Australian marsupial phylogeny
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ABSTRACT:
PROVIDER: PRJEB39788 | ENA |
REPOSITORIES: ENA
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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.
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Project description:Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)
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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.
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Project description:Genome-wide mRNA expression profiles of 70 primary gastric tumors from the Australian patient cohort. Like many cancers, gastric adenocarcinomas (gastric cancers) show considerable heterogeneity between patients. Thus, there is intense interest in using gene expression profiles to discover subtypes of gastric cancers with particular biological properties or therapeutic vulnerabilities. Identification of such subtypes could generate insights into the mechanisms of cancer progression or lay the foundation for personalized treatments. Here we report a robust gene-xpression-based clustering of a large collection of gastric adenocarcinomas from Singaporean patients [GSE34942 and GSE15459]. We developed and validated a classifier for the three subtypes in Australian patient cohort. Profiling of 70 primary gastric tumors on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. All tumors were collected with approvals from Peter MacCallum Cancer Center, Australia; the Research Ethics Review Committee; and signed patient informed consent.
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