Evidence map›Paper›PMID 40087556›Full record

ArticleBMC genomics2025

A near-complete genome assembly of Fragaria iinumae.

Haiyuan Du, Yiying He, Maoxian Chen, Xu Zheng, Daping Gui, Jixing Tang, Yu Fang, Yiwei Huang, Hong Wan, Jiwei Ruan and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Haiyuan DuGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China.
Yiying HeGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China.
Maoxian ChenGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China.
Xu ZhengGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China.
Daping GuiGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China.
Jixing TangGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China.
Yu FangGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China.
Yiwei HuangGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China.
Hong WanHorticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, China.
Jiwei RuanFlower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, China.
Xin JinGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China. jinxin@mail.kib.ac.cn.
Andan ZhuGermplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd, Heilongtan, Kunming, 650201, Yunnan, China. zhuandan@mail.kib.ac.cn.

Funding

High-Level Talent Program of Yunnan Province YDYC20170138Key and Major Program for Basic Research Project 202401AS070094National Natural Science Foundation of China 32270245
6 · The paper itself

Abstract

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.

Indexed as

FragariaGenome, PlantGenomicsChromosomes, PlantMolecular Sequence AnnotationPolyploidyTelomereEarly branchingFragaria iinumaeNear-complete genomeTelomere repeat contraction/expansion

Identifiers

PMID40087556
PMCPMC11909947

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.