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Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)

ABSTRACT: Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)

PROVIDER: PRJNA676111 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13036043_1.fastq.gz	Fastqsanger.gz
	SRR13036043_2.fastq.gz	Fastqsanger.gz
	SRR13036044_1.fastq.gz	Fastqsanger.gz
	SRR13036044_2.fastq.gz	Fastqsanger.gz
	SRR13036045_1.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)

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

Australian marsupial phylogeny

Project description:Australian marsupial phylogeny with denovo assembly of target exons captured sequences.

| PRJEB39788 | ENA

Gene regulatory dynamics during craniofacial development in a carnivorous marsupial

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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Isolation and characterization of melanopsin (Opn4) from the Australian marsupial Sminthopsis crassicaudata (fat-tailed dunnart).

Project description:Melanopsin confers photosensitivity to a subset of retinal ganglion cells and is responsible for many non-image-forming tasks, like the detection of light for circadian entrainment. Recently, two melanopsin genes, Opn4m and Opn4x, were described in non-mammalian vertebrates. However, only one form, Opn4m, has been described in the mammals, although studies to date have been limited to the placentals and have not included the marsupials. We report here the isolation and characterization of an Opn4 gene from an Australian marsupial, the fat-tailed dunnart (Sminthopsis crassicaudata), and present evidence which suggests that the Opn4x gene was lost before the placental/marsupial split. In situ hybridization shows that the expression of Opn4 in the dunnart eye is restricted to a subset of ganglion cells, a pattern previously reported for rodents and primates. These Opn4-positive cells are randomly distributed across the dunnart retina. We also undertook a comparative analysis with the South American marsupial, the grey short-tailed opossum (Monodelphis domestica), and two placental mammals, mouse and human. This approach reveals that the two marsupials show a higher sequence identity than that seen between rodents and primates, despite separating at approximately the same point in time, some 65-85 Myr ago.

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Postnatal development in a marsupial model, the fat-tailed dunnart (Sminthopsis crassicaudata; Dasyuromorphia: Dasyuridae).

Project description:Marsupials exhibit unique biological features that provide fascinating insights into many aspects of mammalian development. These include their distinctive mode of reproduction, altricial stage at birth, and the associated heterochrony that is required for their crawl to the pouch and teat attachment. Marsupials are also an invaluable resource for mammalian comparative biology, forming a distinct lineage from the extant placental and egg-laying monotreme mammals. Despite their unique biology, marsupial resources are lagging behind those available for placentals. The fat-tailed dunnart (Sminthopsis crassicaudata) is a laboratory based marsupial model, with simple and robust husbandry requirements and a short reproductive cycle making it amenable to experimental manipulations. Here we present a detailed staging series for the fat-tailed dunnart, focusing on their accelerated development of the forelimbs and jaws. This study provides the first skeletal developmental series on S. crassicaudata and provides a fundamental resource for future studies exploring mammalian diversification, development and evolution.

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