Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution

Lucas G Kiazim,Rebecca E O’Connor,Michael N Romanov,Valery G Narushin,Darren K Griffin,Denis M Larkin,Evgeni A Brazhnik

doi:10.3390/cells10020362

Lucas G Kiazim, Rebecca E O’Connor + Show 5 more

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https://doi.org/10.3390/cells10020362

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Abstract

Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.

Highlights

Most birds exhibit a highly distinctive, “typical” avian karyotype, where chromosomes are characteristically divided into around 10 macrochromosomes and around 30 -sized, morphologically indistinguishable microchromosomes
Studying overall genome structure is an essential element to understanding avian biology; most avian species have no structural data associated with their genome [4] despite ~460 avian genomes having been sequenced (4% of all species)
Chromosome painting by fluorescence in situ hybridisation (FISH) has resulted in numerous comparative genomic and evolutionary studies in birds (e.g., [3,6,7,8,9,10,11,12]); chromosome paints are limited in their ability to identify intrachromosomal rearrangements such as inversions and duplications

Summary

Introduction

Most birds exhibit a highly distinctive, “typical” avian karyotype, where chromosomes are characteristically divided into around 10 macrochromosomes and around 30 -sized, morphologically indistinguishable microchromosomes. As of May 2019 [5], only 16 genomes have been assembled to a chromosome-level (i.e., a single scaffold for each chromosome from the p- to q-terminus). To address this problem coupling classical cytogenetics with molecular cytogenetics, such as fluorescence in situ hybridisation (FISH), provides a finer resolution of genomic structure and can be used to anchor genome sequence to the chromosomes and thence identify chromosome rearrangements by determining interspecies homology. Chromosome painting by FISH has resulted in numerous comparative genomic and evolutionary studies in birds (e.g., [3,6,7,8,9,10,11,12]); chromosome paints are limited in their ability to identify intrachromosomal rearrangements such as inversions and duplications

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