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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Main Authors: Xin Jin, Haiyuan Du, Maoxian Chen, Xu Zheng, Yiying He, Andan Zhu
Format: Article
Language:English
Published: BMC 2025-02-01
Series:Genome Biology
Subjects:
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.
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institution Kabale University
issn 1474-760X
language English
publishDate 2025-02-01
publisher BMC
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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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