Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time
Tandem duplicate genes are proximally duplicated and as such occur in similar genomic neighborhoods. Using the maize B73 and PH207 de novo genome assemblies, we identified thousands of tandem gene duplicates that account for ∼10% of the annotated genes. These tandem duplicates have a bimodal distrib...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2018-09-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.118.200580 |
| _version_ | 1818889395058507776 |
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| author | Thomas J.Y. Kono Alex B. Brohammer Suzanne E. McGaugh Candice N. Hirsch |
| author_facet | Thomas J.Y. Kono Alex B. Brohammer Suzanne E. McGaugh Candice N. Hirsch |
| author_sort | Thomas J.Y. Kono |
| collection | DOAJ |
| description | Tandem duplicate genes are proximally duplicated and as such occur in similar genomic neighborhoods. Using the maize B73 and PH207 de novo genome assemblies, we identified thousands of tandem gene duplicates that account for ∼10% of the annotated genes. These tandem duplicates have a bimodal distribution of ages, which coincide with ancient allopolyploidization and more recent domestication. Tandem duplicates are smaller on average and have a higher probability of containing LTR elements than other genes, suggesting origins in nonhomologous recombination. Within relatively recent tandem duplicate genes, ∼26% appear to be undergoing degeneration or divergence in function from the ancestral copy. Our results show that tandem duplicates are abundant in maize, arose in bursts throughout maize evolutionary history under multiple potential mechanisms, and may provide a substrate for novel phenotypic variation. |
| first_indexed | 2024-12-19T17:08:20Z |
| format | Article |
| id | doaj.art-bb7c4f6e955c4f1cb6110831ef2066f3 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-19T17:08:20Z |
| publishDate | 2018-09-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-bb7c4f6e955c4f1cb6110831ef2066f32022-12-21T20:13:06ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362018-09-01893049305810.1534/g3.118.20058016Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of TimeThomas J.Y. KonoAlex B. BrohammerSuzanne E. McGaughCandice N. HirschTandem duplicate genes are proximally duplicated and as such occur in similar genomic neighborhoods. Using the maize B73 and PH207 de novo genome assemblies, we identified thousands of tandem gene duplicates that account for ∼10% of the annotated genes. These tandem duplicates have a bimodal distribution of ages, which coincide with ancient allopolyploidization and more recent domestication. Tandem duplicates are smaller on average and have a higher probability of containing LTR elements than other genes, suggesting origins in nonhomologous recombination. Within relatively recent tandem duplicate genes, ∼26% appear to be undergoing degeneration or divergence in function from the ancestral copy. Our results show that tandem duplicates are abundant in maize, arose in bursts throughout maize evolutionary history under multiple potential mechanisms, and may provide a substrate for novel phenotypic variation.http://g3journal.org/lookup/doi/10.1534/g3.118.200580maizetandem duplicategenome evolutioncopy number variationtransposable element |
| spellingShingle | Thomas J.Y. Kono Alex B. Brohammer Suzanne E. McGaugh Candice N. Hirsch Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time G3: Genes, Genomes, Genetics maize tandem duplicate genome evolution copy number variation transposable element |
| title | Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time |
| title_full | Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time |
| title_fullStr | Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time |
| title_full_unstemmed | Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time |
| title_short | Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time |
| title_sort | tandem duplicate genes in maize are abundant and date to two distinct periods of time |
| topic | maize tandem duplicate genome evolution copy number variation transposable element |
| url | http://g3journal.org/lookup/doi/10.1534/g3.118.200580 |
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