Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris)
Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 e...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2016-07-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.116.028761 |
| _version_ | 1819125173875376128 |
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| author | Dongying Gao Dongyan Zhao Brian Abernathy Aiko Iwata-Otsubo Alfredo Herrera-Estrella Ning Jiang Scott A. Jackson |
| author_facet | Dongying Gao Dongyan Zhao Brian Abernathy Aiko Iwata-Otsubo Alfredo Herrera-Estrella Ning Jiang Scott A. Jackson |
| author_sort | Dongying Gao |
| collection | DOAJ |
| description | Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH) analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T). Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome. |
| first_indexed | 2024-12-22T07:35:56Z |
| format | Article |
| id | doaj.art-5ffbd53dfca3400eb7c1c2248c8a583e |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-22T07:35:56Z |
| publishDate | 2016-07-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-5ffbd53dfca3400eb7c1c2248c8a583e2022-12-21T18:33:53ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362016-07-01672091210110.1534/g3.116.02876129Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris)Dongying GaoDongyan ZhaoBrian AbernathyAiko Iwata-OtsuboAlfredo Herrera-EstrellaNing JiangScott A. JacksonTransposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH) analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T). Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome.http://g3journal.org/lookup/doi/10.1534/g3.116.028761DNA transposonCACTAgenome evolutioncommon beanPhaseolus |
| spellingShingle | Dongying Gao Dongyan Zhao Brian Abernathy Aiko Iwata-Otsubo Alfredo Herrera-Estrella Ning Jiang Scott A. Jackson Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris) G3: Genes, Genomes, Genetics DNA transposon CACTA genome evolution common bean Phaseolus |
| title | Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris) |
| title_full | Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris) |
| title_fullStr | Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris) |
| title_full_unstemmed | Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris) |
| title_short | Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris) |
| title_sort | dynamics of a novel highly repetitive cacta family in common bean phaseolus vulgaris |
| topic | DNA transposon CACTA genome evolution common bean Phaseolus |
| url | http://g3journal.org/lookup/doi/10.1534/g3.116.028761 |
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