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Draft genome resources for Chicken Coccidiosis Causal Agents for developing improved control strategies for Avian Coccidosis

Eimeria maxima is considered one of the most important coccidian species because it affects nutrient uptake and predisposes chickens to necrotic enteritis caused by Clostridium perfringens. Differences in the virulence and immunogenicity of E. maxima strains have been observed by researchers. Our laboratory has developed draft genome sequences for a highly virulent strain, namely E. maxima APU1 and a less virulent strain named E. maxima APU2. The genome sequences of these two strains- E. maxima APU1 and APU2 were obtained by long read Oxford Nanopore Technology (ONT). These high-quality reads passed through quality check parameters and assembled into 54.25 Mb with 7693 genes (E. maxima APU1) and 54.78 Mb with 7813 genes (E. maxima APU2) genomes, using hybrid assembly method. The other related Eimeria species (E. acervulina APU1, E. tenella APU2, and E. maxima APU3) are being sequenced followed by downstream analysis i.e., gene annotation, identification on common and unique genic candidates and comparative genomics analyses to understand the biological significance of these predicted genes and their putative roles. The genome sequence and annotations of these genomes of major Eimeria species, including characterizing genetic markers that allow for the development of markers for species identification that could help understand and unravel the basis for pathogenicity of these protozoa

Comprehensive Analyses of 723 Transcriptomes Enhance GWAS Biological Interpretation and Genomic Prediction for Complex Traits in Cattle

In this study, we generated 94 RNA-seq data that were colloced from different tissues in Hereford cow (L1 Dominette 01449) and its relatives. By combining these RNA-seq data with our other data and published data, we uniformly assembled and analyzed a total of 723 transcriptomes from 91 tissues and cell types in cattle, to identify tissue-specific genes with the highest specific expression. We then detected the trait-relevant tissues and cell types, and improved genomic prediction for milk production traits. Overall design: All the tissues were collocted in a previous study (Harhay et al. 2010). total RNA was extracted from snap frozen tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. The quantity and purity of RNA were measured using a NanoDrop 8000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer System (Agilent, Santa Clara, CA, USA)

Eimeria tenella isolate:APU2 Genome sequencing

Coccidia in the genus Eimeria cause economically important disease of poultry and livestock throughout the world. Our laboratory has developed chromosomal level scaffolding of Eimeria tenella (E. tenella APU2) to understand genome architecture of this genome and structural variations with other related Eimeria sequenced at USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Beltsville, United States. The sequences and annotations of genomes of major Eimeria species, will help characterize genetic markers that will allow development of markers for species identification that could help in understanding the basis for pathogenicity of these protozo

Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 2]

In this study, we generated six whole-genome bisufite sequencing (WGBS) data that were colloced from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, and RNA-seq, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes. Overall design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24-h. Briefly, DNA from REPC culture was isolated by phenol/chloroform extraction. DNA (100 ng) was bisulfite-converted and subjected to library preparation using the Pico Methyl-Seqâ„¢ Library Prep Kit (Zymo) following the instructions of the supplier. High-Sensitivity DNA chips were used to assess libraries for quality on the Agilent Bioanalyzer and quantified with Qubit fluorometer. Libraries were sequenced on an Illumina HiSeq2500 (150-bp paired-end sequencing)

Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 4]

In this study, we generated CTCF and four histone modifications, including H3K27ac, H3K27m3, H3K4m1, H3K4m3, which were collected from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing RNA polymerase II, DNA accessibility, and RNA-seq, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes. Overall design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24 hrs. CTCF-seq and ChIP-Seq of H3K27ac, H3K27m3, H3K4m1, H3K4m3, of rumen primary epithelial cells (RPEC) were performed at Active Motif according to proprietary methods. For ChIP-seq, CTCF-seq, the 75-nt single end reads were generated using NextSeq 500 (Active Motif, Inc. Carlsbad, CA, USA)

Analyses of transcriptomes of mammary and lymphocyte tissues in cattle

Analyses of transcriptomes of two tissues in cattle Overall design: We collected 2 tissues (Mammary and Lymphocyte), each tissue has two replicates

Analyses of transcriptomes of multiple tissues in cattle

In this study, we generated 47 RNA-seq data for 14 tissues in Holstein cattle. We analyzed the variations of gene expression among tissues. Overall design: We collected 14 tissues from 4 individuals and generated 47 RNA-seq data