The genome of woodland strawberry (Fragaria vesca)

By Vladimir Shulaev, D. Sargent, R. Crowhurst, Todd C. Mockler, O. Folkerts, Arthur L. Delcher, P. Jaiswal, Keithanne Mockaitis, A. Liston, S. Mane and 61 more. Nature Genetics, 2010

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The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/071f6e13077a57541487422a117dc30f5742971b

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Citations in the corpus

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The genome of melon (Cucumis melo L.) (2012, result): “Our phylogenetic analysis is in agreement with the assignment of Populus in the Malvidae clade (28).”
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses (2012, methodology): “The homologs retrieved from the two sources were further refined, by querying the homolog gene clusters generated in a large-scale analysis (done previously) by using a modified version of the InParanoid (Östlund et al. 2010) program (Shulaev et al. 2011).”
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Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “…and drives AhNRAMP1 cDNA under the control of the –272/–131 region of the barley IDS2 gene containing Fe-deﬁciency-responsive element 1 (IDE1) and IDE2, ﬂanked by the –90/+8 region of the CaMV35S X tobacco ( Nicotiana tabacum L. cv. Petit-Havana SR1) according to the method of Helmer et al. (1984).”
Chloroplast genomes: diversity, evolution, and applications in genetic engineering (2016, background): “Fruits were harvested at ion of red lycopene into orange β-carotene (provitamin A) [154] that facilitates folding.”
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