Biology subjects

Destanovic, D.

Publications and source records attributed to Destanovic, D..

3 recordsLinked to original sources

bioRxiv2025

A Chromosome-Scale Genome of Nanomia septata Reveals Extensive Rearrangement But No Clear Driver of the Unique Colony-Level Organization of Siphonophores

Siphonophores (Cnidaria:Hydrozoa) are pelagic colonial marine invertebrates with many highly specialized bodies (zooids) within a single colony. Their unique biology and ecological importance have made them of particular interest. Recent work revealed siphonophore genomes to be larger than in most other cnidarians. To investigate siphonophores genome biology and develop resources for future studies, we sequenced the genome of a single Nanomia septata to chromosome scale. The haploid genome is 1.5GB across 8 chromosomes, a reduction relative to the 15 chromosomes seen in closely related hydrozoan genomes, and is highly rearranged, consistent with multiple mixing events. Genome expansion occurred through intergenic repeat expansion, with protein-coding genes shorter than in most cnidarians. We found no genomic features clearly associated with siphonophores exceptional colony-level complexity. Gene families that play critical roles in cnidarian development have not expanded, and gene proximity was not generally correlated to their expression across zooids, except in male gonophores. To contextualize these observations, we genome sequenced 20 additional Nanomia specimens across the globe and mapped them to our chromosome-scale reference. Population genomic analyses support three previously recognized species of Nanomia, and at least one additional undescribed species. Overlapping geographic distribution of some Nanomia species suggest reproductive isolation in sympatry. Phylogenetic analyses of genome size indicate Nanomia septata and Nanomia cara have similarly large genomes between 1.5-1.7GB, while Nanomia bijuga and an undescribed species show a secondary reduction to 0.7GB. These results highlight how genomic factors have shaped colony organization and genome diversity within Nanomia.

genomics↗

bioRxiv2024

Topological mixing and irreversibility in animal chromosome evolution

Abstract/Summary ParagraphAnimal chromosomes can persist with recognizable homology over hundreds of millions of years, in spite of homology-obfuscating processes such as chromosomal fusion and translocation. The frequency and pace of these major genome structural changes are unknown, and it remains unclear whether or how they impact long-term genome evolution. Here, we compare whole chromosomal sequences of 3,631 genomes from 2,291 species spanning all major animal clades and show that animal karyotypes evolve primarily via karyotype contraction, associated with increased rates of chromosomal fusion-with-mixing and dispersion that largely obey chromosomal algebra1, or karyotype expansion, which breaks up ancestral linkage groups and forms new chromosomal elements via non-algebraic changes. We show that chromosomal changes can be associated with major extinction events. Using a multi-scale encoding of pan-animal genome homology and a manifold representation of genomic changes, we find that genome evolution is not only driven by changes at the chromosomal level, but that subchromosomal mixing and irreversibility define clade-specific evolution. Using this evolutionary genome topology approach, we calculate extrema of irreversible genomic configurations and identify species that occupy intermediate manifold positions, providing evidence for distinct macro-evolutionary trajectories. We propose that investigation of mixed state accumulation around important gene loci (such as Hox) will be crucial in capturing and further study of clade-specific regulatory innovations.

evolutionary biology↗

bioRxiv2023

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797)

Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio. Octopus vulgaris has been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly is available for O. vulgaris to aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus, O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n=30 chromosomes. Comparisons with other octopus species genomes show a conserved octopus karyotype, and a pattern of local genome rearrangements between species. This new chromosome-scale genome of O. vulgaris will further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.

genomics↗