ArticleScientific reports2017
Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa).
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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71 citing papers in PubMed.
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- Uncovering the genetic basis of fruit volatiles inHorticulture research · 2026Article
- Mitochondrial glutamine synthetase overexpression in tomato source leaves increases assimilate export and fruit yield.The Plant cell · 2026Article
- Genome-Wide Analysis Reveals the Roles ofInternational journal of molecular sciences · 2026Article
- FaRIF as a key regulator of strawberry fruit ripening: deciphering its targets and interaction networks.Horticulture research · 2026Article
- Harnessing genomic resources for passion fruit improvement: Progress and prospects.The plant genome · 2026Review
- Whole-genome sequencing bulked segregant analysis uncovered FW7, a Fusarium wilt resistance gene masked by epistasis in octoploid strawberry.The plant genome · 2025Article
- Article
- Inheritance and enzymatic basis of anthocyanin malonylation in Fragaria × ananassa.The Plant journal : for cell and molecular biology · 2025Article
- Differential expression of CCD4(4B) drives natural variation in fruit carotenoid content in strawberry (Fragaria spp.).Plant biotechnology journal · 2025Article
- Loss-of-function mutations in the fruit softening geneHorticulture research · 2025Article
- CyExpDB: a web-based multi-species tissue-specific gene expression platform for functional genomics in Cyprinidae fish.Database : the journal of biological databases and curation · 2025Article
- Genome-wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits.The plant genome · 2024Article
- Genome-wide gene network uncover temporal and spatial changes of genes in auxin homeostasis during fruit development in strawberry (F. × ananassa).BMC plant biology · 2024Article
- Genome-Wide Analysis of Polygalacturonase Gene Family Reveals Its Role in Strawberry Softening.Plants (Basel, Switzerland) · 2024Article
- Advances in genomics and genome editing for improving strawberry (Frontiers in genetics · 2024Review
- Non-climacteric fruit development and ripening regulation: 'the phytohormones show'.Journal of experimental botany · 2023Review
- A molecular phenology scale of grape berry development.Horticulture research · 2023Article
- QTL analysis for ascorbic acid content in strawberry fruit reveals a complex genetic architecture and association with GDP-L-galactose phosphorylase.Horticulture research · 2023Article
- High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry.Horticulture research · 2023Article
11 more citing papers are in PubMed but not listed here.
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
RNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled. The Trinity program was used for these assemblies, resulting in over 1.4 M isoforms. Filtering by a threshold of 0.3 FPKM, and doing Blastx (E-value < 1 e-30) against the UniProt database of plants reduced the number to 472,476 isoforms. Their assembly with the MIRA program (90% homology) resulted in 26,087 contigs. From these, 91.34 percent showed high homology to Fragaria vesca genes and 87.30 percent Fragaria iinumae (BlastN E-value < 1 e-100). Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, using FREEBAYES, as well as estimate their relative abundance in each sample.
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