GSE161274
Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)
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. Overall design: Fat-tailed dunnarts were bred at the Native Wildlife Teaching and Research Facility at The University of Queensland, Queensland, Australia. Specimens at postnatal ages P12 and P20 (N=3 each age) were used. For each specimen both hemispheres of the neocortex were micro-dissected out followed by total RNA extraction, RNA quality analysis on a Bioanalyzer 2100 RNA Nano assay (Agilent), cDNA library preparation using a Truseq Stranded Total RNA kit v4 (Illumina), and sequencing on an Illumina HiSeq 2000 with 125 bp paired-end reads. A de novo transciptome was assembled using the pooled RNA sequence data of all samples using Trinity, then differential gene expression analysis performed across developmental ages (RSEM, edgeR).