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Fragaria iinumae

ABSTRACT: diploid Fragaria species

PROVIDER: PRJNA243257 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
		Other
	SRR2976090.fastq.gz	Fastqsanger.gz
	SRR9217950_subreads.fastq.gz	Fastqsanger.gz
	SRR9217951_1.fastq.gz	Fastqsanger.gz
	SRR9217951_2.fastq.gz	Fastqsanger.gz

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A near-complete genome assembly of Fragaria iinumae.

Project description: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.

| S-EPMC11909947 | biostudies-literature

Fragaria

Project description:seven Fragaria species Transcriptome

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Fragaria iinumae isolate:FII-19-9

Project description:Fragaria iinumae isolate:FII-19-9 Genome sequencing and assembly

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Fragaria

Project description:RosBREED re-sequencing of Fragaria species

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Comprehensive transcriptomic dataset for early stage fruit development in woodland strawberry Fragaria vesca

Project description:Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacleM-^Rs surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution.

2013-10-01 | E-MTAB-1902 | biostudies-arrayexpress

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