Abstract
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur–theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning.
Highlights
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies
We investigated gene content of those evolutionary breakpoint regions (EBRs) and HSBs identified as being involved in the karyotypic changes from the diapsid ancestor to modern birds and identified genes that may indicate adaptive (EBRs) or conserved (HSBs) phenotypic features or those likely to be involved in gross genomic rearrangement
Our results suggest that most features of a typical ‘avian-like’ karyotype were in place before the divergence of birds and turtles, that the predominant mechanism of change thereafter was intrachromosomal rearrangement and that EBRs were enriched for GO terms associated with chromatin modification and chromosome organisation
Summary
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. In the absence of cellular material and DNA from biological samples of long-extinct, early diverging lineages, data from genome sequence assemblies of extant species can facilitate the reconstruction of gross genome structures (karyotypes) This can be achieved provided those assemblies are at, or close to, chromosome level, i.e. one scaffold per chromosome[1]. Supplementing bioinformatic data with novel molecular cytogenetic approaches on turtle metaphases, we tested the hypothesis that the typical karyotype seen in neornithine birds underwent few interchromosomal rearrangements since the divergence of turtles from archosaurs (birds and crocodilians)
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