S15-1

Karyotype evolution in birds: from conventional staining to chromosome painting, to genome assembly

Edivaldo de Oliveira¹

¹Universidade Federal do Pará, PA, Brazil
²Instituto Evandro Chagas, PA, Brazil

Because of the difficulties in analyzing the karyotype of birds using classical cytogenetics – high diploid numbers and a large amount of microchromosomes - only a small percentage of species have been characterized Cytogenetically. Advances, such as chromosome painting, have helped to overcome the limitations of conventional and banding analyses. The use of whole chromosome paints, as well as BACs for microchromosomes, allowed the exploration of different aspects of the genome organization and evolution. Currently, considering that reference genomes are important tools to investigate many biological aspects of a species, the number of species of birds with assembled genomes has grown drastically. The advances in genome sequencing technology and the availability of new mathematical algorithms used in the genome assembly have revolutionized the study of chromosome evolution. However, a direct information link between the assembled genomes and the standard karyotype of the target species is not always provided. In some cases, the comparison of chromosomal data shows that the assembled genomes, especially the ones based on short reads, have some regions or even entire chromosomes missing, especially in birds. In addition, the assembled scaffolds are often not ordered and anchored into chromosomes. In addition, information about the positions of the centromeres is often lacking, and the p and q arms of a chromosome are not identified. It should be pointed out, however, that the species present in cytogenetic data, in which the chromosome numbering was based not only in size, but on chromosomal morphology, bands, and usually have information concerning gene content and homology with other species. Thus, the association of the data obtained from the assembly of the genome with cytogenetic studies makes the results much more informative, allowing for the mapping of repetitive sequences and genes of interest, and better adjustment of the data in silica with the physical genome.

S15-2

Microchromosomes are building blocks of bird, reptile and mammal chromosomes

Jennifer A. Marshall Graves¹

¹School of Life science, La Trobe University, Melbourne, Australia
²Institute of Applied Ecology, University of Canberra, Australia

Microchromosomes, once considered unimportant shreds of the chicken genome, are gene rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds, and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles, that are atypical.

S15-3

How to evolve an 'alien': a distinct mode of chromosomal evolution in cephalopods

Oleg Simakov¹

¹University of Vienna

Conservation of chromosomal synteny (macrosynteny) has been observed for many animal species dating back to the cradle of animal life over 600 million years ago. In the majority of animal genomes the karyotype conservation is striking, yet in some clades there have been substantial modifications to this ancestral scheme. In vertebrates, the two rounds of whole genome duplications have not only created additional chromosomal copies but also have allowed for chromosomal fusions, bringing together genes that existed separately on different chromosomes before. In this context, the

S15-4

Chromosome-wide translocation repatterned recombination rates and accumulated reproductive isolations during nematode speciation

Kohta Yoshida¹, Christian Rödelsperger¹, Ralf J. Sommer¹

¹Max Planck Institute for Developmental Biology

Chromosomal translocations are one of the major types of genetic mutations that diverge genomes of different species. Classic cytogenetic studies suggested the effect of translocation on reproductive isolation via meiotic abnormality. More recently, evolution of hybrid incompatibility caused by reduced recombination rates at translocation breakpoints was proposed. However, empirical studies to test these hypotheses were scares especially in animals. In the present study, we study genomic divergence and reproductive isolation in closely related nematodes; the hermaphroditic model organism Pristionchus pacificus and the closely related, but gonochoristic sister-species Pristionchus exspectatus. We first generated a chromosome-wide genome assembly of P. exspectatus using single-molecule and Hi-C sequencing to compare with the high-quality genome of P. pacificus. We found a large chromosome-wide translocation although inter-chromosomal translocation were thought to be rare in nematodes. Chromosomal patterns of gene density, repeat density and GC content suggest two recent independent chromosomal fusions with the same chromosome. Indeed, cytogenetic studies of the outgroup species indicate yet another karyotype supporting two independent fusion events. To test the effect of this translocation on reproductive isolation, we conducted QTL analyses for hybrid sterility of BC1 in different sexes. We observed that the QTLs with the largest effect on hybrid sterility of any sex were indeed located at the translocation. Female sterility was explained by trisomy of BC1 by unbalanced segregation in F1 meiosis, while neither QTLs of male nor hermaphrodite sterility could be explained. When we investigated genetic linkage of P. exspectatus we found the translocation to alter the chromosome-wide pattern of recombination rates with gene clusters containing more than 15% expressed genes tightly linked with each other. In the F1 hybrid meiosis, we observed abnormal recombination pattern that broke the linkage of the gene cluster and facilitated male sterility. Taken together, we found a rapid pace of chromosomal translocations repatterning recombination rate and driving reproductive isolation during nematode speciation.

S15-5

Chromatin conformation shapes chromosome evolution in Drosophila and plants

Yi Liao¹, J.J. Emerson^1,2

¹Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
²Center for Complex Biological Systems, University of California, Irvine, California 92697, USA

The general patterns of three-dimensional (3D) chromatin organization are very similar between animals and plants with major higher-order chromatin structures shared between each other, though the formation and function may be considerably different. In an attempt to resolve some of these differences, we investigated the relationship of 3D chromatin organization and genomic structural variations at varying evolutionary time scales both in Drosophila and Solanum species. In Drosophila, we find that TADs remain relatively well conserved between D. melanogaster and D. pseudoobscura despite the presence of substantial shuffling of synteny between the pair over 50 million years of evolution. This suggests that genome rearrangements that disrupt TAD integrity are subject to purifying selection. By using high-confidence structural variant (SV) datasets from high-quality PacBio assemblies of 14 D. melanogaster strains and its 3 closest sibling species from the D. simulans species complex, and three obscura clade species, we find evidence of selection on structural variants at the TAD boundaries in Drosophila genomes, with the pattern differing between SV types. For example, deletions are significantly depleted at TAD boundaries for both divergent and polymorphic SVs, pointing to possible purifying selection, whereas divergent tandem duplications are enriched at TAD boundaries compared to polymorphism indicative of positive selection. In contrast to Drosophila and other well-studied animals (e.g. human and birds), in plants, TADs appear to not be prominent, though similar features are bioinformatically annotated in some plant species. This raises the question as to whether a similar pattern is also operating in plant genomes. To test this, we used both divergent and polymorphic SV datasets and Hi-C data from Solanum genomes to answer this question. We found similar patterns at the TAD-like boundaries of Solanum genomes, contrasting previous observations in rice (Oryza). Whether this is influenced by more dynamic chromatin domains and sequence content among plant genomes or other reasons requires further investigation. Our results suggest that in animals and plants, the role of the spatial organization (i.e. TADs) in genome activity and regulation has followed similar evolutionary trajectories at least in some cases.