Characterising genome architectures using genome decomposition analysis
Abstract Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie biological processes such as chromosomal segregation and the regulation of gene expression. We present a new tool called Genome D...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-05-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-022-08616-3 |
| _version_ | 1811324502881075200 |
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| author | Eerik Aunin Matthew Berriman Adam James Reid |
| author_facet | Eerik Aunin Matthew Berriman Adam James Reid |
| author_sort | Eerik Aunin |
| collection | DOAJ |
| description | Abstract Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie biological processes such as chromosomal segregation and the regulation of gene expression. We present a new tool called Genome Decomposition Analysis (GDA) that characterises genome architectures and acts as an accessible approach for discovering hidden features of a genome assembly. With the imminent deluge of high-quality genome assemblies from projects such as the Darwin Tree of Life and the Earth BioGenome Project, GDA has been designed to facilitate their exploration and the discovery of novel genome biology. We highlight the effectiveness of our approach in characterising the genome architectures of single-celled eukaryotic parasites from the phylum Apicomplexa and show that it scales well to large genomes. |
| first_indexed | 2024-04-13T14:15:30Z |
| format | Article |
| id | doaj.art-8ae74ced5d2e492c9b27c788d5c950d3 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T14:15:30Z |
| publishDate | 2022-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-8ae74ced5d2e492c9b27c788d5c950d32022-12-22T02:43:39ZengBMCBMC Genomics1471-21642022-05-0123111510.1186/s12864-022-08616-3Characterising genome architectures using genome decomposition analysisEerik Aunin0Matthew Berriman1Adam James Reid2Wellcome Sanger InstituteWellcome Sanger InstituteWellcome Sanger InstituteAbstract Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie biological processes such as chromosomal segregation and the regulation of gene expression. We present a new tool called Genome Decomposition Analysis (GDA) that characterises genome architectures and acts as an accessible approach for discovering hidden features of a genome assembly. With the imminent deluge of high-quality genome assemblies from projects such as the Darwin Tree of Life and the Earth BioGenome Project, GDA has been designed to facilitate their exploration and the discovery of novel genome biology. We highlight the effectiveness of our approach in characterising the genome architectures of single-celled eukaryotic parasites from the phylum Apicomplexa and show that it scales well to large genomes.https://doi.org/10.1186/s12864-022-08616-3Genome architectureChromosome structureGenome assemblyParasitesApicomplexaPlasmodium |
| spellingShingle | Eerik Aunin Matthew Berriman Adam James Reid Characterising genome architectures using genome decomposition analysis BMC Genomics Genome architecture Chromosome structure Genome assembly Parasites Apicomplexa Plasmodium |
| title | Characterising genome architectures using genome decomposition analysis |
| title_full | Characterising genome architectures using genome decomposition analysis |
| title_fullStr | Characterising genome architectures using genome decomposition analysis |
| title_full_unstemmed | Characterising genome architectures using genome decomposition analysis |
| title_short | Characterising genome architectures using genome decomposition analysis |
| title_sort | characterising genome architectures using genome decomposition analysis |
| topic | Genome architecture Chromosome structure Genome assembly Parasites Apicomplexa Plasmodium |
| url | https://doi.org/10.1186/s12864-022-08616-3 |
| work_keys_str_mv | AT eerikaunin characterisinggenomearchitecturesusinggenomedecompositionanalysis AT matthewberriman characterisinggenomearchitecturesusinggenomedecompositionanalysis AT adamjamesreid characterisinggenomearchitecturesusinggenomedecompositionanalysis |