Biology subjects

Frankenberg, S. R.

Publications and source records attributed to Frankenberg, S. R..

5 recordsLinked to original sources

bioRxiv2024

Enrichment of spermatogonial stem cells and staging of the testis cycle in a dasyurid marsupial, the fat-tailed dunnart

There is increasing interest in use of marsupial models in research, for use in next-generation conservation by improving fitness through genetic modification, and in de-extinction efforts. Specifically this includes dasyurid marsupials such as the Thylacine, Tasmanian devil, quolls and the small rodent-like dunnarts. Technologies for generating genetically modified Australian marsupials remains to be established. Given the need to advance research in this space, the fat-tailed dunnart (Sminthopsis crassicaudata) is being established as a model for marsupial spermatogonial stem cell isolation, modification and testicular transplantation. This species is small (60-90mm body size), polyovulatory (8-12 pups per birth), and can breed in standard rodent facilities when housed in a 12:12 light cycle. To develop the fat tailed dunnart as a model for next-generation marsupial conservation, this study aimed to enrich dunnart spermatogonial stem cells from whole testis digestions using a fluorescent dye technology and fluorescence-activated cell sorting. This approach is not dependent on antibodies or genetic reporter animals that are limiting factors when performing cell sorting on species separated from human and mouse by large evolutionary timescales. This study also assessed development of spermatogonia and spermatogenesis in the fat-tailed dunnart, by making the first definition of the cycle of the seminiferous epithelium in any dasyurid. Overall, this is the first detailed study to assess the cycle of dasyurid spermatogenesis and provides a valuable method to enrich marsupial spermatogonial stem cells for cellular, functional and molecular analysis.

cell biology↗

bioRxiv2024

Genetically engineered resistance to bufotoxin in marsupial ATP1A1

The introduction of the bufotoxin-secreting cane toad (Rhinella marina) to Queensland in 1935 has had a devastating impact on wildlife in the Australian tropics. Having evolved for millions of years in the absence of cane toads or other bufotoxin-secreting organisms, many of the Australias native predators that include cane toads in their diet suffered large population declines following cane toad invasion to their habitat. One marsupial species, the northern quoll (Dasyurus hallucatus), is now classified as endangered (IUCN Red List) largely due to bufotoxin ingestion. This study aimed to introduce bufotoxin resistance into a marsupial cell line by editing part of the ATP1A1 gene encoding the extracellular H1-H2 domain - the binding target of bufotoxin. To this end, CRISPR prime editing was used to replace the part of the wildtype ATP1A1 gene encoding the H1-H2 domain in fibroblasts of a related marsupial model, the fat-tailed dunnart (Sminthopsis crassicaudata), with modifications known to be associated with bufotoxin resistance. The genetically modified cell population showed a >45-fold increase in resistance to bufalin (an active component of bufotoxin) compared to wild type. This study provides a proof of concept towards engineering genetic resistance in the northern quoll to halt or even reverse its current population decline.

bioengineering↗

bioRxiv2023

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata)

Marsupials exhibit highly specialized patterns of reproduction and development, making them uniquely valuable for comparative genomics studies with their sister lineage, eutherian (also known as placental) mammals. However, marsupial genomic resources still lag far behind those of eutherian mammals, limiting our insight into mammalian diversity. Here, we present a series of novel genomic resources for the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-like marsupial that, due to its ease of husbandry and ex-utero development, is emerging as a laboratory model. To enable wider use, we have generated a multi-tissue de novo transcriptome assembly of dunnart RNA-seq reads spanning 12 tissues. This highly representative transcriptome is comprised of 2,093,982 assembled transcripts, with a mean transcript length of 830 bp. The transcriptome mammalian BUSCO completeness score of 93% is the highest amongst all other published marsupial transcriptomes. Additionally, we report an improved fat-tailed dunnart genome assembly which is 3.23 Gb long, organized into 1,848 scaffolds, with a scaffold N50 of 72.64 Mb. The genome annotation, supported by assembled transcripts and ab initio predictions, revealed 21,622 protein-coding genes. Altogether, these resources will contribute greatly towards characterizing marsupial biology and mammalian genome evolution.

genomics↗

bioRxiv2023

Reference genome of the endangered eastern quoll (Dasyurus viverrinus)

The eastern quoll (Dasyurus viverrinus) is an endangered marsupial mesopredator native to Australia. Since the extirpation of the last mainland Australian populations in the late 20th century, wild populations of this species have been restricted to two islands at the far southern end of its historical range. Eastern quolls are the subject of captive breeding programs and attempts have recently been made to re-establish a population in mainland Australia through translocations. However, few resources currently exist to guide the genetic management of this species. Here, we generated a chromosome-scale reference genome for the eastern quoll, along with gene annotations supported by multi-tissue transcriptomes. Through comparisons with related species, we find that our reference genome is among the most complete marsupial assemblies currently available. Using this assembly, we infer the species demographic history and identify potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely drives differences in pelage color between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii). The genomic resources we present are valuable new tools for evolutionary and conservation genomic studies.

genomics↗

bioRxiv2022

Evolutionary Origin of Vertebrate OCT4/POU5 Functions in Supporting Pluripotency

The support of pluripotent cells over time is an essential feature of development. In eutherian embryos, pluripotency is maintained from naive states in peri-implantation to primed pluripotency at gastrulation. To understand how these states emerged, we reconstruct the evolutionary trajectory of the Pou5 gene family, which contains the central pluripotency factor OCT4. By coupling evolutionary sequence analysis with functional studies in mouse Embryonic Stem Cells (ESCs), we found that the ability of POU5 proteins to support pluripotency originated in the gnathostome lineage, prior to the generation of two paralogues, Pou5f1 and Pou5f3 via gene duplication. In osteichthyans, retaining both genes, the paralogues differ in their support of naive and primed pluripotency. This specialization of these duplicates enables the diversification of function in self-renewal and differentiation. By integrating sequence evolution, ESC phenotypes, developmental contexts and structural modelling, we pinpoint OCT4 regions sufficient for naive pluripotency and describe their adaptation over evolutionary time.

developmental biology↗