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Background: MYB transcription factors regulate anthocyanin biosynthesis across numerous plant species. However, comprehensive genome-wide investigations regarding the R2R3-MYB gene family and its involvement in regulating anthocyanin biosynthesis in the red and white fruit color morphs of Fragaria pentaphylla remain scarce. Results: A total of 101 FpR2R3-MYB genes were identified from the F. pentaphylla genome and were divided into 34 subgroups based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were particularly conserved among the FpR2R3-MYB genes, especially members within the same subgroup. The FpR2R3-MYB genes were distributed over seven F. pentaphylla chromosomes. Analysis of gene duplication events revealed five pairs of tandem duplication genes and 16 pairs of segmental duplication genes, suggesting that segmental duplications are the major pattern for expansion of the FpR2R3-MYB gene family expansion in F. pentaphylla. Cis-regulatory elements of the FpR2R3-MYB promoters were involved in cellular development, phytohormones, environmental stress and photoresponse. Based on the analysis of the FpR2R3-MYB gene family and transcriptome sequencing (RNA-seq) data, FpMYB9 was identified as a key transcription factor involved in the regulation of anthocyanin synthesis in F. pentaphylla fruits. The expression of FpMYB9 increases significantly during the ripening stage of red fruits, as confirmed by reverse transcription quantitative real-time PCR. In addition, subcellular localization experiments further confirmed the nuclear presence of FpMYB9, supporting its role as a transcription factor involved in anthocyanin biosynthesis. Conclusion: Our results showed that the FpR2R3-MYB genes are highly conserved and play important roles in the anthocyanin biosynthesis in F. pentaphylla fruits. Our results also provide a compelling basis for further understanding of the regulatory mechanism underlying the role of FpMYB9 in anthocyanin formation in F. pentaphylla fruits. [ABSTRACT FROM AUTHOR]

Abstract Background MYB transcription factors regulate anthocyanin biosynthesis across numerous plant species. However, comprehensive genome-wide investigations regarding the R2R3-MYB gene family and its involvement in regulating anthocyanin biosynthesis in the red and white fruit color morphs of Fragaria pentaphylla remain scarce. Results A total of 101 FpR2R3-MYB genes were identified from the F. pentaphylla genome and were divided into 34 subgroups based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were particularly conserved among the FpR2R3-MYB genes, especially members within the same subgroup. The FpR2R3-MYB genes were distributed over seven F. pentaphylla chromosomes. Analysis of gene duplication events revealed five pairs of tandem duplication genes and 16 pairs of segmental duplication genes, suggesting that segmental duplications are the major pattern for expansion of the FpR2R3-MYB gene family expansion in F. pentaphylla. Cis-regulatory elements of the FpR2R3-MYB promoters were involved in cellular development, phytohormones, environmental stress and photoresponse. Based on the analysis of the FpR2R3-MYB gene family and transcriptome sequencing (RNA-seq) data, FpMYB9 was identified as a key transcription factor involved in the regulation of anthocyanin synthesis in F. pentaphylla fruits. The expression of FpMYB9 increases significantly during the ripening stage of red fruits, as confirmed by reverse transcription quantitative real-time PCR. In addition, subcellular localization experiments further confirmed the nuclear presence of FpMYB9, supporting its role as a transcription factor involved in anthocyanin biosynthesis. Conclusion Our results showed that the FpR2R3-MYB genes are highly conserved and play important roles in the anthocyanin biosynthesis in F. pentaphylla fruits. Our results also provide a compelling basis for further understanding of the regulatory mechanism underlying the role of FpMYB9 in anthocyanin formation in F. pentaphylla fruits.

Fragaria pentaphylla, a wild diploid quinquefoliolate species of Fragaria, is native to Southwest China. It has two morphs of red and white fruit color in nature and has characteristics of unique fragrance and resistance, which made it not only a valuable breedingmaterial but also a potentialmodel plant for molecular function researches. Here, we generate a high-quality chromosome-level genome assembly of a F. pentaphylla accession, BAAFS-FP039 employing a combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. The assembled genome contained 256.74 Mb and a contig N50 length of 32.38 Mb, accounting for 99.9% of the estimated genome (256.77 Mb). Based on Hi-C data, seven pseudo-chromosomes of F. pentaphylla-FP039 genome were assembled, covering 99.39% of the genome assembly. The genome was composed of 44.61% repetitive sequences and 29,623 protein-coding genes, 97.62% of protein-coding genes could be functionally annotated. Phylogenetic and chromosome syntenic analysis revealed that F. pentaphylla-FP039 was closely related to F. nubicola. This high-quality genome could provides fundamental molecular resources for evolutionary studies, breeding efforts, and exploring the unique biological characteristics of F. pentaphylla. [ABSTRACT FROM AUTHOR]

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BACKGROUND Strawberries have become one of the most popular fruits because of their unique flavor and high nutritional value. Fruit quality and price are the most important criteria that determine consumer acceptability. Fragaria nilgerrensis and Fragaria pentaphylla are two wild Asian diploid strawberry species that differ in fruit color, taste, and aroma. To understand the molecular mechanisms involved in the formation of high‐quality strawberry fruit, we integrated transcriptomics and metabolomics research methods to compare the metabolic and biosynthetic mechanisms of the two Fragaria species. RESULTS: F. nilgerrensis fruit has higher amino acid and lipid contents and a higher sugar‐to‐acid ratio than F. pentaphylla fruit does, underlying their superior nutritional value, aroma, firmness, and taste. Compared with F. nilgerrensis fruit, F. pentaphylla fruit contained more flavonoids, indicating its enhanced color and health benefits. In addition, candidate structural genes that regulate the biosynthesis of flavonoids, amino acids, and glycerophospholipids in the two strawberry fruit were screened. CONCLUSIONS: The differences in aroma, firmness, and taste between F. nilgerrensis fruit and F. pentaphylla fruit are probably due to differences in their amino acid and lipid contents, as well as the difference in their sugar‐to‐acid ratios. Eight key structural genes that may play important roles in the biosynthesis of amino acids, lipids, and flavonoids were identified. © 2021 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Aims Fruit color polymorphisms are widespread in plants, but what maintains them is largely unclear. One hypothesis is that some morphs are preferred by dispersers while others have higher pre- or postdispersal fitness. This leads to the prediction that fruit color morphs will differ in pre- or postdispersal fitness. Methods We compared genetic and clonal diversity, mating system, morphological traits that might be associated with resistance to freezing, and germination, survival and seed production of progeny of the red and white fruit morphs in a population of a diploid, wild strawberry, Fragaria pentaphylla , from south-central China. Important Findings The red morph was much more abundant than the white but did not show higher genetic diversity as measured by observed and effective numbers of alleles, Shannon information index, or expected or observed heterozygosities. AMOVA showed that most of the genetic variation in the population was within rather than between morphs. Morphs did not differ in mating system parameters, and no significant biparental inbreeding was found in either morph. Gene flow between two morphs was high (N m = 6.89). Seeds of the red morph germinated about 2 days earlier and had a 40% higher rate of germination than those of the white morph, but survival of seedlings and seed production by surviving offspring did not differ between morphs. The whole postdispersal fitness of the red morph was about two times higher than that of the white morph. Red morphs had hairier petioles but not more surface wax on leaves. Overall, results showed partial evidence for difference in pre- and postdispersal fitness between fruit color morphs in F. pentaphylla. Differences in fitness independent of dispersal may thus partially account for fruit color polymorphism in all cases. [ABSTRACT FROM AUTHOR]

Fragaria pentaphylla has fragmented distribution in southwest China, and its populations have been shrinking. In the present study, we report the complete chloroplast genome sequence of F. pentaphylla using next-generation sequencing technology. The complete chloroplast genome size is 155,640 bp. The genome contained 128 genes, including 30 tRNA genes, 78 protein-coding genes, and four rRNA genes, and multiple copies of 19 of these genes. Phylogenetic analysis based on nine complete chloroplast genomes revealed that F. pentaphylla is closely related to Fragaria vesca subsp. vesca. The complete chloroplast genome of F. pentaphylla would provide a good foundation for understanding the diversification and evolution of the genus Fragaria, and might help in conserving the precious natural populations of wild white strawberry. [ABSTRACT FROM AUTHOR]

Fragaria pentaphylla , a wild diploid quinquefoliolate species of Fragaria , is native to Southwest China. It has two morphs of red and white fruit color in nature and has characteristics of unique fragrance and resistance, which made it not only a valuable breeding material but also a potential model plant for molecular function researches. Here, we generate a high-quality chromosome-level genome assembly of a F. pentaphylla accession, BAAFS-FP039 employing a combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. The assembled genome contained 256.74 Mb and a contig N50 length of 32.38 Mb, accounting for 99.9% of the estimated genome (256.77 Mb). Based on Hi-C data, seven pseudo-chromosomes of F. pentaphylla -FP039 genome were assembled, covering 99.39% of the genome assembly. The genome was composed of 44.61% repetitive sequences and 29,623 protein-coding genes, 97.62% of protein-coding genes could be functionally annotated. Phylogenetic and chromosome syntenic analysis revealed that F. pentaphylla -FP039 was closely related to F. nubicola . This high-quality genome could provides fundamental molecular resources for evolutionary studies, breeding efforts, and exploring the unique biological characteristics of F. pentaphylla ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Sun, Li, Chang, Dong, Zhong, Zhang, Wei, Gao, Wang, Zhang and Sun.)

Fragaria pentaphylla is a perennial herb with two morphs that produce either white or red fruit. A combined metabolomic and transcriptomic analysis of the red and white fruits was conducted to reveal the different accumulated metabolites and differentially expressed genes between the red and white fruits. Red fruits of F. pentaphylla had higher quality with abundant flavonoids, free amino acids, and vitamins, compared with white fruits. Four anthocyanins, one procyanidin and 15 flavonoids in red morphs were significantly higher than in white morphs. The low level of pelargonin O-hexosyl-O-hexoside, pelargonidin O-hexoside and petunidin O-rutinoside might contribute to the white color of the F. pentaphylla flesh. Eighteen amino acids, except glycine or glutamine, were found in both the red and white morphs. Red fruits had a higher content of amino acids than white fruits. No DEG was involved in the pathway for amino acids synthesis, indicating that the higher levels of amino acids in red fruits than in white were not due to an increased amino acid biosynthesis. Integrated metabolomic and transcriptomic data suggested that COR , CHI , DFR , PKS and COMT genes might be related to the synthesis of flavonoids. Besides, 7OMT and PKS genes were shown to be closely associated with alkaloid and polyphenol synthesis. These results provide new insights into the molecular mechanisms of the color and nutrients in strawberries. • The white flesh of F. pentaphylla has low levels of flavonoids and anthocyanins. • The red fruits of F. pentaphylla are rich in free amino acids and vitamins. • No DEG is involved in amino acids biosynthesis. [ABSTRACT FROM AUTHOR]