Diversity of reptile sex chromosome evolution revealed by cytogenetic and linked-read sequencing

Reptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about mechanisms of sex chromosome turnover. Recent studies have made significant progress in better understanding diversity and conservation of reptile sex chromosomes, with however no reptile master sex determination genes identified. Here we describe an integrated genomics and cytogenetics pipeline, combining probes generated from the microdissected sex chromosomes with transcriptome and genome sequencing to explore the sex chromosome diversity in non-model Australian reptiles. We tested our pipeline on a turtle, two species of geckos, and a monitor lizard. Genes identified on sex chromosomes were compared to the chicken genome to identify homologous regions among the four species. We identified candidate sex determining genes within these regions, including conserved vertebrate sex-determining genes pdgfa, pdgfra amh and wt1, and demonstrated their testis or ovary-specific expression. All four species showed gene-by-gene rather than chromosome-wide dosage compensation. Our results imply that reptile sex chromosomes originated by independent acquisition of sex-determining genes on different autosomes, as well as translocations between different ancestral macro- and microchromosomes. We discuss the evolutionary drivers of the slow differentiation and turnover of reptile sex chromosomes

Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes

The Consortium for Snake Genomics is in the process of sequencing the genome and creating transcriptomic resources for the Burmese python. Here, we describe how this will be done, what analyses this work will include, and provide a timeline

Report from the First Snake Genomics and Integrative Biology Meeting

This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems.Organismic and Evolutionary Biolog

Report from the First Snake Genomics and Integrative Biology Meeting

This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems

Report from the first snake genomics and integrative biology meeting

Animal science

Chromosomal evolution in the Ridge-tailed goannas

Chromosomes were the first genetic molecules used for evolutionary studies and are a complex arrangement of proteins and DNA sequences that organise into stable structures for the faithful replication of genetic material. These structures are conserved in all domains of life. Chromosomal evolution often occurs in tandem with species evolution, and the diversity of form and number of chromosomes is highly variable across taxa. The relationship between chromosome evolution and species divergence is a topic of ongoing research with a rich history dating back over a century. Despite this, several questions remain unanswered about the fundamental mechanisms that drive chromosome evolution and the direct impacts that these changes have on the sequence of events that lead to species adaptation, diversification and finally speciation. This thesis addresses fundamental questions regarding the molecular processes that occur during species evolution, and what role chromosome evolution plays during these events. The chromosomal, genic, and geographic processes are typically considered independent variables, but often there are events that occur simultaneously or with considerable overlap, and integrated studies merging technologies and theory are needed for the interpretation of contradictions revealed by one-dimensional studies. In this thesis, I explore the role of chromosome polymorphisms in the divergence of Ridge-tailed goannas, (Varanus acanthurus BOULENGER), a species complex of dwarf monitor lizards from the Subgenus Odatria. This unique group of monitor lizards have a broad distribution across northern Australia and widespread chromosome polymorphisms across a significant portion of their range. However, some populations have fixed karyotypes typical of all other Varanus species in which clusters of species (clades) are defined by their karyotype identity, and the clades differ by chromosome morphology characterised by pericentric inversions on chromosomes 5-8. It is unknown if the chromosome polymorphisms represent a genetic barrier between individuals with different karyotypes, represent a hybrid population, or what genes are involved in these rearrangements. To test for the role these polymorphisms play in species divergence, I used a multidisciplinary, chromosomics approach integrating field ecology, population genetics, genomics, and cytogenetics. Specifically, I tested for geneflow between individuals with chromosome rearrangements within and between populations to address the question: are chromosome polymorphisms a by-product or a driver of population divergence? I proceed to characterise the rearrangements identified on both autosomes and the sex chromosomes. This thesis shows that polymorphisms occurring within chromosomes are central to driving genetic divergence and are actively occurring within populations, and these transitions have occurred de novo in different populations multiple times resulting in a rapid diversification of species in the Varanidae lineage in Australia. I further apply the logic that de novo chromosome rearrangements are drivers of divergence to the broader understanding of vertebrate chromosome evolution and highlight the methodology and its application for addressing these fundamental questions in other vertebrates. Similar structural transitions characterise the diversification of the primates and other vertebrate lineages that have undergone recent and rapid speciation

Precocious myelination in a mouse model of autism.

Autism spectrum disorder (ASD) has been hypothesized to be a result of altered connectivity in the brain. Recent imaging studies suggest accelerated maturation of the white matter in young children with ASD, with underlying mechanisms unknown. Myelin is an integral part of the white matter and critical for connectivity; however, its role in ASD remains largely unclear. Here, we investigated myelin development in a model of idiopathic ASD, the BTBR mice. Magnetic resonance imaging revealed that fiber tracts in the frontal brain of the BTBR mice had increased volume at postnatal day 6, but the difference reduced over time, reminiscent of the findings in young patients. We further identified that myelination in the frontal brain of both male and female neonatal BTBR mice was increased, associated with elevated levels of myelin basic protein. However, myelin pattern was unaltered in adult BTBR mice, revealing accelerated developmental trajectory of myelination. Consistently, we found that signaling of platelet-derived growth factor receptor alpha (PDGFRα) was reduced in the frontal brain of neonatal BTBR mice. However, levels of microRNA species known to regulate PDGFRα signaling and myelination were unaltered. Together, these results suggest that precocious myelination could potentially contribute to increased volume and connectivity of the white matter observed in young children with ASD