et al., 2017). A significant amount of single-cell transcriptome data has been produced as a result of the technology’s quick development and widespread adoption.Research on other model species has also gathered a sizable quantity of transcriptome data at the single-cell level.

Liver DNA methylation and transcriptome between 1- and 3-year-old grass carp

Diseases of grass carps often occur in juveniles but not in adults that may have established disease resistance during development.We performed both DNA bisulfite and transcriptome sequencing on liver libraries of 1-and 3-year-old grass carps.Differential DNA-methylation analysis exhibited a declined methylation level through development.Functional annotation revealed that identified differentially methylated genes(DMGs)and differentially expressed genes were enriched in immune-related pathways such as PI3K-Akt signaling pathway and its related pathways.Both differentially methylated and differentially expressed genes were clustered into the growth-and immune-related function networks.Subcellular localization analysis indicated that the DMGs localized on cell membrane were significantly enriched in calcium signaling pathway and neuroactive ligand-receptor interaction pathway,implying the importance of G protein-coupled receptors to development.These findings will broaden our understanding of the key genes and pathways that affect the immune system at different development stages and the developing protective strategies in grass carp.