ArticleGenome biology2018
Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
- The complete genome of a songbird.bioRxiv : the preprint server for biology · 2025Article
- Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).BMC biology · 2025Article
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- Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge.Scientific reports · 2024Article
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- Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human.Scientific reports · 2023Article
- A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa).Scientific data · 2023Article
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- Fixed Allele Differences Associated With the Centromere Reveal Chromosome Morphology and Rearrangements in a Reptile (Varanus acanthurus BOULENGER).Molecular biology and evolution · 2023Article
- Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights.BMC genomics · 2023Article
- The gyrfalcon (Falco rusticolus) genome.G3 (Bethesda, Md.) · 2023Article
- A conserved karyotype? Chromosomal rearrangements in Charadrius collaris detected by BAC-FISH.PloS one · 2023Article
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- Dinosaurs: Comparative Cytogenomics of Their Reptile Cousins and Avian Descendants.Animals : an open access journal from MDPI · 2022Review
- Microchromosome BAC-FISH Reveals Different Patterns of Genome Organization in Three Charadriiformes Species.Animals : an open access journal from MDPI · 2022Article
- Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux.Genome biology and evolution · 2022Article
- Comparative chromosome maps between the stone curlew and three ciconiiform species (the grey heron, little egret and crested ibis).BMC ecology and evolution · 2022Article
- Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots.Nature communications · 2022Article
- Fourth Report on Chicken Genes and Chromosomes 2022.Cytogenetic and genome research · 2022Review
- Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity.Genome biology and evolution · 2021Article
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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.
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