Kylie Munyard
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View article: Identification of six genomic regions associated with pigment intensity in alpacas
Identification of six genomic regions associated with pigment intensity in alpacas Open
Context Currently, there is a growing consumer demand for more ecologically sustainable practices in the textile industry. Fabric dyeing is highly pollutive, and one way to avoid dyeing is to use naturally coloured fibres. Alpacas exhibit …
View article: A copy number variant near KITLG is associated with the roan pattern in alpacas
A copy number variant near KITLG is associated with the roan pattern in alpacas Open
Context The alpaca roan pattern is characterised by white and coloured fibre interspersed together, with a distinctive lighter body and darker extremities, and commonly is believed to be inherited in an autosomal dominant manner. It is of …
View article: Variants of HCMV UL18 Sequenced Directly from Clinical Specimens Associate with Antibody and T-Cell Responses to HCMV
Variants of HCMV UL18 Sequenced Directly from Clinical Specimens Associate with Antibody and T-Cell Responses to HCMV Open
Around 80% of adults worldwide carry human cytomegaloviris (HCMV). The HCMV gene UL18 is a homolog of HLA class I genes and encodes a protein with high affinity for the NK and T-cell cytotoxicity inhibitor LIR-1. UL18 was deep sequenced fr…
View article: Sequencing of the Viral UL111a Gene Directly from Clinical Specimens Reveals Variants of HCMV-Encoded IL-10 That Are Associated with Altered Immune Responses to HCMV
Sequencing of the Viral UL111a Gene Directly from Clinical Specimens Reveals Variants of HCMV-Encoded IL-10 That Are Associated with Altered Immune Responses to HCMV Open
Human cytomegalovirus (HCMV) is a beta-herpesvirus carried by ~80% of adults worldwide. Acute infections are often asymptomatic in healthy individuals but generate diverse syndromes in neonates, renal transplant recipients (RTR), and peopl…
View article: Sequencing Directly from Clinical Specimens Reveals Genetic Variations in HCMV-Encoded Chemokine Receptor US28 That May Influence Antibody Levels and Interactions with Human Chemokines
Sequencing Directly from Clinical Specimens Reveals Genetic Variations in HCMV-Encoded Chemokine Receptor US28 That May Influence Antibody Levels and Interactions with Human Chemokines Open
Human cytomegalovirus (HCMV) is a common viral pathogen of solid organ transplant recipients, neonates, and HIV-infected individuals. HCMV encodes homologs of several host genes with the potential to influence viral persistence and/or path…
View article: Microbiome analysis of the skin of sheep that are resistant or susceptible to breech flystrike
Microbiome analysis of the skin of sheep that are resistant or susceptible to breech flystrike Open
Context Breech strike is a serious disease for wool sheep. Skin wrinkle and dags are known predisposing factors for breech strike; however, a large part of the variation among sheep is unknown. Aims We studied the natural diversity and dif…
View article: New Species and New Records of Sponge-Inhabiting Barnacles (Cirripedia, Balanidae, Acastinae) from Australia
New Species and New Records of Sponge-Inhabiting Barnacles (Cirripedia, Balanidae, Acastinae) from Australia Open
The subfamily Acastinae contains a diverse group of barnacles that are obligate symbionts of sponges and alcyonacean and antipatharian corals. Integrating morphological and genetic (COI) data to compare against known species, this paper re…
View article: GWAS Identifies a Region Containing the<i>SALL1</i>Gene in Variation of Pigmentation Intensity Within the Chestnut Coat Color of Horses
GWAS Identifies a Region Containing the<i>SALL1</i>Gene in Variation of Pigmentation Intensity Within the Chestnut Coat Color of Horses Open
Chestnut coat color in horses is determined by a missense mutation within the MC1R gene. However, the intensity of the chestnut color can vary widely within individuals possessing this genotype. Here, we investigated this variation using s…
View article: Human Cytomegalovirus-Encoded microRNAs Can Be Found in Saliva Samples from Renal Transplant Recipients
Human Cytomegalovirus-Encoded microRNAs Can Be Found in Saliva Samples from Renal Transplant Recipients Open
Human cytomegalovirus (HCMV) infections are common following renal transplantation and may have long-lasting effects. HCMV can be measured directly by viral DNA or indirectly via host immune responses. HCMV-encoded microRNA (miRNA) may alt…
View article: MOESM9 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM9 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 9 ATAC-seq peaks (coordinates, quantification, positional classification): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains the following si…
View article: MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 4 Reference DE genes (all combinations): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains itself two subfolders, one for each model: diffcou…
View article: MOESM5 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM5 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 5 FR-AgENCODE genes and transcripts (structure, expression, positional and coding classes).• bos_taurus_cuff_tpm0.1_2sample_complete.gff• bos_taurus_cuff_tpm0.1_2sample_trid_4posclasses_3codingclasses_booleans.tsv• bos_taur…
View article: MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 8 lncRNAs (information from FEELnc, orthology, structure, etc). Archive content:• bos_taurus.lncrna.TPM0.1in2samples.classif.tsv• capra_hircus.lncrna.TPM0.1in2samples.classif.tsv• ConservedLncRNABySynteny_73_19_6.xlsx• gall…
View article: MOESM11 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM11 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 11 Four livestock species ATAC-seq peak orthology.
View article: MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 3 Orthologs between the 4 livestock species. We used Biomart to retrieve the 1 to 1 orthology relationships between chicken, pig and cattle and added goat via gene name. The human gene id is given for reference.
View article: MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 2 Reference genes and transcripts (structure, expression) of the 4 species. Archive content:• bos_taurus.gtf• bos_taurus.refgn.tpm.tsv• capra_hircus.gtf• capra_hircus.refgn.tpm.tsv• gallus_gallus.gtf• gallus_gallus.refgn.tp…
View article: MOESM12 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM12 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 12 Hi-C TADs and A/B compartments: the archive contains three folders, one for each species (capra_hircus, gallus_gallus, sus_scrofa). Each folder contains the following two files:• compartments.bed• mat.40000.longest25chr.…
View article: MOESM6 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM6 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 6 Four livestock species FR-AgENCODE gene orthology.
View article: MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 8 lncRNAs (information from FEELnc, orthology, structure, etc). Archive content:• bos_taurus.lncrna.TPM0.1in2samples.classif.tsv• capra_hircus.lncrna.TPM0.1in2samples.classif.tsv• ConservedLncRNABySynteny_73_19_6.xlsx• gall…
View article: MOESM7 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM7 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 7 FR-AgENCODE DE genes (all combinations). The archive has the same structure than de.refgn.tar.gz with names starting with cuffgenes instead of refgenes.
View article: MOESM13 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM13 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 13 Three livestock species TAD boundary orthology.
View article: MOESM10 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM10 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 10 DA ATAC-seq peaks (all combinations). The archive has the same structure as de.refgn.tar.gz with names starting with mergedpeaks.peaknb.allexp.readnb instead of refgenes.counts.min2tpm0.1.
View article: Multi-species annotation of transcriptome and chromatin structure in domesticated animals
Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Background Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relatio…
View article: Description of a new species of Membranobalanus (Crustacea, Cirripedia) from southern Australia
Description of a new species of Membranobalanus (Crustacea, Cirripedia) from southern Australia Open
A new species of sponge-inhabiting barnacle, Membranobalanus porphyrophilus sp. nov. , is described herein. This species can be distinguished from all other congeners by a combination of characters, in particular by the shapes of the tergu…
View article: 32 Functional annotation of livestock genomes: chromatin structure and regulation of gene expression
32 Functional annotation of livestock genomes: chromatin structure and regulation of gene expression Open
Improving the functional annotation of animal genomes is a key challenge in bridging the gap between genotype and phenotype, thus enabling predictive biology. Regarding livestock production, major outcomes are expected from a better unders…
View article: Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids
Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids Open
The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological signi…
View article: MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 4 Reference DE genes (all combinations): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains itself two subfolders, one for each model: diffcou…
View article: MOESM9 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM9 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 9 ATAC-seq peaks (coordinates, quantification, positional classification): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains the following si…