Marsupial gammaherpesviruses
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB23311 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:marsupial metagenome Targeted loci environmental
| PRJNA473283 | ENA
Project description:We study the genomic and developmental basis of the mammalian gliding membrane, or patagium, an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of fifteen new marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. We confirm our finding via epigenomics, transcriptomics, and in vivo marsupial transgenics.
2024-05-22 | GSE256507 | GEO
Project description:Australian marsupial phylogeny with denovo assembly of target exons captured sequences.
| PRJEB39788 | ENA
Project description:Marsupials and placental mammals exhibit significant differences in reproductive and life history strategies. Marsupials are born highly underdeveloped after an extremely short period of gestation, leading to prioritization of the development of structures critical for post-birth survival in the pouch. Critically, they must undergo accelerated development of the oro-facial region compared to placentals. Previously we described the accelerated development of the oro-facial region in the carnivorous Australian marsupial, the fat-tailed dunnart Sminthopsis crassicaudata that has one of the shortest gestations of any mammal. By combining genome comparisons of the mouse and dunnart with functional data for the enhancer-associated chromatin modifications, H3K4me3 and H3K27ac, we investigated divergence of craniofacial regulatory landscapes between these species. While genes involved in regulating facial development were largely conserved in mouse and dunnart, the regulatory landscape varied significantly. Additionally, a subset of dunnart-specific enhancers were associated with genes highly expressed only in dunnart relating to cranial neural crest proliferation, embryonic myogenesis and epidermis development. Comparative RNA-seq analyses of facial tissue revealed dunnart-specific expression of genes involved in the development of the mechanosensory system. Accelerated development of the dunnart sensory system likely relates to the sensory cues received by the nasal-oral region during the postnatal journey to the pouch. Together these data suggest that accelerated development in the dunnart can be driven by dunnart-specific enhancer activity. Our study highlights the power of marsupial-placental comparative genomics for understanding the role of enhancers in driving temporal shifts in development.
2023-03-15 | GSE188990 | GEO
Project description:Oz Mammals Genomics Consortia collection of marsupial specimens Genome sequencing and assembly
| PRJNA650593 | ENA
Project description:We generated genome-wide histone maps of four histone modifications, H3K4me3, H3K9Ac, H3K9me3, and H3K27me3, by ChIP-seq in male fibroblasts isolated from a model marsupial, Monodelphis domestica. We assayed the correlation and association of these histone modifications with each other, certain genomic elements such as CpG islands and predicted promoters, and the transcriptional states of the genes they mark. Generally, we found that promoters of actively transcribed genes are associated with H3K4me3 and H3K9Ac and lack H3K9me3 and H3K27me3. We also show that transcriptionally opposing, mutually exclusive histone modifications mark monoallelically expressed and imprinted genes in our samples.
2014-11-07 | GSE47723 | GEO
Project description:The six-layered neocortex is exclusively present in mammals and mediates sensory-motor and higher-order functions. Key differences in this structure and its connections exist between the main mammalian groups: eutherians and marsupials, however, the molecular changes that underlie these known morphological differences remain unknown. This question is particularly difficult to address because small and transient changes in gene expression during development may be crucial to brain formation, which would not be detectable in adult transcriptomic analyses. To address this question of the developmental origin of changes in the evolution of the mammalian neocortex, we performed transcriptomic analysis on the marsupial fat-tailed dunnart (Sminthopsis crassicaudata) at postnatal ages P12 and P20 corresponding to the generation of infragranular (layers 5/6) and supragranular (layers 2/3) neurons, respectively. We assembled a de novo transcriptome of the neocortex of fat-tailed dunnarts using RNA-seq data from all samples, then differential gene expression analysis performed across the two ages. Additional cross-species analysis was performed against existing mouse neocortical datasets in the NCBI Sequence Read Archive at equivalent developmental ages embryonic (E) day 12.5 (SRR1509162, SRR1509163, SRR1509164) and E16 (SRR5755669, SRR5755670, SRR5755671, SRR5755672). We identified 12,632 protein-coding transcripts orthologous to mouse RNA reference sequences (Refseq) in the dunnart neocortical transciptome. The results also revealed divergences in gene sets known to be enriched in different neuronal populations, revealing a more advanced stage of maturation in the marsupial neocortex at the period of infragranular birth compared to the eutherian mouse.
2022-01-17 | GSE161274 | GEO
Project description:The objective of our study is to investigate the effect of PFOA and GenX on the gene expression levels in Monodelphis domestica whole blood cultures by RNA-seq and identify the major susceptible genes. We identified 578 differentially expressed genes (DEGs) in the PFOA treatment group and 148 DEGs in the GenX treatment group. 10 genes were selected for qRT-PCR validation and were confirmed to be DEGs. Pathway enrichment analysis revealed that several developmental processes were altered after PFOA exposure and showed an up-regulated pattern. And down-regulated DEGs after PFOA exposure were enriched for metabolic process and immune system process. GenX exposure is associated with up-regulated fatty acid transport pathways and inflammatory process. Our study is the first one to investigate the effects of PFASs on marsupial animals, providing supportive evidence of the similar transcriptomic alterations caused by PFOA and a fluorinated alternative GenX, which can work as a complement of the previous studies of PFASs effects on rodent or human.
2022-10-15 | GSE208237 | GEO
Project description:Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. The majority (152/176) of X-linked genes exhibited paternally imprinted expression with nearly 100% maternal allele expression, whereas 24 loci (14%) escaped inactivation showing varying levels of biallelic expression. In addition to regulation by the non-coding RSX transcript, strong depletion of H3K27me3 at escaper gene loci indicates that histone states also influence opossum XCI. Notably, the opossum does not show an association between X-linked gene expression and promoter DNA methylation. Our study provides the first comprehensive catalogue of parent-of-origin expression status for X-linked genes in a marsupial and sheds light on the regulation and evolution of imprinted XCI in mammals. Profiling of four histone modifications in embryonic day 13 opossum (Monodelphis domestica) fetal brain by Illumina ChIP-seq
2013-09-23 | E-GEOD-45186 | biostudies-arrayexpress