An mRNA expression atlas for the duck with public RNA-seq datasets

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 18, 2025

Ducks are globally important poultry species and a major source of farm animal products, including meat, eggs, feathers. A thorough understanding the functional genomic transcriptomic sequences is crucial for improving production efficiency. This study constructed largest duck mRNA expression atlas among all waterfowl to date. The encompasses 1,257 tissue samples across 30 types, representing organ systems. Using advanced clustering analysis, we established co-expression network clusters describe transcriptional features in and, when feasible, assign these unique types or pathways. Additionally, identified 27 low-variance, highly expressed housekeeping genes suitable gene experiments. Furthermore, in-depth analysis revealed potential sex-biased patterns within tissues specific profiles meat-type egg-type ducks, providing valuable resources understand genetic basis sex differences particular phenotypes. research elucidates biological processes affecting productivity. presents most extensive any These findings significant value advancing industrial applications.

Language: Английский

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A Multi-Tissue Gene Expression Atlas of Water Buffalo (Bubalus bubalis) Reveals Transcriptome Conservation between Buffalo and Cattle

Genes, Journal Year: 2023, Volume and Issue: 14(4), P. 890 - 890

Published: April 10, 2023

We generated 73 transcriptomic data of water buffalo, which were integrated with publicly available in this species, yielding a large dataset 355 samples representing 20 major tissue categories. established multi-tissue gene expression atlas buffalo. Furthermore, by comparing them 4866 cattle from the genotype-tissue (CattleGTEx), we found that transcriptomes two species exhibited conservation their overall patterns, tissue-specific and house-keeping expression. further identified conserved divergent genes between largest number differentially expressed skin, may be related to structural functional differences skin species. This work provides source annotation buffalo genome lays foundations for future genetic evolutionary studies

Language: Английский

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Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Feb. 1, 2024

Abstract Enhancers and the enhancer RNAs (eRNAs) have been strongly implicated in regulations of transcriptions. Based multi-omics data (ATAC-seq, ChIP-seq RNA-seq) from public databases, Pig-eRNAdb is a dataset that comprehensively integrates enhancers eRNAs for pigs using machine learning strategy, which incorporates 82,399 37,803 607 samples across 15 tissues pigs. This user-friendly covers comprehensive depth annotation The coordinates expression patterns are downloadable. Besides, thousands regulators on eRNAs, target genes tissue-specific housekeeping also accessible as well sequence similarity with humans. Moreover, eRNA-trait associations encompass 652 traits provided. It will crucially facilitate investigations reference

Language: Английский

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De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: May 11, 2024

Abstract Domesticated herbivores are an important agricultural resource that play a critical role in global food security, particularly as they can adapt to varied environments, including marginal lands. An understanding of the molecular basis their biology would contribute better management and sustainable production. Thus, we conducted transcriptome sequencing 100 105 tissues from two females each seven species herbivore (cattle, sheep, goats, sika deer, horses, donkeys, rabbits) breeds sheep. The quality raw trimmed reads was assessed terms base quality, GC content, duplication sequence rate, overrepresented k-mers, score distribution with FastQC. high-quality filtered RNA-seq were deposited public database which provides approximately 54 billion paired-end total, average mapping rate ~93.92%. Transcriptome databases represent valuable resources be used study patterns gene expression, pathways related key biological processes, economic traits herbivores.

Language: Английский

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Genome-wide scan for runs of homozygosity in South American Camelids

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Aug. 21, 2023

Abstract Background Alpaca ( Vicugna pacos ), llama Lama glama vicugna ) and guanaco guanicoe are the camelid species distributed over Andean high-altitude grasslands, Altiplano, Patagonian arid steppes. Despite wide interest on these animals, most of loci under selection still unknown. Using whole-genome sequencing (WGS) data we investigated occurrence distribution Runs Of Homozygosity (ROHs) across South American Camelids (SACs) genome to identify genetic relationship between four potential signatures selection. Results A total 37 WGS samples covering was included in final analysis. The multi-dimensional scaling approach showed a clear separation species; however, admixture analysis suggested strong introgression from alpaca. Conversely, very low with other SACs found. did not show significant differences number, length ROHs (100-500 kb) genomic inbreeding values. Longer (> 500 were found almost exclusively Seven overlapping shared by alpacas, encompassing nine FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 RIC8B while twenty-five annotated ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 RCOR1 ). Four ROHs, three DLG1, KAT6B PDE4D seven genes ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 LOC107034552 detected for guanaco, respectively. Conclusions revealed areas potentially selected production traits as well natural adaptation harsh environment. hint driven environment farming purpose signals Interesting, gene identified both suggesting positive effect wild populations fitness. Such information may be further ecological animal studies.

Language: Английский

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Transcriptomic analysis reveals diverse expression patterns underlying the fiber diameter of oxidative and glycolytic skeletal muscles in steers

Meat Science, Journal Year: 2023, Volume and Issue: 207, P. 109350 - 109350

Published: Oct. 4, 2023

Skeletal muscles consist of heterogeneous fibers with various contractile and metabolic properties that affect meat quality. The size muscle contributes to mass myopathy. Thus, improved understanding the expression patterns underlying fiber might open possibilities change them using genetic methods. aim this study was reveal transcriptomic landscapes one oxidative (Psoas major) three glycolytic (Longissimus lumborum, Triceps brachii, Semimembranosus) muscles. Principal component analysis (PCA) showed significant differences in gene among four Specifically, 2777 differentially expressed genes (DEGs) were detected between six pairwise comparisons Weighted co-expression network (WGCNA) identified modules, which significantly associated diameter. We also 23 candidate genes, enrichment biosynthesis amino acids (bta01230), sarcomere (GO:0030017), regulation actin cytoskeleton (bta04810) overlapped DEGs WGCNA. Nineteen these (e.g., EEF1A2, FARSB, PINK1) have been reported promote or inhibit growth development. Our findings contribute muscles, may provide a basis for breeding improve yield.

Language: Английский

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Gene coexpression network analysis reveals the genes and pathways in pectoralis major muscle and liver associated with wooden breast in broilers

Poultry Science, Journal Year: 2024, Volume and Issue: 103(10), P. 104056 - 104056

Published: July 6, 2024

Wooden breast (WB) is a myopathy mainly affecting pectoralis major (PM) muscle in modern commercial broiler chickens, causing enormous economic losses the poultry industry. Recent studies have observed hepatic and PM injury broilers affected by WB, but relationships between WB 2 tissues are mostly unclear. In current study, RNA-seq raw data of liver were downloaded from GSE144000, we constructed gene coexpression networks to explore using weighted network analysis (WGCNA) method. Six modules significantly correlated with networks, respectively. TGF-beta signaling, Toll-like receptor signaling mTOR pathways enriched genes within 6 network. Meanwhile, pathway was consensus across tissues, salmon module (r = -0.5 p 0.05) negatively which apoptosis, autophagy enriched. The related 3 pathways, myeloid differentiation primary response 88 (MYD88), interferon regulatory factor 7 (IRF7), mitogen-activated protein kinase 14 (MAPK14), FBJ murine osteosarcoma viral oncogene homolog (FOS), jun proto-oncogene (JUN), caspase-10, unc-51 like activating (ULK2) serine/threonine 11 (LKB1), identified module. this found that cell inflammation, apoptosis might influence broilers.

Language: Английский

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Expression patterns of housekeeping genes and tissue-specific genes in black goats across multiple tissues

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Sept. 19, 2024

Language: Английский

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Comparative analyses of dynamic transcriptome profiles highlight key response genes and dominant isoforms for muscle development and growth in chicken

Genetics Selection Evolution, Journal Year: 2023, Volume and Issue: 55(1)

Published: Oct. 23, 2023

Modern breeding strategies have resulted in significant differences muscle mass between indigenous chicken and specialized broiler. However, the molecular regulatory mechanisms that underlie these remain elusive. The aim of this study was to identify key genes underlying breast development broiler.Two time-series RNA-sequencing profiles muscles were generated from commercial Arbor Acres (AA) broiler (fast-growing) Chinese Lushi blue-shelled-egg (LS) (slow-growing) at embryonic days 10, 14, 18, post-hatching day 1 weeks 1, 3, 5. Principal component analysis transcriptome showed top four principal components accounted for more than 80% total variance each breed. developmental axes AA LS overlapped stages but gradually separated adult stages. Integrative investigation differentially-expressed transcripts contained identified 44 formed a network associated with two breeds. In addition, alternative splicing revealed multiple isoforms always had one dominant transcript exhibited significantly higher expression level others. Among genes, TNFRSF6B gene, mediator signal transduction pathways cell proliferation, harbored isoforms, TNFRSF6B-X1 TNFRSF6B-X2. isoform both breeds before age week. A switching event occurred week age, resulting TNFRSF6B-X2 being broiler, whereas remained chicken. Gain-of-function assays demonstrated promoted proliferation primary myoblasts, only augmented differentiation intracellular protein content myoblasts.For first time, we several may be responsible slow-growing fast-growing These findings provide new insights into

Language: Английский

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Characterization and analysis of transcriptomes of multiple tissues from estrus and diestrus in pigs

International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 256, P. 128324 - 128324

Published: Nov. 23, 2023

Language: Английский

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