Chromosome Science 21: 1-44, 2018 APCC6 (the 6th Asia-Pacic Chromosome Colloquium) Held on July 4th to 5th, 2018 At University of Canberra Australia Local Organizing Committee Tariq Ezaz University of Canberra, Australia Janine Deakin University of Canberra, Australia Jenny Graves University of Canberra, Australia Craig Moritz Australian National University, Australia Mark Eldridge Australian Museum, Australia Sally Potter Australian National University, Australia Kornsorn Srikulnath Kasetsart University, Bangkok, Thailand APCC6 University of Canberra, Australia 1 Chromosomes in the light of evolution Harris Lewin University of California Davis, USA Chromosome rearrangements are a hallmark of ge- nome evolution and essential for understanding the mechanisms of speciation and adaptation. Determining the types and chronology of chromosome rearrange- ments over evolutionary time scales has been a difficult problem due primarily to the lack of high quality, chro- mosome-scale genome assemblies that are necessary ORAL PRESENTATION for reliable reconstruction of ancestral genomes. In addi- tion, for genome-wide comparisons that require resolv- Plenary Lectures ing large numbers of rearrangements of varying scale, determining ancestral chromosomal states is challenging both methodologically and computationally. We recently developed a new computational tool for reconstructing ancestral chromosomes at high resolution, called DE- SCHRAMBLER, which uses syntenic fragments construct- ed from whole-genome comparisons of both high qual- ity chromosome-scale and fragmented assemblies in a phylogenetic probabilistic framework. We applied DE- SCHRAMBLER to sequenced genomes of 21 species that included representatives of 10 eutherian orders. Seven ancestral genomes leading to human were reconstruct- ed, including the ancestor of all placental mammals. These reconstructions revealed a detailed history of chromosome rearrangements that occurred during ~105 million years of eutherian evolutionOur results provide an evolutionary basis for comparison of the genome or- ganization of all eutherians that will facilitate greater un- derstanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases. With ongoing ef- forts to sequence vertebrate genomes from all classes, it will be possible to extend chromosome reconstructions deeper into evolutionary time. Sequence-based recon- struction of ancestral chromosomes thus provides a new opportunity to bridge the gap between traditional cy- togenetics and genomics by illuminating the origins of ancestral synteny and the timing of chromosome rear- rangements during evolution. 2 APCC6 University of Canberra, Australia Unique sex chromosome and sex- determining mechanism in Japanese native mammals, genus Tokudaia Asato Kuroiwa Faculty of Science, Hokkaido University, Japan In placenta mammals, a sex is genetically directed by inheritance of sex chromosomes at the time of fertiliza- tion. If the sex chromosome constitution is XX, the fer- tilized egg develops into a female, whereas if the con- stitution is XY, it becomes a male. Sex determination is actually carried out by the SRY (sex-determining region on Y) gene located on the Y chromosome. The expres- sion starts in supporting cell precursors derived from coelomic epithelium and induces SOX9 (SRY-box 9) ex- pression. The genus Tokudaia, Muridae, Rodentia does not adopt this sex-determining mechanism that is strictly conserved in mammals. Tokudaia consists of three spe- cies. Remarkably, two species, Tokudaia osimensis (Amami spiny rat) and Tokudaia tokunoshimensis (Tokunoshima spiny rat) have XO/XO sex chromosome constitution caused by lacking the Y chromosome. The SRY gene is also absent in these species. By contrast, the remaining one, Tokudaia muenninki (Okinawa spiny rat) has XX/ XY sex chromosome constitution same as general mam- mals. However, their sex chromosomes have acquired the neo-X and neo-Y regions due to a fusion of a pair of autosomes to the X and Y chromosomes. Excessive duplicated copies of SRY are distributed on the Y chro- mosome, whereas, our previous studies indicated these were not functional. Tokudaia therefore have acquired a unique sex-determining mechanism independent of SRY. All species inhabit the southernmost islands in Japan. All are on the verge of extinction and successful artificial breeding has not been achieved, hence, we have stud- ied Tokudaia using limited materials. In this session, I will show recent data of the unique sex chromosome evolu- tion and the sex-determining mechanism in Tokudaia. APCC6 University of Canberra, Australia 3 Chromosome-level genome assembly and reconstruction of evolutionary events in birds and other dinosaurs Darren K. Griffin1*, Rebecca E. O’Connor1, Michael N. Romanov1, Joana Damas2, Marta Farra2, Henry Mar- tell1, Lucas Kiazim1, Rebecca Jennings1, Anjali Man- dawala3, Sunitha Joseph1, Katie E. Fowler3, Eden A. Slack2, Emily Allanson2, Malcolm Ferguson-Smith4, Paul M. Barrett5, Nicole Valenzuela6, Denis M. Larkin2 1School of Biosciences, University of Kent, Canterbury, UK 2Department of Comparative Biomedical Sciences, Royal Veteri- nary College, University of London, London, UK Section: Cytogenetics in the 3School of Human and Life Sciences, Canterbury Christchurch University, Canterbury, Kent, UK genomics 4Department of Veterinary Medicine, Cambridge University, Cam- bridge, UK 5Department of Earth Sciences, Natural History Museum, Crom- well Road, London SW7 5BD, UK 6Department of Ecology, Evolution, and Organismal Biology, Iowa State University, USA The ultimate aim of a genome assembly is to create a contiguous length of sequence from the p- to q- termi- nus of each chromosome. Most assemblies are however highly fragmented, limiting their use in studies of gene mapping, phylogenomics and genomic organisation. To overcome these limitations, we developed a novel scaf- fold-to-chromosome anchoring method combining ref- erence-assisted chromosome assembly (RACA) and fluo- rescence in situ hybridisation (FISH) to position scaffolds from de novo genomes onto chromosomes. Using RACA, scaffolds were ordered and orientated into predicted chromosome fragments (PCFs) against a reference and outgroup genome. PCFs were verified using PCR prior to FISH mapping. A universal set of FISH probes devel- oped through the selection of conserved regions were then used to map PCFs of peregrine falcon (Falco pereg- rinus), pigeon (Columba livia), ostrich (Struthio camelus), saker falcon (Falco cherrug) the budgerigar (Melopsit- tacus undulatus). Using this approach, we were able im- prove the N50 of genomes seven-fold. Results revealed that Interchromosomal breakpoint regions are limited to regions with low sequence conservation, shedding light on why most avian species have very stable karyotypes. Our combined FISH and bioinformatics approach repre- sents a step-change in the mapping of genome assem- blies, allowing comparative genomic research at a higher resolution than previously possible. The universal probe set, facilitates research into avian karyotype evolution and the role of chromosome rearrangements in adapta- tion and phenotypic diversity in birds. Indeed, they have been used on over 20 avian species plus non-avian rep- tiles (including turtles), shedding light into the evolu- tion of dinosaur species. Non-avian dinosaurs remain subjects of intense biological enquiry while pervading popular culture and the creative arts. While organismal studies focus primarily on their morphology, relation- ships, likely behaviour, and ecology there have been few 4 APCC6 University of Canberra, Australia academic studies that have made extensive extrapola- Testing the Integrative Breakage Model: A tions about the nature of non-avian dinosaur genome multidisciplinary approach for the study of structure prior to the emergence of modern birds. We have used multiple avian whole genome sequences as- genome plasticity sembled at a chromosomal level, to reconstruct the most likely gross genome organization of the overall genome Aurora Ruiz-Herrera, Andreu Paytuvì-Gallart and structure of the diapsid ancestor and reconstruct the se- Covadonga Vara quence of inter and intrachromosomal events that most likely occurred along the Archosauromorpha-Archosau- Universitat Autonoma Barcelona, Spain ria-Avemetatarsalia-Dinosauria-Theropoda-Manirapto- ra-Avialae lineage from the lepidosauromorph-archo- sauromorph divergence ~275 mya through to extant Unlocking the genomic basis of speciation is a re- neornithine birds. search priority in biology fuelled by the ongoing debate on species concepts and facilitated by the availability of an unprecedented large number of genomic resources. Through comparative genomics of both closely and dis- tantly related mammalian species our research group, along with others, has contributed to models that ex- plain genome structure and evolution. Such reconstruc- tions have revealed that the genomic regions implicated in structural evolutionary changes, disrupt genomic syn- teny, and are clustered in regions more prone to break and reorganize. In searching for the origin (and conse- quences) of this evolutionary instability, we provided in- sights on the genomic features that characterize evolu- tionary regions. In addition, we have also observed that changes in gene expression that are caused by genome reshuffling may have a selective advantage through the development of new adaptive characters specific to mammalian