Peter Temple-Smith | bioRxiv Science

bioRxiv2016

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Background: Spiny mice of the genus Acomys are small desert-dwelling rodents that display physiological characteristics not typically found in rodents. Recent investigations have reported a menstrual cycle and scar free-wound healing in this species; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique physiological traits, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research. However, little genetic information is currently available for Acomys, limiting the application of some modern investigative techniques. This project aimed to generate a reference transcriptome assembly for the common spiny mouse (Acomys cahirinus).\n\nResults: Illumina RNA sequencing of male and female spiny mice produced 451 million, 150bp paired-end reads from 15 organ types. An extensive survey of de novo transcriptome assembly approaches of high-quality reads using Trinity, SOAPdenovo-Trans, and Velvet/Oases at multiple kmer lengths was conducted with 49 single-kmer assemblies generated from this dataset, with and without in silico normalization and probabilistic error correction. Merging transcripts from 49 individual single-kmer assemblies into a single meta-assembly of non-redundant transcripts using the EvidentialGene tr2aacds pipeline produced the highest quality transcriptome assembly, comprised of 880,080 contigs, of which 189,925 transcripts were annotated using the SwissProt/Uniprot database.\n\nConclusions: This study provides the first detailed characterization of the spiny mouse transcriptome. It validates the application of the EvidentialGene tr2aacds pipeline to generate a high-quality reference transcriptome assembly in a mammalian species, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.

Bioinformatics↗

bioRxiv2016

First evidence of a menstruating rodent: the spiny mouse (Acomys cahirinus)

BackgroundAdvances in research relating to menstruation and associated disorders (such as endometriosis and pre-menstrual syndrome) have been hindered by the lack of an appropriate animal model. Thus, many aspects of this phenomenon remain poorly understood limiting the development of efficacious treatment for women. Menstruating species account for only 1.5% of mammals, and less than 0.09% of these are non-primates. Menstruation occurs as a consequence of progesterone priming of the endometrial stroma and a spontaneous decidual reaction. At the end of each infertile cycle as progesterone levels decline the uterus is unable to maintain this terminally differentiated stroma and the superficial endometrium is shed. True menstruation has never been reported in rodents.\n\nObjectiveHere we describe the first observation of menstruation in a rodent, the spiny mouse (Acomys cahirinus).\n\nStudy DesignVirgin female spiny mice (n=14) aged 12-16 weeks were sampled through daily vaginal lavage for 2 complete reproductive cycles in our in-house colony at Monash Medical Centre, Clayton, Australia. Stage-specific collection of reproductive tissue and plasma was used for histology, prolactin immunohistochemistry, and ELISA assay of progesterone (n=5 / stage of the menstrual cycle). Normally distributed data are reported as the mean {+/-} standard error and significant differences calculated using a one-way ANOVA. Non-normal data are displayed as the median values of replicates (with interquartile range) and significant differences calculated using Kruskal-Wallis test.\n\nResultsMean cycle length was 8.7 {+/-} 0.4 days with red blood cells observed in the lavages over 3.0 {+/-} 0.2 days. Cyclic endometrial shedding and blood in the vaginal canal concluding with each infertile cycle was confirmed in all virgin females. The endometrium was thickest during the luteal phase, when plasma progesterone peaked at ~102.1 ng/mL and the optical density for prolactin immunoreactivity was strongest. The spiny mouse undergoes spontaneous decidualisation, demonstrating for the first time menstruation in a rodent.\n\nConclusionThe spiny mouse is the first rodent species known to menstruate and provides an unprecedented natural non-primate model to study the mechanisms of menstrual shedding and repair, and may be useful in furthering our understanding of human specific menstrual and pregnancy associated diseases.

Physiology↗