Rebecca O'Connor

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

BackgroundThe availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.ResultsFocusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species’ genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.ConclusionsResults suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly

Summary Balanced chromosomal aberrations have been shown to affect fertility in most species studied, often leading to hypoprolificacy (reduced litter size) in domestic animals such as pigs. With an increasing emphasis in modern food production on the use of a small population of high quality males for artificial insemination, the potential economic and environmental costs of hypoprolific boars, bulls, rams etc. are considerable. There is therefore a need for novel tools to facilitate rapid, cost‐effective chromosome translocation screening. This has previously been achieved by standard karyotype analysis; however, this approach relies on a significant level of expertise and is limited in its ability to identify subtle, cryptic translocations. To address this problem, we developed a novel device and protocol for translocation screening using subtelomeric probes and fluorescence in situ hybridisation. Probes were designed using BACs (bacterial artificial chromosomes) from the subtelomeric region of the short (p‐arm) and long (q‐arm) of each porcine chromosome. They were directly labelled with FITC or Texas Red (p‐arm and q‐arm respectively) prior to application of a ‘Multiprobe’ device, thereby enabling simultaneous detection of each individual porcine chromosome on a single slide. Initial experiments designed to isolate BACs in subtelomeric regions led to the discovery of a series of incorrectly mapped regions in the porcine genome assembly (from a total of 82 BACs, only 45 BACs mapped correctly). Our work therefore highlights the importance of accurate physical mapping of newly sequenced genomes. The system herein described allows for robust and comprehensive analysis of the porcine karyotype, an adjunct to classical cytogenetics that provides a valuable tool to expedite efficient, cost effective food production.

[Avian cytogenetics goes functional] Third report on chicken genes and chromosomes 2015

Opening insights into new technologies in avian genomics The chicken has long been a model organism for genetic and developmental studies. It is now beginning to take its place as a model genome, opening up the fields of phylogenetics and comparative genomics like never before. This report comes at a time of huge technological advances (particularly in sequencing methodologies) and summarizes the current efforts to complete the gaps in the genome. It describes the progress that has been made in genomic annotation, particularly with respect to noncoding RNAs and genetic variants. Reviews of comparative genomics, avian evolution and sex determination are included as well as transcriptomic case studies and developments in epigenetic studies. The Third Report on Chicken Genes and Chromosomes also features the National Avian Research Facility and how it has developed into a resource for the study of avian biology, genetics, infection and disease. In this volume researchers interested in genetics, genomics and evolution will find detailed information that has not been available until now.

Avian cytogenetics goes functional

Chromosomal abnormalities in secondary bovine oocytes matured in vitro up to 48 hours Abstract Chromosomal abnormalities in secondary bovine oocytes matured in vitro up to 48 hours. 21st International Colloquium on Animal Cytogenetics and Gene Mapping Rubessa M., Pauciullo A., Peretti V., Iannuzzi L., Ramunno L., Di Berardino D.Edited by: L. Iannuzzi, A. Perucatti, A. Iannuzzi, A. Pauciullo, V. Genualdo, D. Incarnato, L. Keller (CNRISPAAM, Naples, Italy)Sister Chromatid exchange (SCE) test in river buffalo cells treated with Furocoumarins. / Iannuzzi A.; Perucatti A.; Genualdo V.; Pauciullo A.; Pucciarelli L.; Incarnato D.; Melis R.; Porqueddu C.; Marchetti M.; Iannuzzi L.. In: CHROMOSOME RESEARCH. ISSN 0967-3849. 22(2014), pp. 421-421. Original Citation: Sister Chromatid exchange (SCE) test in river buffalo cells treated with Furocoumarins.Comparative FISH-mapping of TNF, STAT5A and MNTR1A fecundity genes on river buffalo, cattle, sheep and goat. / Iannuzzi A.; Perucatti A.; Pauciullo A.; Genualdo V.; Incarnato D.; Pucciarelli L.; De Lorenzi L.; Parma P.; Iannuzzi L.. In: CHROMOSOME RESEARCH. ISSN 0967-3849. 22(2014), pp. 418-418. Original Citation: Comparative FISH-mapping of TNF, STAT5A and MNTR1A fecundity genes on river buffalo, cattle, sheep and goat.Multicolor FISH with 10 specific painting probes for the rapid identification of the sub-metacentric river buffalo autosomes (Bubalus bubalis, 2n=50) / Pauciullo A.; Perucatti A.; Iannuzzi A.; Incarnato D.; Genualdo V.; Pucciarelli L.; Di Berardino D.; Iannuzzi L.. In: CHROMOSOME RESEARCH. ISSN 0967-3849. 22(2014), pp. 410-410. Original Citation: Multicolor FISH with 10 specific painting probes for the rapid identification of the sub-metacentric river buffalo autosomes (Bubalus bubalis, 2n=50)

Gross genome evolution in the Dinosauria

Book 22 International Colloquium on Animal Cytogenetics and Genomics 2–5 July 2016, Toulouse France Dedicated to the memory of Florence Richard Edited by: Martine Yerle-Bouissou & Alain Pinton GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France (martine.yerle@toulouse.inra.fr) Published online: 16 August 2016 # Springer Science+Business Media Dordrecht 2016The Dinosaurs dominated the terrestrial environment for around 170 million years and are probably the most successful land vertebrate group to have existed. They survived several mass extinction events before finally all non-avian species were wiped out 66 million years ago in the Cretaceous-Paleogene extinction event. The neornithes (modern birds) are their living descendants. Despite the huge phenotypic diversity seen in birds, they, and some non-avian reptiles (e.g. some turtle species) display remarkably similar karyotypes with a characteristic pattern of macro and micro chromosomes, small genome size and few repetitive elements. This suggests that these were features present early in their evolution. The availability whole genome sequences and the recent sequencing of around 50 avian genomes, 6 of which were assembled at sufficient read depth and coverage to permit visualization at the chromosomal level, has facilitated the reconstruction of the overall genome structure (karyotype) of both Saurian (bird-reptile) and Avian ancestors. Subsequent use of bioinformatic tools permitted the retracing of the gross evolutionary changes that have occurred along the Dinosaur (and various avian) lineages. Gene ontology analysis of homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) of chromosomes has allowed us to search for enrichment for genes involved in chromosome rearrangement (consistent with the formation of the signature fragmented karyotype of birds (and probably dinosaurs)). Preliminary analyses of EBRs suggest that they appear to be enriched for genes involved in body size, consistent with the overall gross reduction in body size as dinosaurs evolved into birds. Our results also suggest a period of inter-and intra-chromosomal rearrangements up until around the divergence of turtles (approximately 210 MYA) with a relatively “fixed” pattern thereafter where intra-chromosomal rearrangement plus a few identifiable fissions predominated. It is reasonable therefore to speculate that this ‘avianstyle’ genome may be one of the key factors in the success of this extraordinarily diverse animal group, allowing rapid speciation through increased propensity for random segregation and genetic recombination.

Upgrading Molecular Cytogenetics to Study Reproduction and Reproductive Isolation in Mammals, Birds, and Dinosaurs

amazing diversity of life, including over 2,000 species of vascular plants, exotic mammals such as tapirs, giant anteaters, howler monkeys, ocelots, and jaguars, in addition to hundreds of different bird species and thousands of different insects, the choice of Foz is an excellent analogy for the diverse approaches and systems chromosome biologists explore, and that will be emphasized throughout this conference. The 2016 ICC program offers seven sessions, beginning with a session on Chromosome Structure and Nuclear Architecture, highlighting the influences and interactions chromosomes have on the three-dimensional space of the nucleus. Session II will focus on Specialized Chromosomes, such as sex chromosomes and B chromosomes, whose structure and behavior are often distinguished from that of autosomal chromosomes. Population and Evolutionary Chromosome Biology, the third session, covers a synthesis of chromosome biology and The International Chromosome Conferences (ICC) originated from the Oxford Chromosome Conferences, inaugurated by C.D. Darlington and K.R. Lewis in 1964 and held subsequently in England in 1967 and 1970. The Chromosome Conference grew to an international event with its fourth meeting, held in Jerusalem, Israel in 1972, heralding the beginning of 40 years of technological advances that have expanded our understanding of chromosome biology in model and non-traditional biological systems. Having been hosted in Europe and the United States 16 times since then, this year the ICC will be held across the equator in Foz do Iguaçu, Brazil, on July 10–13, 2016. The event will bring scientists from across the globe to a biannual meeting focused on modern advances in chromosome biology, technology and theory. The Iguaçu National Park, a UNESCO World Heritage Centre, includes the Iguaçu Falls and has been chosen as one of the ‘New Natural Seven Wonders of the World’. Home to an Published online: June 2, 2016I.O. Furo a , R. Kretschmer b , R.J. Gunski c , A.D.V. Garnero c , M.A. Ferguson-Smith d , P.C.M. O ́Brien d , E.H.C. de Oliveira e, f a Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, b PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, and c Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Brazil; d Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; e Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, and f Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Brazil

Reconstruction of the putative Saurian karyotype and the hypothetical chromosome rearrangements that occurred along the Dinosaur lineage

Universidade Estadual Paulista Julio de Mesquita Filho, Instituto de Biociencias, Rio Claro, BrasilThe advent of the next generation sequencing (NGS) made sequencing and scaffolding of an entire animal genome a routine procedure. As the result we face a fast increase in the number of animal genomes available due to the activities of large international genome sequencing initiatives e.g., Genome 10K (G10K) or smaller projects. However, the full informative power of a sequenced genome could only be achieved when it is assembled into chromosomes. Usually, a draft or nearly complete animal chromosome assembly is achieved through three steps: (i) constructing contigs based on read overlaps, (ii) merging contigs into scaffolds using pair-end reads, and (iii) mapping scaffolds on chromosomes with the use of physical or genetic maps. As the cost of mapping techniques is still much higher than sequencing, the genetic and physical maps are not available for the majority of the de novo sequenced genomes. To overcome this problem for assemblies that employ long-insert libraries (5 – 40 Kbp) we recently developed the reference-assisted chromosome assembly (RACA) algorithm (Kim et al., 2013). This method relies on both the raw sequencing data (reads) and comparative information; the latter is obtained from alignments between the target (de novo sequenced), a closely related (reference) and more distantly related (outgroup) genomes. Using RACA followed by the manual FISH or PCR verification steps we are reconstructing the chromosome organisation of 19 bird species sequenced by the G10K community. We use the publically available chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) chromosome assemblies as either reference or outgroup for each reconstruction depending on their phylogenetic relationships with each target species. Initially, we established the optimal RACA parameters for a bird chromosome assembly reconstruction using the duck (Anas platyrhynchos) and budgerigar (Melopsittacus undulatus) super-scaffolds assembled with the support from physical maps. This step allowed us to test the reliability of RACA reconstructions for bird genomes. Due to a higher evolutionary conservation of the bird karyotype compared to the mammalian one, we have achieved ~97% accuracy of scaffold adjacencies in our predicted chromosome fragments compared to the ~93-96% accuracies reported for mammals (Kim et al., 2013). We detected ~4-28% of scaffolds in different target bird genomes that are either chimeric or containing genuine lineage-specific evolutionary breakpoint regions. Some of these scaffolds will be selected for follow up PCR or FISH verifications. All RACA reconstructions will become publicly available from our Evolution Highway comparative chromosome browser http://evolutionhighway.ncsa.uiuc.edu/birds/ and will be further utilised to study connections between the chromosome evolution, adaptation and phenotypic diversity in birds and other vertebrates.Universidade Estadual Paulista, Nucleo de Pesquisa e Conservacao de Cervideos, Faculdade de Ciencias Agrarias e Veterinarias, Jaboticabal, Brasil• Invited speaker abstracts have the prefix “S” • Selected Oral presentations have the prefix “O” • Poster abstracts have the prefix “P” S1: 50th Anniversary of the first Oxford Chromosome Conference and some reflections on chromosome synapsis Malcolm A Ferguson-Smith Department of Veterinary Medicine, University of Cambridge, Cambridge, UK. Cyril Darlington, who organised the first Oxford Chromosome Conference 50 years ago, was one of the great pioneers of cytogenetics. He brought new understanding to the mechanisms of mitosis and meiosis and the uniformity of chromosome behaviour in all plants and animals with its implications for evolution. His major conclusions relate to the origin of chiasmata and the properties of sex chromosomes and were based on light microscopy before the era of molecular cytogenetics in the 1970s. Since his day the field has been transformed by electron microscopy, FISH, immunofluorescence of chromosomal proteins, meiotic mutants in yeast and mice and by DNA mapping and sequencing. Progress in understanding chromosome structure and synapsis in meiotic and somatic cells since Darlington will be briefly summarised with emphasis on the unknown. Genome conservation and the nature of non-coding DNA at synapsis sites, and the threedimensional structure of chromosomal proteins (eg, those of axial filaments), should be among the topics for discussion at this and future Chromosome Conferences. 20th International Chromosome Conference (ICCXX) 35120th International Chromosome Conference (ICCXX). 50th Anniversary, University of Kent, Canterbury, 1st–4th September 2014.Dinosaurs hold a unique place both in the history of the earth and the imagination of many. They dominated the terrestrial environment for around 170 million years during which time they diversified into at least 1000 different species. Reptilia, within which they are placed is one of the most remarkable vertebrate groups, consisting of two structurally and physiologically distinct lineages – the birds and the non-avian reptiles, of which there are 10,000 and 7,500 extant species respectively. The dinosaurs are without doubt the most successful group of vertebrate to have existed. They survived several mass extinction events before finally non-avian dinosaurs were defeated 66 million years ago in the Cretaceous-Paleogene extinction event, leaving the neornithes (modern birds) as their living descendants. Aside from the huge phenotypic diversity seen in this group, the birds and non-avian reptiles interestingly display similar karyotypic patterns (with the exception of crocodilians); with the characteristic pattern of macro and micro chromosomes, small genome size and few repetitive elements, suggesting that these were features exhibited in their common ancestor. In this study, the availability of multiple reptile genome sequences (including birds) on an interactive browser (Evolution Highway) allowed us to identify multi species homologous synteny blocks (msHSBs) between the putative avian ancestor (derived from six species of extant birds), the Lizard (Anolis carolensis) and the Snake (Boa constrictor). From these msHSBs we were able to produce a series of contiguous ancestral regions (CARs) representing the most likely ancestral karyotype of the Saurian (ancestor of archosaurs and lepidosaurs) that diverged from the mammalian lineage 280 mya. From this we have hypothesised the series of inter and intra-chromosomal rearrangements that have occurred along the dinosaur (archosaur) lineage to the ancestor of modern birds (100 mya) and along the lepidosaur lineage to the modern snake and lizard using the model of maximum parsimony. Our study shows that relatively few chromosomal rearrangements took place over this period with an average of one inter or intra-chromosomal (translocations and inversions respectively) rearrangement occurring approximately every 2 million years. The majority of these rearrangements appear to be intra-chromosomal suggesting an overall karyotypic stability, which is consistent with that of that of modern birds. Our results support the hypothesis that the characteristically avian genome was present in the saurian ancestor and that it has remained remarkably stable in the 280 million years since. It is credible therefore to suggest that this ‘avian-style’ genome may be one of the key factors in the success of this extraordinarily diverse animal group.

AVIAN ANCESTRAL KARYOTYPE RECONSTRUCTION AND DIFFERENTIAL RATES OF INTER-AND INTRA-CHROMOSOMAL CHANGE IN DIFFERENT LINEAGES

Universidade Estadual Paulista Julio de Mesquita Filho, Instituto de Biociencias, Rio Claro, BrasilThe advent of the next generation sequencing (NGS) made sequencing and scaffolding of an entire animal genome a routine procedure. As the result we face a fast increase in the number of animal genomes available due to the activities of large international genome sequencing initiatives e.g., Genome 10K (G10K) or smaller projects. However, the full informative power of a sequenced genome could only be achieved when it is assembled into chromosomes. Usually, a draft or nearly complete animal chromosome assembly is achieved through three steps: (i) constructing contigs based on read overlaps, (ii) merging contigs into scaffolds using pair-end reads, and (iii) mapping scaffolds on chromosomes with the use of physical or genetic maps. As the cost of mapping techniques is still much higher than sequencing, the genetic and physical maps are not available for the majority of the de novo sequenced genomes. To overcome this problem for assemblies that employ long-insert libraries (5 – 40 Kbp) we recently developed the reference-assisted chromosome assembly (RACA) algorithm (Kim et al., 2013). This method relies on both the raw sequencing data (reads) and comparative information; the latter is obtained from alignments between the target (de novo sequenced), a closely related (reference) and more distantly related (outgroup) genomes. Using RACA followed by the manual FISH or PCR verification steps we are reconstructing the chromosome organisation of 19 bird species sequenced by the G10K community. We use the publically available chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) chromosome assemblies as either reference or outgroup for each reconstruction depending on their phylogenetic relationships with each target species. Initially, we established the optimal RACA parameters for a bird chromosome assembly reconstruction using the duck (Anas platyrhynchos) and budgerigar (Melopsittacus undulatus) super-scaffolds assembled with the support from physical maps. This step allowed us to test the reliability of RACA reconstructions for bird genomes. Due to a higher evolutionary conservation of the bird karyotype compared to the mammalian one, we have achieved ~97% accuracy of scaffold adjacencies in our predicted chromosome fragments compared to the ~93-96% accuracies reported for mammals (Kim et al., 2013). We detected ~4-28% of scaffolds in different target bird genomes that are either chimeric or containing genuine lineage-specific evolutionary breakpoint regions. Some of these scaffolds will be selected for follow up PCR or FISH verifications. All RACA reconstructions will become publicly available from our Evolution Highway comparative chromosome browser http://evolutionhighway.ncsa.uiuc.edu/birds/ and will be further utilised to study connections between the chromosome evolution, adaptation and phenotypic diversity in birds and other vertebrates.Universidade Estadual Paulista, Nucleo de Pesquisa e Conservacao de Cervideos, Faculdade de Ciencias Agrarias e Veterinarias, Jaboticabal, Brasil• Invited speaker abstracts have the prefix “S” • Selected Oral presentations have the prefix “O” • Poster abstracts have the prefix “P” S1: 50th Anniversary of the first Oxford Chromosome Conference and some reflections on chromosome synapsis Malcolm A Ferguson-Smith Department of Veterinary Medicine, University of Cambridge, Cambridge, UK. Cyril Darlington, who organised the first Oxford Chromosome Conference 50 years ago, was one of the great pioneers of cytogenetics. He brought new understanding to the mechanisms of mitosis and meiosis and the uniformity of chromosome behaviour in all plants and animals with its implications for evolution. His major conclusions relate to the origin of chiasmata and the properties of sex chromosomes and were based on light microscopy before the era of molecular cytogenetics in the 1970s. Since his day the field has been transformed by electron microscopy, FISH, immunofluorescence of chromosomal proteins, meiotic mutants in yeast and mice and by DNA mapping and sequencing. Progress in understanding chromosome structure and synapsis in meiotic and somatic cells since Darlington will be briefly summarised with emphasis on the unknown. Genome conservation and the nature of non-coding DNA at synapsis sites, and the threedimensional structure of chromosomal proteins (eg, those of axial filaments), should be among the topics for discussion at this and future Chromosome Conferences. 20th International Chromosome Conference (ICCXX) 35120th International Chromosome Conference (ICCXX). 50th Anniversary, University of Kent, Canterbury, 1st–4th September 2014.Dinosaurs hold a unique place both in the history of the earth and the imagination of many. They dominated the terrestrial environment for around 170 million years during which time they diversified into at least 1000 different species. Reptilia, within which they are placed is one of the most remarkable vertebrate groups, consisting of two structurally and physiologically distinct lineages – the birds and the non-avian reptiles, of which there are 10,000 and 7,500 extant species respectively. The dinosaurs are without doubt the most successful group of vertebrate to have existed. They survived several mass extinction events before finally non-avian dinosaurs were defeated 66 million years ago in the Cretaceous-Paleogene extinction event, leaving the neornithes (modern birds) as their living descendants. Aside from the huge phenotypic diversity seen in this group, the birds and non-avian reptiles interestingly display similar karyotypic patterns (with the exception of crocodilians); with the characteristic pattern of macro and micro chromosomes, small genome size and few repetitive elements, suggesting that these were features exhibited in their common ancestor. In this study, the availability of multiple reptile genome sequences (including birds) on an interactive browser (Evolution Highway) allowed us to identify multi species homologous synteny blocks (msHSBs) between the putative avian ancestor (derived from six species of extant birds), the Lizard (Anolis carolensis) and the Snake (Boa constrictor). From these msHSBs we were able to produce a series of contiguous ancestral regions (CARs) representing the most likely ancestral karyotype of the Saurian (ancestor of archosaurs and lepidosaurs) that diverged from the mammalian lineage 280 mya. From this we have hypothesised the series of inter and intra-chromosomal rearrangements that have occurred along the dinosaur (archosaur) lineage to the ancestor of modern birds (100 mya) and along the lepidosaur lineage to the modern snake and lizard using the model of maximum parsimony. Our study shows that relatively few chromosomal rearrangements took place over this period with an average of one inter or intra-chromosomal (translocations and inversions respectively) rearrangement occurring approximately every 2 million years. The majority of these rearrangements appear to be intra-chromosomal suggesting an overall karyotypic stability, which is consistent with that of that of modern birds. Our results support the hypothesis that the characteristically avian genome was present in the saurian ancestor and that it has remained remarkably stable in the 280 million years since. It is credible therefore to suggest that this ‘avian-style’ genome may be one of the key factors in the success of this extraordinarily diverse animal group.

AVIAN CHROMONOMICS GOES FUNCTIONAL

Universidade Estadual Paulista Julio de Mesquita Filho, Instituto de Biociencias, Rio Claro, BrasilThe advent of the next generation sequencing (NGS) made sequencing and scaffolding of an entire animal genome a routine procedure. As the result we face a fast increase in the number of animal genomes available due to the activities of large international genome sequencing initiatives e.g., Genome 10K (G10K) or smaller projects. However, the full informative power of a sequenced genome could only be achieved when it is assembled into chromosomes. Usually, a draft or nearly complete animal chromosome assembly is achieved through three steps: (i) constructing contigs based on read overlaps, (ii) merging contigs into scaffolds using pair-end reads, and (iii) mapping scaffolds on chromosomes with the use of physical or genetic maps. As the cost of mapping techniques is still much higher than sequencing, the genetic and physical maps are not available for the majority of the de novo sequenced genomes. To overcome this problem for assemblies that employ long-insert libraries (5 – 40 Kbp) we recently developed the reference-assisted chromosome assembly (RACA) algorithm (Kim et al., 2013). This method relies on both the raw sequencing data (reads) and comparative information; the latter is obtained from alignments between the target (de novo sequenced), a closely related (reference) and more distantly related (outgroup) genomes. Using RACA followed by the manual FISH or PCR verification steps we are reconstructing the chromosome organisation of 19 bird species sequenced by the G10K community. We use the publically available chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) chromosome assemblies as either reference or outgroup for each reconstruction depending on their phylogenetic relationships with each target species. Initially, we established the optimal RACA parameters for a bird chromosome assembly reconstruction using the duck (Anas platyrhynchos) and budgerigar (Melopsittacus undulatus) super-scaffolds assembled with the support from physical maps. This step allowed us to test the reliability of RACA reconstructions for bird genomes. Due to a higher evolutionary conservation of the bird karyotype compared to the mammalian one, we have achieved ~97% accuracy of scaffold adjacencies in our predicted chromosome fragments compared to the ~93-96% accuracies reported for mammals (Kim et al., 2013). We detected ~4-28% of scaffolds in different target bird genomes that are either chimeric or containing genuine lineage-specific evolutionary breakpoint regions. Some of these scaffolds will be selected for follow up PCR or FISH verifications. All RACA reconstructions will become publicly available from our Evolution Highway comparative chromosome browser http://evolutionhighway.ncsa.uiuc.edu/birds/ and will be further utilised to study connections between the chromosome evolution, adaptation and phenotypic diversity in birds and other vertebrates.Universidade Estadual Paulista, Nucleo de Pesquisa e Conservacao de Cervideos, Faculdade de Ciencias Agrarias e Veterinarias, Jaboticabal, Brasil• Invited speaker abstracts have the prefix “S” • Selected Oral presentations have the prefix “O” • Poster abstracts have the prefix “P” S1: 50th Anniversary of the first Oxford Chromosome Conference and some reflections on chromosome synapsis Malcolm A Ferguson-Smith Department of Veterinary Medicine, University of Cambridge, Cambridge, UK. Cyril Darlington, who organised the first Oxford Chromosome Conference 50 years ago, was one of the great pioneers of cytogenetics. He brought new understanding to the mechanisms of mitosis and meiosis and the uniformity of chromosome behaviour in all plants and animals with its implications for evolution. His major conclusions relate to the origin of chiasmata and the properties of sex chromosomes and were based on light microscopy before the era of molecular cytogenetics in the 1970s. Since his day the field has been transformed by electron microscopy, FISH, immunofluorescence of chromosomal proteins, meiotic mutants in yeast and mice and by DNA mapping and sequencing. Progress in understanding chromosome structure and synapsis in meiotic and somatic cells since Darlington will be briefly summarised with emphasis on the unknown. Genome conservation and the nature of non-coding DNA at synapsis sites, and the threedimensional structure of chromosomal proteins (eg, those of axial filaments), should be among the topics for discussion at this and future Chromosome Conferences. 20th International Chromosome Conference (ICCXX) 35120th International Chromosome Conference (ICCXX). 50th Anniversary, University of Kent, Canterbury, 1st–4th September 2014.Dinosaurs hold a unique place both in the history of the earth and the imagination of many. They dominated the terrestrial environment for around 170 million years during which time they diversified into at least 1000 different species. Reptilia, within which they are placed is one of the most remarkable vertebrate groups, consisting of two structurally and physiologically distinct lineages – the birds and the non-avian reptiles, of which there are 10,000 and 7,500 extant species respectively. The dinosaurs are without doubt the most successful group of vertebrate to have existed. They survived several mass extinction events before finally non-avian dinosaurs were defeated 66 million years ago in the Cretaceous-Paleogene extinction event, leaving the neornithes (modern birds) as their living descendants. Aside from the huge phenotypic diversity seen in this group, the birds and non-avian reptiles interestingly display similar karyotypic patterns (with the exception of crocodilians); with the characteristic pattern of macro and micro chromosomes, small genome size and few repetitive elements, suggesting that these were features exhibited in their common ancestor. In this study, the availability of multiple reptile genome sequences (including birds) on an interactive browser (Evolution Highway) allowed us to identify multi species homologous synteny blocks (msHSBs) between the putative avian ancestor (derived from six species of extant birds), the Lizard (Anolis carolensis) and the Snake (Boa constrictor). From these msHSBs we were able to produce a series of contiguous ancestral regions (CARs) representing the most likely ancestral karyotype of the Saurian (ancestor of archosaurs and lepidosaurs) that diverged from the mammalian lineage 280 mya. From this we have hypothesised the series of inter and intra-chromosomal rearrangements that have occurred along the dinosaur (archosaur) lineage to the ancestor of modern birds (100 mya) and along the lepidosaur lineage to the modern snake and lizard using the model of maximum parsimony. Our study shows that relatively few chromosomal rearrangements took place over this period with an average of one inter or intra-chromosomal (translocations and inversions respectively) rearrangement occurring approximately every 2 million years. The majority of these rearrangements appear to be intra-chromosomal suggesting an overall karyotypic stability, which is consistent with that of that of modern birds. Our results support the hypothesis that the characteristically avian genome was present in the saurian ancestor and that it has remained remarkably stable in the 280 million years since. It is credible therefore to suggest that this ‘avian-style’ genome may be one of the key factors in the success of this extraordinarily diverse animal group.