Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

Rebecca E O’Connor,Lucas Kiazim,Emily Allanson,Sophie Bennett,Joana Damas,Darren K Griffin,Rebecca Jennings,Sunitha Joseph,Eden A Slack,Marta Farré,Denis M Larkin

doi:10.1186/s13059-018-1550-x

Rebecca E O’Connor, Lucas Kiazim + Show 9 more

Open Access

https://doi.org/10.1186/s13059-018-1550-x

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Abstract

BackgroundThe number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions.ResultsWe used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest.ConclusionsThe tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.

Highlights

The number of de novo genome sequence assemblies is increasing exponentially; relatively few contain one scaffold/contig per chromosome
We further studied the fate of coding elements (CNEs) in the evolutionary breakpoint regions (EBRs) flanking interchromosomal rearrangements of a highly rearranged avian genome, finding that, in the peregrine falcon, interchromosomal EBRs contain 12 times fewer CNEs than intrachromosomal ones [15]
Predicted chromosome fragments for three new species Predicted chromosome fragments were generated for fragmented saker falcon, budgerigar, and ostrich whole-genome sequences using Reference-Assisted Chromosome Assembly (RACA) [17]

Summary

Introduction

The number of de novo genome sequence assemblies is increasing exponentially; relatively few contain one scaffold/contig per chromosome Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. To achieve a chromosome-level assembly often requires a combination of technologies to integrate the sequence data, e.g., Hi-C [14], linkage mapping, pre-existing chromosome-level reference assemblies, and/or molecular cytogenetics [15, 16]. To this end, we made use of bioinformatic approaches, e.g., the Reference-Assisted Chromosome Assembly (RACA) algorithm [17]. Only two genomes—the pigeon (Columba livia) and the Peregrine falcon (Falco peregrinus)—have been assembled in this way [15]

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