NEW YORK (GenomeWeb) – Using genome sequences from present-day birds and reptiles, a research team has attempted to reconstruct the genome for an ancestral group of four-limbed amniotes known as diapsids from which birds, reptiles, and dinosaurs descended.
The researchers brought together chromosome-level genome assemblies for four birds and reptiles, using bioinformatic analyses and new cytogenetic data to reconstruct ancestral genome organization patterns, adaptive genetic changes, and conserved sequences in the lineage with the help of evolutionary breakpoint region (EBR) and homologous synteny blocks (HSBs) gleaned from the extant genome data. With these data, the team was able to reach back some 260 million years, predicting the chromosome structure of the diapsid Eunotosaurus ancestor of birds, reptiles, dinosaurs, and pterosaurs. The findings appeared online yesterday in Nature Communications.
"It is fascinating to see how the knowledge we collect about extant species' genomes coupled with smart computation technologies allow us to go back in time and learn about the genomes and biology of species that existed long before humans appeared and for which we would never have a biological sample," co-senior author Denis Larkin, a comparative biomedical sciences researcher at the University of London's Royal Veterinary College, said in a statement.
Building on a prior chromosomal reconstruction study based on half a dozen extant bird genomes, the team used a "multiple-genome rearrangement and analysis" (MGRA2) analytical tool to retrace karyotypic patterns in the diapsid ancestral genome using genome assemblies for the chicken, zebra finch, mallard, Carolina anole lizard, and the grey short-tailed opossum, which represents a mammalian outgroup. The search uncovered nearly 400 multi-species HSBs, making it possible to reconstruct 19 chromosome-like "contiguous ancestral regions" with MGRA2 analyses.
The researchers also evaluated genome assemblies for several other extant species such as the turkey, budgerigar, and ostrich, but did not include those genomes in their subsequent analyses due to sequence fragmentation or genome misassembly issues that cropped up when they assessed the genomes cytogenetically using fluorescence in situ hybridization.
In addition to the bioinformatic look at the genomes, the team used cross-species molecular cytogenetics approaches to profile and compare chromosomal patterns in the chicken, Caroline anole lizard, red-eared slider turtle, and spiny soft-shelled turtle. It also did pairwise genome alignments with the Evolution Highway chromosome browser to look at HSB positions across species.
Together, these data provided a peek at ancestral diapsid genomes, as well as the within- and between-chromosome rearrangements that occurred in the diverse dinosaur, reptile, and bird descendants of the diapsids.
The researchers made several findings — for example, when comparing the chicken genome and predicted diapsid ancestor genome they noticed that inter-chromosomal rearrangements were relatively rare, while intra-chromosomal inversions turned up a few dozen times. Digging into the genes falling in conserved HSBs and the divergent EBRs provided them still more clues to the adaptations arising in the species over time.
"Remaining largely unchanged interchromosomally through the dinosaur-theropod route that led to modern birds," the authors explained, "intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organization and transcription."
They estimated that the advent of a bird-like genome organization comprised of 40 pairs of chromosome and 30 microchromosomes goes back more than 255 million years, before the split between lineages leading to birds and turtles. Moreover, they reported, the overall genome organization in this lineage seems to stretch back to ancestors that emerged well before lineages leading to early dinosaurs and the flying pterosaur reptiles.
"This genome organization … predates the emergence of early dinosaurs and pterosaurs and the evolution of flight," Larkin and his co-authors wrote, noting that the genome structure in this lineage "appears highly stable yet contributes to a large degree of phenotypic diversity."