Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease

Long-read RNA Sequencing Improves the Annotation of the Equine Transcriptome

A high-quality reference genome assembly, a biobank of diverse equine tissues from the Functional Annotation of the Animal Genome (FAANG) initiative, and incorporation of long-read sequencing technologies, have enabled efforts to build a comprehensive and tissue-specific equine transcriptome. The equine FAANG transcriptome reported here provides up to 45% improvement in transcriptome completeness across tissue types when compared to either RefSeq or Ensembl transcriptomes. This transcriptome also provides major improvements in the identification of alternatively spliced isoforms, novel noncoding genes, and 3’ transcription termination site (TTS) annotations. The equine FAANG transcriptome will empower future functional studies of important equine traits while providing future opportunities to identify allele-specific expression and differentially expressed genes across tissues

Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression

BACKGROUND: In mammals, an important source of genomic variation is insertion polymorphism of retrotransposons. These may acquire a functional role when inserted inside genes or in their proximity. The aim of this work was to carry out a genome wide analysis of ERE1 retrotransposons in the horse and to analyze insertion polymorphism in relation to evolution and function. The effect of an ERE1 insertion in the promoter of the myostatin gene, which is involved in muscle development, was also investigated. RESULTS: In the horse population, the fraction of ERE1 polymorphic loci is related to the degree of similarity to their consensus sequence. Through the analysis of ERE1 conservation in seven equid species, we established that the level of identity to their consensus is indicative of evolutionary age of insertion. The position of ERE1s relative to genes suggests that some elements have acquired a functional role. Reporter gene assays showed that the ERE1 insertion within the horse myostatin promoter affects gene expression. The frequency of this variant promoter correlates with sport aptitude and racing performance. CONCLUSIONS: Sequence conservation and insertion polymorphism of ERE1 elements are related to the time of their appearance in the horse lineage, therefore, ERE1s are a useful tool for evolutionary and population studies. Our results suggest that the ERE1 insertion at the myostatin locus has been unwittingly selected by breeders to obtain horses with specific racing abilities. Although a complex combination of environmental and genetic factors contributes to athletic performance, breeding schemes may take into account ERE1 insertion polymorphism at the myostatin promoter. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0281-1) contains supplementary material, which is available to authorized users

Neocentromere formation and evolution in the genus Equus

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Neocentromere formation and evolution in the genus Equus

The living species of the genus Equus (horses, asses and zebras) are particularly valuable for comparative cytogenetic studies because their karyotypes differ extensively in spite of their recent divergence, morphological similarity and capacity to interbreed. We have shown that the formation of evolutionary new centromeres (ENCs), that is the shift of centromeres without DNA sequence rearrangement, played a key role during the rapid evolution of this genus; therefore, these animals are an ideal model system to study the formation and evolution of mammalian centromeres

Evolution and molecular dynamics of centromeres in the genus Equus

The centromere is the locus directing chromosome segregation at cell division. The mechanism by which centromere identity is specified on chromosomal DNA sequences has been deeply enigmatic, with a clear dependence on the epigenetic inheritance of the centromeric histone, CENP-A. While a degree of autonomy of centromere placement along the chromosome has been established by studies of human neocentromeres and observation of evolutionary centromere repositioning, a role for DNA sequence in driving centromere location remains to be elucidated. The typical association of mammalian centromeres with extensive arrays of highly repetitive satellite DNA, has so far hampered a detailed molecular dissection of centromere function and evolution. In previous work, we discovered that, in the genus Equus (horses, asses and zebras), centromere repositioning during evolution was exceptionally frequent and that satellite DNA and centromeres are often uncoupled in this genus (Piras et al, PLoS Genet 2010, 6 e1000845). We then described the first native satellite-free centromere discovered in a mammal, that of horse chromosome 11 (Wade et al, Science 2009, 326: 865-867); using a combination of molecular and cytogenetic approaches we recently demonstrated that the precise positioning of this native mammalian centromere is highly variable, even on the two homologous chromosomes in a single individual. These results corroborate the hypothesis that CENP-A is the principal determinant of centromere identity, but they make a much deeper point: CENP-A location along the DNA polymer is not fixed but rather exhibits a diffusion-like behavior. We are now characterizing a number of satellite-less centromeres in asses and zebras; preliminary observations on the molecular organization of centromeres, based on the exploitation of this powerful model system, will be presented

Description of the telomeric RNA, TERRA, in human oocytes

Introduction: The ends of lineal chromosomes are organized in ribonucleoproteic complexes called telomeres, essential to maintain genome integrity. Furthermore, in oogenesis telomeres play an important role throughout meiotic chromosome events since they tether telomeres together promoting alignment, synapsis and recombination between homologue chromosomes. The recently discovered telomeric repeat-containing RNA (TERRA) is a structural component of the telomeric complex that also acts as a telomerase inhibitor. Until now, TERRA has been described in several somatic cell lines and tissues of different eukaryotic organisms. In this study, TERRA was identified for the first time at telomeres of human oocytes, and its presence and localization was established all through the first stages of meiotic prophase I

Micro-Raman mapping of the strain field in GaAsN/GaAsN:H planar heterostructures: A brief review and recent evolution

Raman scattering is an effective tool for the investigation of the strain state of crystalline solids. In this brief review, we show how the analysis of the GaAs-like longitudinal optical phonon frequency allowed to map the strain behavior across interfaces in planar heterostructures consisting of GaAsN wires embedded in GaAsN:H matrices. Moreover, we recently showed how the evolution of the longitudinal optical frequency with increasing H dose strongly depends on polarization geometry. In a specific geometry, we observed a relaxation of the GaAs selection rules. We also present new results which demonstrate how laser irradiation intensity-even at low levels-may affect the line shape of the GaAs-like spectral features in GaAsN hydrogenated materials