Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana.
Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can...
| Main Authors: | , , , , |
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| Format: | Journal Article |
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Oxford University Press
2011
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| Online Access: | http://hdl.handle.net/20.500.11937/21062 |
| _version_ | 1848750485743337472 |
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| author | Lai, A. Denton-Giles, Matthew Mueller-Roeber, B. SChippers, J. Dijkwel, P. Dijkwel, P. |
| author_facet | Lai, A. Denton-Giles, Matthew Mueller-Roeber, B. SChippers, J. Dijkwel, P. Dijkwel, P. |
| author_sort | Lai, A. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a 3 ~71-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (>100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions. |
| first_indexed | 2025-11-14T07:37:35Z |
| format | Journal Article |
| id | curtin-20.500.11937-21062 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T07:37:35Z |
| publishDate | 2011 |
| publisher | Oxford University Press |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-210622017-09-13T13:45:15Z Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. Lai, A. Denton-Giles, Matthew Mueller-Roeber, B. SChippers, J. Dijkwel, P. Dijkwel, P. comparative genomics genome partitioning drafted genomes haplotype allelic variants Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a 3 ~71-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (>100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions. 2011 Journal Article http://hdl.handle.net/20.500.11937/21062 10.1093/gbe/evr038 Oxford University Press fulltext |
| spellingShingle | comparative genomics genome partitioning drafted genomes haplotype allelic variants Lai, A. Denton-Giles, Matthew Mueller-Roeber, B. SChippers, J. Dijkwel, P. Dijkwel, P. Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. |
| title | Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. |
| title_full | Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. |
| title_fullStr | Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. |
| title_full_unstemmed | Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. |
| title_short | Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana. |
| title_sort | positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of arabidopsis thaliana. |
| topic | comparative genomics genome partitioning drafted genomes haplotype allelic variants |
| url | http://hdl.handle.net/20.500.11937/21062 |