Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives
Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S r...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2016-04-01
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| Series: | G3: Genes, Genomes, Genetics |
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| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.115.024984 |
| _version_ | 1818669202119065600 |
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| author | Aiko Iwata-Otsubo Brittany Radke Seth Findley Brian Abernathy C. Eduardo Vallejos Scott A. Jackson |
| author_facet | Aiko Iwata-Otsubo Brittany Radke Seth Findley Brian Abernathy C. Eduardo Vallejos Scott A. Jackson |
| author_sort | Aiko Iwata-Otsubo |
| collection | DOAJ |
| description | Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species. |
| first_indexed | 2024-12-17T06:48:28Z |
| format | Article |
| id | doaj.art-05d7213142e643bbbc5f4e6607b9f82b |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-17T06:48:28Z |
| publishDate | 2016-04-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-05d7213142e643bbbc5f4e6607b9f82b2022-12-21T21:59:40ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362016-04-01641013102210.1534/g3.115.02498421Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and RelativesAiko Iwata-OtsuboBrittany RadkeSeth FindleyBrian AbernathyC. Eduardo VallejosScott A. JacksonFluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.http://g3journal.org/lookup/doi/10.1534/g3.115.024984common beankaryotypingfluorescence in situ hybridizationsatellite repeatschromosome evolution |
| spellingShingle | Aiko Iwata-Otsubo Brittany Radke Seth Findley Brian Abernathy C. Eduardo Vallejos Scott A. Jackson Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives G3: Genes, Genomes, Genetics common bean karyotyping fluorescence in situ hybridization satellite repeats chromosome evolution |
| title | Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives |
| title_full | Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives |
| title_fullStr | Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives |
| title_full_unstemmed | Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives |
| title_short | Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives |
| title_sort | fluorescence in situ hybridization fish based karyotyping reveals rapid evolution of centromeric and subtelomeric repeats in common bean phaseolus vulgaris and relatives |
| topic | common bean karyotyping fluorescence in situ hybridization satellite repeats chromosome evolution |
| url | http://g3journal.org/lookup/doi/10.1534/g3.115.024984 |
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