Bioinformatics in horses involves the application of computational tools and techniques to analyze and interpret biological data related to equine species. This interdisciplinary field integrates biology, computer science, and information technology to study genetic, genomic, and proteomic information in horses. Bioinformatics can be used to investigate genetic variations, understand disease mechanisms, and assist in the development of targeted therapies and breeding programs. Key areas of focus include genome sequencing, gene expression analysis, and the identification of genetic markers associated with specific traits or conditions. This page compiles peer-reviewed research studies and scholarly articles that explore the application and impact of bioinformatics on equine genetics, health, and breeding.
Fransson LA, Havsmark B.The structure of dermatan sulfate-chondroitin sulfate
copolymers, isolated from horse aorta, has been examined.
It was found that a large proportion of the galactosaminoglycans of this tissue was obtained as a discrete polysaccharide fraction with an L-iduronic acid to D-glucuronic
acid ratio of approximately 1: 2. This finding together with
infrared data indicated that the polymer contained approximately equimolar proportions of the three repeating disaccharide units glucuronosyl-N-acetylgalactosamine 4-sulfate
(A), iduronosyl-N-acetylgalactosamine 4-sulfate (B), and
glucuronosyl-N-acet...
Richter GW, Moppert GA, Lee JC.1. Fingerprints of tryptic digests of apoferritins from a human liver, horse spleens and ACI rat livers were made by means of electrophoresis and chromatography on microcrystalline cellulose, and were compared.
2. All tryptic peptides also present in apoferritins from the human liver and the horse spleens were also present in apoferritin from the rat livers.
3. In the digests of horse and of rat apoferritin there was a peptide that was not present in the digests of human apoferritin. Another peptide was obtained from human and from rat apoferritin, but not from horse apoferritin.
4. T...
Breckenridge WC, Kuksis A.The triglyceride compositions of the milk fats of man, dog, guinea pig, cow, sheep, goat, and horse were compared by gas-liquid chromatography of the intact triglycerides and of the butyl esters of the component fatty acids. The milk fats of man, dog, and guinea pig, which were largely made up of long-chain fatty acids, showed a common pattern with major contributions made by the glycerides with 48-54 acyl carbon atoms. The milk fats of cow, sheep, and goat, which were rich in short-chain acids, showed significant proportions of triglycerides with 28-54 acyl carbon atoms. Horse milk, which con...
RANDALL CC, LAWSON LA.The research article discusses the successful adaptation of the Equine Abortion Virus (EAV) to L-M 929 cells, the impact on infected cultures, and possible reasons for earlier unsuccessful attempts. It […]
Riley CB, McClure JT, Low-Ying S, Dolenko BK, Somorjai RL, Shaw RA.To assess the feasibility of a serum-based test using infrared spectroscopy to identify a subpopulation of mares at risk of producing foals susceptible to failure of passive transfer of immunity (FPT) because of mare-associated factors. Methods: Serum was collected from post-parturient mares (n = 126) and their foals at 24-72 h of age. A radial immunodiffusion IgG test was used to determine each foal's serum IgG concentration. Infrared absorbance spectra of dam sera were collected in the wave number range of 400-4000 cm(-1). Following data preprocessing, pattern recognition techniques were use...
Kim MC, Lee SW, Ryu DY, Cui FJ, Bhak J, Kim Y.The role of microRNAs (miRNAs) as a post-transcriptional gene regulator has been elucidated in a broad range of organisms including domestic animals. Characterization of miRNAs in normal tissues is an important step to investigate the functions of miRNAs in various physiological and pathological conditions. Using Illumina Next Generation Sequencing (NGS) technology, we identified a total of 292 known and 329 novel miRNAs in normal horse tissues including skeletal muscle, colon and liver. Distinct sets of miRNAs were differentially expressed in a tissue-specific manner. The miRNA genes were dis...
Chopineau M, Martinat N, Pourchet C, Stewart F, Combarnous Y, Guillou F.Although donkey luteinizing hormone exhibits a very high degree of amino acid sequence identity with horse LH, its FSH activity in non-equine species is tenfold lower. The coding regions of the common zebra (Equus burchelli) glycoprotein hormone alpha-subunit and LH beta-subunit transcripts were cloned by reverse transcription-PCR from pituitary gland RNA to investigate more precisely the structure-function relationships of this gonadotrophin family. Zebra LH was then expressed in COS-7 cells and its LH and FSH activities were assessed in a rat Leydig cell bioassay (for LH) and in a cell line ...
Handing KB, Shabalin IG, Szlachta K, Majorek KA, Minor W.Serum albumin (SA) is the main transporter of drugs in mammalian blood plasma. Here, we report the first crystal structure of equine serum albumin (ESA) in complex with antihistamine drug cetirizine at a resolution of 2.1Å. Cetirizine is bound in two sites--a novel drug binding site (CBS1) and the fatty acid binding site 6 (CBS2). Both sites differ from those that have been proposed in multiple reports based on equilibrium dialysis and fluorescence studies for mammalian albumins as cetirizine binding sites. We show that the residues forming the binding pockets in ESA are highly conserved in h...
Lauková A, Styková E, Focková V, Maďar M.Nowadays, developed more precisious identification techniques have allowed to validate newer enterococcal species. Among them, the species Enterococcus moraviensis was also validated, at first from surface waters. However, in this study, characteristics and potential to bacteriocin production by the strain E. moraviensis EMo 1-1Nik isolated from buccal mucosa of Slovak warm-blood horse breed has been studied. BLASTn analysis allotted this strain to the species E. moraviensis with percentage identity BLASTn 16S rRNA sequence in the strain up to 100% (99.93% similarity with E. moraviensis NR1139...
Whan G, Runciman RJ, Hurtig M.Whole bone in vitro biomechanical compressive testing can be complicated by three factors: sample asymmetry, heterogeneous material properties, and unknown effective centroid location. Methods: The technique presented here facilitates the calculation of effective centroid position, modulus of elasticity and equivalent uniform strain magnitude for a cross section of bone from a simple whole bone compressive test. Simplification of section response to load is achieved through a combination of linear beam and simple planer geometry theory. The technique requires three longitudinal strain gauges b...
Cieslak J, Mackowski M, Czyzak-Runowska G, Wojtowski J, Puppel K, Kuczynska B, Pawlak P.Apart from the well-known role of somatic cell count as a parameter reflecting the inflammatory status of the mammary gland, the composition of cells isolated from milk is considered as a valuable material for gene expression studies in mammals. Due to its unique composition, in recent years an increasing interest in mare's milk consumption has been observed. Thus, investigating the genetic background of horse's milk variability presents and interesting study model. Relying on 39 milk samples collected from mares representing three breeds (Polish Primitive Horse, Polish Cold-blooded Horse, Pol...
Palomino Lago E, Baird A, Blott SC, McPhail RE, Ross AC, Durward-Akhurst SA, Guest DJ.Fractures caused by bone overloading are a leading cause of euthanasia in Thoroughbred racehorses. The risk of fatal fracture has been shown to be influenced by both environmental and genetic factors but, to date, no specific genetic mechanisms underpinning fractures have been identified. In this study, we utilised a genome-wide polygenic risk score to establish an in vitro cell system to study bone gene regulation in horses at high and low genetic risk of fracture. Candidate gene expression analysis revealed differential expression of and genes in osteoblasts derived from high- and low-risk...
Connard SS, Gaesser AM, Clarke EJ, Linardi RL, Even KM, Engiles JB, Koch DW, Peffers MJ, Ortved KF.The objective of this study was to characterize extracellular vesicles (EVs) in plasma and synovial fluid obtained from horses with and without naturally occurring post-traumatic osteoarthritis (PTOA). Methods: EVs were isolated from plasma and synovial fluid from horses with (n = 6) and without (n = 6) PTOA. Methods: Plasma and synovial fluid EVs were characterized with respect to quantity, size, and surface markers. Small RNA sequencing was performed, and differentially expressed microRNAs (miRNAs) underwent bioinformatic analysis to identify putative targets and to explore potential associa...
Hu L, Li X, Li C, Wang L, Han L, Ni W, Zhou P, Hu S.The gut microbiota is a treasure trove of carbohydrate-active enzymes (CAZymes). To explore novel and efficient CAZymes, we analyzed the 4,142 metagenome-assembled genomes (MAGs) of the horse gut microbiota and found the MAG117.bin13 genome (Bacteroides fragilis) contains the highest number of polysaccharide utilisation loci sites (PULs), indicating its high capability for carbohydrate degradation. Bioinformatics analysis indicate that the PULs region of the MAG117.bin13 genome encodes many hypothetical proteins, which are important sources for exploring novel CAZymes. Interestingly, we discov...
Wang J, Ren W, Sun Z, Han Z, Zeng Y, Meng J, Yao X.This study conducted a thorough analysis of the myofiber type composition in the extensor digitorum longus muscle (EDL) and soleus muscle (SOL) of Kazakh horses, across different genders (male and female). The results showed significant differences in myofiber type composition between EDL and SOL, with a higher proportion of Type I fibers in SOL muscles and a greater prevalence of Type II fibers in EDL muscles. Additionally, the myofiber diameter in Kazakh horses was relatively small, potentially related to the tenderness and edible quality of their muscles. Using high-throughput sequencing te...
Ustyantsev IG, Kosushkin SA, Borodulina OR, Vassetzky NS, Kramerov DA.Short Interspersed Elements (SINEs) are eukaryotic retrotransposons transcribed by RNA polymerase III (pol III). Many mammalian SINEs (T SINEs) contain a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail in their 3'-end. The RNAs of such SINEs have the capacity for AAUAAA-dependent polyadenylation, which is unique to pol III-generated transcripts. The structure, evolution, and polyadenylation of the Ere SINE of ungulates (horses, rhinos, and tapirs) were investigated in this study. A bioinformatics analysis revealed the presence of up to ~4 × 10 Ere copie...
Data in briefJune 10, 2024
Volume 55 110603 doi: 10.1016/j.dib.2024.110603
Groot M, Schmidtová D, Fernandes R.This paper presents an archaeozoological dataset listing numbers of identified fragments for domestic cattle, sheep/goat, pig and horse from archaeological sites in the Netherlands dating from the Bronze Age to the Early Medieval period (c. 2000 BC - AD 1050) [1]. In addition to fragment numbers per species, the geo-referenced dataset includes chronological information, site descriptions, and bibliographic references. Data were collected from tables listing numbers of bone fragments per animal species as found in published and unpublished reports. Number of identified bone fragments per animal...
Wagner LH, Aurich J, Claaßen S, Melchert M, Kaps M, Aurich C.Transrectal and transabdominal ultrasonography is an established method to monitor pregnancy, fetal growth and wellbeing in different species. Growth charts with multiple bio-morphometric parameters to estimate days of gestation and days before parturition exist in small companion animals, sheep and goats, riding type horses and large ponies but not in small horse breeds like Shetland ponies. The aim of this study was to apply fetal biometric assessment and detailed description of physiologic fetal development to mid and late term pregnancies in Shetland mares and to generate reference data fo...
Semik-Gurgul E, Pawlina-Tyszko K, Gurgul A, Szmatoła T, Rybińska J, Ząbek T.DNA methylation and microRNA (miRNA) expression are epigenetic mechanisms essential for regulating tissue-specific gene expression and metabolic processes. However, high-resolution transcriptome, methylome, or miRNAome data is only available for a few model organisms and selected tissues. Up to date, only a few studies have reported on gene expression, DNA methylation, or miRNA expression in adult equine tissues at the genome-wide level. In the present study, we used RNA-Seq, miRNA-seq, and reduced representation bisulfite sequencing (RRBS) data from the heart, lung, and liver tissues of healt...
Tahir AM, Guo L, Ward RK, Yu X, Rideout A, Hore M, Wang ZJ.Laryngeal hemiplegia (LH) is a major upper respiratory tract (URT) complication in racehorses. Endoscopy imaging of horse throat is a gold standard for URT assessment. However, current manual assessment faces several challenges, stemming from the poor quality of endoscopy videos and subjectivity of manual grading. To overcome such limitations, we propose an explainable machine learning (ML)-based solution for efficient URT assessment. Specifically, a cascaded YOLOv8 architecture is utilized to segment the key semantic regions and landmarks per frame. Several spatiotemporal features are then ex...
Guo L, Tahir AM, Hore M, Collins A, Rideout A, Wang ZJ.Sesamoiditis is a common equine disease with varying severity, leading to increased injury risks and performance degradation in horses. Accurate grading of sesamoiditis is crucial for effective treatment. Although deep learning-based approaches for grading sesamoiditis show promise, they remain underexplored and often lack clinical interpretability. To address this issue, we propose a novel, clinically interpretable multi-task learning model that integrates clinical knowledge with machine learning. The proposed model employs a dual-branch decoder to simultaneously perform sesamoiditis grading ...
Bailey E, Finno CJ, Cullen JN, Kalbfleisch T, Petersen JL.Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5-5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Indi...
In this paper, we report a comprehensive and consistent annotation of the locus encoding the β-chain of the equine T-cell receptor (TRB), as inferred from recent genome assembly using bioinformatics tools. The horse TRB locus spans approximately 1 Mb, making it the largest locus among the mammalian species studied to date, with a significantly higher number of genes related to extensive duplicative events. In the region, 136 TRBV (belonging to 29 subgroups), 2 TRBD, 13 TRBJ, and 2 TRBC genes, were identified. The general genomic organization resembles that of other mammals, with a V cluster o...
Parsad R, Bagiyal M, Ahlawat S, Arora R, Gera R, Chhabra P, Sharma U.Donkeys (Equus asinus) have played a vital role in agriculture, transportation, and companionship, particularly in developing regions where they are indispensable working animals. The domestication of donkeys marked a significant turning point in human history, as they became essential for transportation, agriculture, and trade, especially in arid and semi-arid areas where their resilience and endurance were highly valued. In modern society, donkeys are indispensable due to their diversified applications, including meat, dairy, medicine, and functional bioproducts, supporting economic, cultura...
Toft K, Honoré ML, Ripley NE, Nielsen MK, Fromm B, Mardahl M, Nielsen LN, Nejsum P, Thamsborg SM, Cirera S, Pihl TH.The equine bloodworm, Strongylus vulgaris, is a highly pathogenic parasite causing potentially fatal vascular and intestinal damage. Parasites express and release microRNAs (miRNAs) for internal regulation and to modulate host immunity. The complete set of miRNAs expressed by S. vulgaris (the S. vulgaris miRNAome) remains unannotated and the aim of this study was to annotate the miRNAome of L4 and L5 stages of S. vulgaris, and to examine differences in miRNA abundance between larval stages and sexes. Furthermore, we aimed to determine if miRNAs were detectable in excretory/secretory products (...
Lou X, Shao W, Wu Y, Ma H, Chen H, Zheng N, Zhao Y.Active peptides in mare milk have unique biological activities, but how the bioactive protein in mare's milk changes under the influence of temperature has not been fully studied. Therefore, in this study, the differential expression of bioactive peptides potentially present in horse milk under different heat treatment conditions was investigated for the first time using peptidomic and bioinformatic techniques. We collected a total of 15 samples. In this study, we divided the samples into five groups, specifically, 65 °C, 30 min; 72 °C, 15 min; 83 °C; 10 min; 95 °C, 5 min; and an untreated...
Ma L, Li J, He J, Jiang T, Hao Y, Bu Y.Cylicostephanus longibursatus is a common parasite in equine animals. Hosts infected by these nematodes might face disease or death. This study utilized next-generation sequencing technology to sequence the complete mitochondrial genome (mt genome) of C. longibursatus. Through bioinformatics techniques, the genomic base composition, codon usage, tRNA secondary structures, evolutionary relationships, and taxonomic status were analyzed. The results revealed that the mitochondrial genome of C. longibursatus is a double-stranded, 13,807-bp closed circular molecule with an AT content of 76.0%, indi...
Ahlawat S, Sharma U, Niranjan SK, Chhabra P, Arora R, Sharma R, Singh KV, Vijh RK, Mehta SC.This study explored the maternal genetic diversity of six indigenous Indian horse and pony breeds (Bhutia, Kathiawari, Manipuri, Marwari, Spiti, and Zanskari) using comprehensive mitochondrial genome (mitogenome) analysis. Blood samples from 53 horses across diverse agro-climatic zones of India were analyzed, revealing 36 distinct haplotypes, with a haplotype diversity of 0.889 and nucleotide diversity of 0.00347. These indices suggest significant maternal genetic diversity in Indian equines. A median-joining (MJ) network, based on the hypervariable region of the D-loop along with sequences of...
Smith MZ, York M, Townsend KS, Martin LM, Gull T, Coghill LM, Ericsson AC, Johnson PJ.Whereas restoration of fecal consistency after treatment with clioquinol for chronic diarrhea and free fecal water syndrome has been attributed to its antiprotozoal properties, actions of clioquinol on the colonic bacterial microbiota have not been investigated. Objective: Characterize the dynamics of fecal microbial diversity before, during, and after PO administration of clioquinol to healthy horses. Methods: Experimental prospective cohort study using a single horse group. Methods: Eight healthy adult horses received PO clioquinol (10 g, daily) for 7 days. Feces were obtained daily for ...
Walters M, Skovgaard K, Heegaard PMH, Fang Y, Kharaz YA, Bundgaard L, Skovgaard LT, Jensen HE, Andersen PH, Peffers MJ, Jacobsen S.MicroRNAs, a class of small noncoding RNAs, serve as post-transcriptional regulators of gene expression and are present in a stable and quantifiable form in biological fluids. MicroRNAs may influence intra-articular responses and the course of disease, but very little is known about their temporal changes in osteoarthritis. Objective: To identify miRNAs and characterise the temporal changes in their abundance in SF from horses with experimentally induced osteoarthritis. We hypothesised that the abundance of miRNA would change during disease progression. Methods: In vivo experiments. Methods: R...
Chakraborty A, Dutta P, Amrit R, Dey P, Osborne WJ.Endosymbiotic bacteria are known to synthesize bioactive compounds which have biotechnological potentials that enhance immune responses by stimulating the production of immune cells. Horse milk is widely known to have nutraceutical and antimicrobial activities; however, there are no scientific reports on its inhibitory effects. VITAPRJS1, isolated from horse milk, showed non-hemolytic properties and was significantly tolerant to bile salt and NaCl. The isolate also exhibited potent antibacterial activity against pathogenic bacterial strains such as Escherichia coli, Pseudomonas aeruginosa, Sta...
Faulk C.Sequencing a genome by students has now become practical as we demonstrated with our recent publication of the Przewalski's horse (Equus ferus przewalskii) genome. In this review, I describe my experience teaching genome assembly in the classroom. In my course, students sequenced, assembled, and published a high-quality genome for Przewalski's horse using Oxford Nanopore long-read sequencing with only $4000 of materials. Along with the genome, we assembled the mitochondrial genome, sequence variants, predicted gene annotations, and DNA methylation levels. Our genome statistics far exceeded the...
Li X, Wang Z, Zhu M, Wang B, Teng S, Yan J, Wang H, Yuan P, Cao S, Qu X, Wang Z, Zhan K, Choudhury MP, Yang X, Bao Q, He S, Liu L, Zhao P, Jiang J....Horse domestication revolutionizes human civilization by transforming transportation, agriculture, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures underlying pony size remain unexplored. Here, a high-quality genome assembly of the Chinese Debao pony is presented, and 452 qualified individuals from 64 horse breeds worldwide are extensively analyzed. The authors' results reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and Western pony lineages...
Frontiers in geneticsFebruary 27, 2025
Volume 16 1534461 doi: 10.3389/fgene.2025.1534461
Barber AM, Kingsley NB, Peng S, Giulotto E, Bellone RR, Finno CJ, Kalbfleisch T, Petersen JL.The Functional Annotation of Animal Genomes (FAANG) consortium aims to annotate animal genomes across species, and work in the horse has substantially contributed to that goal. As part of this initiative, chromatin immunoprecipitation with sequencing (ChIP-seq) was performed to identify histone modifications corresponding to enhancers (H3K4me1), promoters (H3K4me3), activators (H3K27ac), and repressors (H3K27me3) in eight tissues from two Thoroughbred stallions: adipose, parietal cortex, heart, lamina, liver, lung, skeletal muscle, and testis. The average genome coverage of peaks identified by...
