Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha
Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and asse...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
GigaScience Press
2021-12-01
|
| Series: | GigaByte |
| Online Access: | https://gigabytejournal.com/articles/36 |
| _version_ | 1797871039038881792 |
|---|---|
| author | Anna E. Syme Todd G. B. McLay Frank Udovicic David J. Cantrill Daniel J. Murphy |
| author_facet | Anna E. Syme Todd G. B. McLay Frank Udovicic David J. Cantrill Daniel J. Murphy |
| author_sort | Anna E. Syme |
| collection | DOAJ |
| description |
Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found that different assemblies revealed contrasting arrangements of genomic segments; a hypothesis supported by mapped reads spanning alternate paths.
|
| first_indexed | 2024-04-10T00:37:57Z |
| format | Article |
| id | doaj.art-e3efa66186db44c2b8bb4fa0c291137b |
| institution | Directory Open Access Journal |
| issn | 2709-4715 |
| language | English |
| last_indexed | 2024-04-10T00:37:57Z |
| publishDate | 2021-12-01 |
| publisher | GigaScience Press |
| record_format | Article |
| series | GigaByte |
| spelling | doaj.art-e3efa66186db44c2b8bb4fa0c291137b2023-03-14T11:58:11ZengGigaScience PressGigaByte2709-47152021-12-0110.46471/gigabyte.36Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnanthaAnna E. Syme 0https://orcid.org/0000-0002-9906-0673Todd G. B. McLay 1https://orcid.org/0000-0001-6405-8007Frank Udovicic 2https://orcid.org/0000-0003-1697-8444David J. Cantrill 3https://orcid.org/0000-0002-1185-4015Daniel J. Murphy 4https://orcid.org/0000-0002-8358-363XRoyal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia, Melbourne Bioinformatics, The University of Melbourne, Parkville 3010, AustraliaRoyal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia, School of BioSciences, The University of Melbourne, Parkville 3010, Australia, Centre for Australian National Biodiversity Research, CSIRO, GPO Box 1700, Canberra 2601, AustraliaRoyal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, AustraliaRoyal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, AustraliaRoyal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found that different assemblies revealed contrasting arrangements of genomic segments; a hypothesis supported by mapped reads spanning alternate paths. https://gigabytejournal.com/articles/36 |
| spellingShingle | Anna E. Syme Todd G. B. McLay Frank Udovicic David J. Cantrill Daniel J. Murphy Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha GigaByte |
| title | Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha |
| title_full | Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha |
| title_fullStr | Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha |
| title_full_unstemmed | Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha |
| title_short | Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha |
| title_sort | long read assemblies reveal structural diversity in genomes of organelles an example with acacia pycnantha |
| url | https://gigabytejournal.com/articles/36 |
| work_keys_str_mv | AT annaesyme longreadassembliesrevealstructuraldiversityingenomesoforganellesanexamplewithacaciapycnantha AT toddgbmclay longreadassembliesrevealstructuraldiversityingenomesoforganellesanexamplewithacaciapycnantha AT frankudovicic longreadassembliesrevealstructuraldiversityingenomesoforganellesanexamplewithacaciapycnantha AT davidjcantrill longreadassembliesrevealstructuraldiversityingenomesoforganellesanexamplewithacaciapycnantha AT danieljmurphy longreadassembliesrevealstructuraldiversityingenomesoforganellesanexamplewithacaciapycnantha |