Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
Abstract Background The 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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-10-01
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| Series: | Genome Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s13059-018-1550-x |
| _version_ | 1818996657872699392 |
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| author | Rebecca E O’Connor Marta Farré Sunitha Joseph Joana Damas Lucas Kiazim Rebecca Jennings Sophie Bennett Eden A Slack Emily Allanson Denis M Larkin Darren K Griffin |
| author_facet | Rebecca E O’Connor Marta Farré Sunitha Joseph Joana Damas Lucas Kiazim Rebecca Jennings Sophie Bennett Eden A Slack Emily Allanson Denis M Larkin Darren K Griffin |
| author_sort | Rebecca E O’Connor |
| collection | DOAJ |
| description | Abstract Background The 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. Results We 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. Conclusions The 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. |
| first_indexed | 2024-12-20T21:33:14Z |
| format | Article |
| id | doaj.art-0b18948a14f848fea3a9fc271a73a4b4 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-20T21:33:14Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-0b18948a14f848fea3a9fc271a73a4b42022-12-21T19:26:00ZengBMCGenome Biology1474-760X2018-10-0119111510.1186/s13059-018-1550-xChromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomesRebecca E O’Connor0Marta Farré1Sunitha Joseph2Joana Damas3Lucas Kiazim4Rebecca Jennings5Sophie Bennett6Eden A Slack7Emily Allanson8Denis M Larkin9Darren K Griffin10School of Biosciences, University of KentDepartment of Comparative Biomedical Sciences, Royal Veterinary College, University of LondonSchool of Biosciences, University of KentDepartment of Comparative Biomedical Sciences, Royal Veterinary College, University of LondonSchool of Biosciences, University of KentSchool of Biosciences, University of KentSchool of Biosciences, University of KentDepartment of Comparative Biomedical Sciences, Royal Veterinary College, University of LondonDepartment of Comparative Biomedical Sciences, Royal Veterinary College, University of LondonDepartment of Comparative Biomedical Sciences, Royal Veterinary College, University of LondonSchool of Biosciences, University of KentAbstract Background The 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. Results We 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. Conclusions The 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.http://link.springer.com/article/10.1186/s13059-018-1550-xChromosome-level genome assemblyGenome evolutionCNEEBR |
| spellingShingle | Rebecca E O’Connor Marta Farré Sunitha Joseph Joana Damas Lucas Kiazim Rebecca Jennings Sophie Bennett Eden A Slack Emily Allanson Denis M Larkin Darren K Griffin Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes Genome Biology Chromosome-level genome assembly Genome evolution CNE EBR |
| title | Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| title_full | Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| title_fullStr | Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| title_full_unstemmed | Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| title_short | Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| title_sort | chromosome level assembly reveals extensive rearrangement in saker falcon and budgerigar but not ostrich genomes |
| topic | Chromosome-level genome assembly Genome evolution CNE EBR |
| url | http://link.springer.com/article/10.1186/s13059-018-1550-x |
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