A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites
Abstract We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. “EA78” (2n = 8x = 56). We identify 147 bp canonical centromeric repeats across 50 strawber...
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BMC
2025-02-01
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Online Access: | https://doi.org/10.1186/s13059-025-03482-0 |
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author | Xin Jin Haiyuan Du Maoxian Chen Xu Zheng Yiying He Andan Zhu |
author_facet | Xin Jin Haiyuan Du Maoxian Chen Xu Zheng Yiying He Andan Zhu |
author_sort | Xin Jin |
collection | DOAJ |
description | Abstract We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. “EA78” (2n = 8x = 56). We identify 147 bp canonical centromeric repeats across 50 strawberry chromosomes and uncover the formation of six neocentromeres through centromere turnover. Our findings indicate strawberry genomes have diverged centromeric satellite arrays among chromosomes, particularly across homoeologs, while maintaining high sequence similarity between homologs. We trace the evolutionary dynamics of centromeric repeats and find substantial centromere size expansion in wild and cultivated octoploids compared to the diploid ancestor, F. vesca. |
format | Article |
id | doaj-art-8c2c8035a0b74b149a0aa385aa672814 |
institution | Kabale University |
issn | 1474-760X |
language | English |
publishDate | 2025-02-01 |
publisher | BMC |
record_format | Article |
series | Genome Biology |
spelling | doaj-art-8c2c8035a0b74b149a0aa385aa6728142025-02-09T12:39:26ZengBMCGenome Biology1474-760X2025-02-0126111610.1186/s13059-025-03482-0A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellitesXin Jin0Haiyuan Du1Maoxian Chen2Xu Zheng3Yiying He4Andan Zhu5Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesAbstract We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. “EA78” (2n = 8x = 56). We identify 147 bp canonical centromeric repeats across 50 strawberry chromosomes and uncover the formation of six neocentromeres through centromere turnover. Our findings indicate strawberry genomes have diverged centromeric satellite arrays among chromosomes, particularly across homoeologs, while maintaining high sequence similarity between homologs. We trace the evolutionary dynamics of centromeric repeats and find substantial centromere size expansion in wild and cultivated octoploids compared to the diploid ancestor, F. vesca.https://doi.org/10.1186/s13059-025-03482-0Octoploid strawberryFully phasedSynthetic allopolyploidsCentromeric satellitesEvolutionary turnover |
spellingShingle | Xin Jin Haiyuan Du Maoxian Chen Xu Zheng Yiying He Andan Zhu A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites Genome Biology Octoploid strawberry Fully phased Synthetic allopolyploids Centromeric satellites Evolutionary turnover |
title | A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites |
title_full | A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites |
title_fullStr | A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites |
title_full_unstemmed | A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites |
title_short | A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites |
title_sort | fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites |
topic | Octoploid strawberry Fully phased Synthetic allopolyploids Centromeric satellites Evolutionary turnover |
url | https://doi.org/10.1186/s13059-025-03482-0 |
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