Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

Joana Damas,Denis M Larkin,Marta Farré,Jaebum Kim,Darren K Griffin

doi:10.1186/s13059-018-1544-8

Joana Damas, Denis M Larkin + Show 3 more

Open Access

https://doi.org/10.1186/s13059-018-1544-8

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Abstract

BackgroundReconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history. However, this is impeded by both the fragmented nature of the majority of genome assemblies and the limitations of the available software to work with them. These limitations are particularly apparent in birds, with only 10 chromosome-level assemblies reported thus far. Algorithmic approaches applied to fragmented genome assemblies can nonetheless help define patterns of chromosomal change in defined taxonomic groups.ResultsHere, we make use of the DESCHRAMBLER algorithm to perform the first large-scale study of ancestral chromosome structure and evolution in birds. This algorithm allows us to reconstruct the overall genome structure of 14 key nodes of avian evolution from the Avian ancestor to the ancestor of the Estrildidae, Thraupidae and Fringillidae families.ConclusionsAnalysis of these reconstructions provides important insights into the variability of rearrangement rates during avian evolution and allows the detection of patterns related to the chromosome distribution of evolutionary breakpoint regions. Moreover, the inclusion of microchromosomes in our reconstructions allows us to provide novel insights into the evolution of these avian chromosomes, specifically.

Highlights

Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes
They revealed that evolutionary breakpoint regions (EBRs) are often reused in evolution, that EBRs locate in gene-dense regions and that lineage-specific EBRs are usually associated with the location of segmental duplications in mammals [6,7,8]
These findings demonstrated the importance of genome sequence comparisons for the detection of the overall pattern of chromosomal events that shaped extant genomes and stimulated the development of several algorithms to perform the reconstruction of ancestral karyotypes based on genome sequence data

Summary

Introduction

Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. These reconstructions allowed the identification of novel genome rearrangements and the detection of varied rates of change in different animal lineages They revealed that evolutionary breakpoint regions (EBRs) are often reused in evolution, that EBRs locate in gene-dense regions and that lineage-specific EBRs are usually associated with the location of segmental duplications in mammals [6,7,8]. These findings demonstrated the importance of genome sequence comparisons for the detection of the overall pattern of chromosomal events that shaped extant genomes and stimulated the development of several algorithms to perform the reconstruction of ancestral karyotypes based on genome sequence data. It showed that, amongst the 10 orders studied, the primates had the largest number of chromosomes structurally identical to the Eutherian ancestor (orangutan exhibiting the largest) with chimps displaying more structural changes than humans [11]

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