文献类型： 外文期刊
作者： Du, Haiyuan 1 ; He, Yiying 1 ; Chen, Maoxian 1 ; Zheng, Xu 1 ; Gui, Daping 1 ; Tang, Jixing 1 ; Fang, Yu 1 ; Huang, Yiwei 1 ; Wan, Hong 4 ; Ruan, Jiwei 5 ; Jin, Xin 1 ; Zhu, Andan 1 ;
作者机构： 1.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, 132 Lanhei Rd, Kunming 650201, Yunnan, Peoples R China
2.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Crop Wild Relat Om, 132 Lanhei Rd, Kunming 650201, Yunnan, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Yunnan Acad Agr Sci, Hort Res Inst, Kunming 650205, Yunnan, Peoples R China
5.Yunnan Acad Agr Sci, Flower Res Inst, Kunming 650205, Yunnan, Peoples R China
关键词：
期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）
ISSN： 1471-2164
年卷期： 2025 年 26 卷 1 期
页码：
收录情况： SCI
摘要： Fragaria iinumae, a diploid progenitor species of octoploid strawberries, likely occupies a basal position within the genus Fragaria. In this study, we report a near-complete genome assembly of F. iinumae v2.0, totaling 241.14 Mb with a contig N50 of 33.31 Mb. We identified 14 telomeric and 7 centromeric regions across its seven chromosomes. Compared to previous assemblies, F. iinumae v2.0 demonstrates substantial improvements in both genome continuity (gaps reduced from 29 to 0) and annotation completeness, including the annotation of 4,144 new genes and 395 new gene clusters. Notably, several large structural variants were identified between the F. iinumae v1.0 and F. iinumae v2.0 genomes, with most gaps in the v1.0 assembly overlapping with structural variant breakpoints. Additionally, we found a significant expansion of telomeric repeats in the B subgenome of octoploid strawberries compared to F. iinumae. Interestingly, two telomeres consistently exhibited low repeat abundance in both the diploid and octoploid B subgenomes, suggesting significant contraction early in the evolution of F. iinumae. Furthermore, through multiple lines of genomic evidence-including phylogenetic analyses, genetic distance matrices, a burst of LTR insertions, and the distribution of NLR resistance genes, we conclude that F. iinumae may represent an early-diverging lineage within the strawberry genus. This updated assembly provides a crucial genomic resource for understanding of the origin and structural dynamics of the strawberry genus and facilitates further exploration of genome-wide consequences of polyploidy.
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