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Nam, Young‐Woo; Tichit, L.; Leperlier, Monique; Cuerq, B.; Marty, Isabelle; Lelièvre, Jean-Marc

doi:10.1023/a:1006179928312

Cited by 86 publications

(7 citation statements)

References 27 publications

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“…The over-expression of metallothionein-like proteins was detected during the quality check of the NGS libraries. The same discovery has been reported in similar studies performed during the development and ripening of pineapple and other Fragaria fruit species (Nam et al, 1999 ; Moyle et al, 2005 ).…”

Section: Discussionsupporting

confidence: 81%

RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit

et al. 2022

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Fragaria chiloensis (Chilean strawberry) is a native species that produces fruit with an exotic pinkish color and a fruity aroma. It has a non-climacteric pattern of fruit ripening, and it is the mother of the commercial Fragaria x ananassa. The ripening of F. chiloensis fruit seems stimulated by ABA, and a complete set of genes participate in its softening, color, and aroma development. In addition, a set of transcription factors regulate the entire process, but few of them have been described. Over the last two decades, RNA-seq was used to identify genes at three fruit development/ripening stages, named C2 (unripe, large green) to C4 (full ripe), in whole fruit and fruit without achenes. A total of 204,754 contigs were assembled considering all samples, obtaining an N50 of 1.125 bp. Differentially expressed genes (DEGs) between two samples were identified, obtaining a total of 77,181 DEGs. Transcripts for genes involved in ABA biosynthesis present high and differential expression during the C2, C3, and C4 stages. Besides, contigs corresponding to ABA receptors, which interact with a regulatory network, are also differentially expressed. Genes associated with cell wall remodeling and those involved in flavonoid synthesis were also differentially expressed. An interaction network was built considering differentially expressed genes for the phenylpropanoid and flavonoid molecular pathways and having FcMYB1 as a transcription factor regulator. Identifying key genes could give an option to control the ripening of this non-climacteric fruit.

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Section: Discussionsupporting

confidence: 81%

RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit

et al. 2022

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“…Most members of the MLP/RRP subfamily are expressed in fruits with their expression upregulated during ripening. Examples are a ripening-induced protein from wild strawberry [45], Csf-2 from cucumber [46] and Sn-1 from bell pepper, whose expression can also be induced by wounding in unripe fruits [47]. A wound-induced transcript from Mesembryanthemum crystallinum [Uniprot:O65178] also belongs to this subfamily.…”

Section: Resultsmentioning

confidence: 99%

The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands

2008

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BackgroundThe major birch pollen allergen, Bet v 1, is a member of the ubiquitous PR-10 family of plant pathogenesis-related proteins. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. In addition, determination of the Bet v 1 structure revealed the existence of a large superfamily of structurally related proteins. In this study, we aimed to identify and classify all Bet v 1-related structures from the Protein Data Bank and all Bet v 1-related sequences from the Uniprot database.ResultsStructural comparisons of representative members of already known protein families structurally related to Bet v 1 with all entries of the Protein Data Bank yielded 47 structures with non-identical sequences. They were classified into eleven families, five of which were newly identified and not included in the Structural Classification of Proteins database release 1.71. The taxonomic distribution of these families extracted from the Pfam protein family database showed that members of the polyketide cyclase family and the activator of Hsp90 ATPase homologue 1 family were distributed among all three superkingdoms, while members of some bacterial families were confined to a small number of species. Comparison of ligand binding activities of Bet v 1-like superfamily members revealed that their functions were related to binding and metabolism of large, hydrophobic compounds such as lipids, hormones, and antibiotics. Phylogenetic relationships within the Bet v 1 family, defined as the group of proteins with significant sequence similarity to Bet v 1, were determined by aligning 264 Bet v 1-related sequences. A distance-based phylogenetic tree yielded a classification into 11 subfamilies, nine exclusively containing plant sequences and two subfamilies of bacterial proteins. Plant sequences included the pathogenesis-related proteins 10, the major latex proteins/ripening-related proteins subfamily, and polyketide cyclase-like sequences.ConclusionThe ubiquitous distribution of Bet v 1-related proteins among all superkingdoms suggests that a Bet v 1-like protein was already present in the last universal common ancestor. During evolution, this protein diversified into numerous families with low sequence similarity but with a common fold that succeeded as a versatile scaffold for binding of bulky ligands.

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“…During fruit development and ripening, the types and contents of strawberry volatile components are one of the most critical factors to determine the quality of the strawberry [ 46 ]. The changes in strawberry fruit quality result from changes in gene expression and enzymatic activity during strawberry fruit development and ripening [ 47 , 48 ]. The content of volatile components in the fruits of ‘Sachinoka’ and its somaclonal mutant ‘Mixue’ gradually increased with the development of fruit.…”

Section: Discussionmentioning

confidence: 99%

An Integrated Metabolomic and Gene Expression Analysis of ‘Sachinoka’ Strawberry and Its Somaclonal Mutant Reveals Fruit Color and Volatiles Differences

Bian

Song

et al. 2022

Plants

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Plant tissue culture produces a wide range of genetic variations which are useful for quality improvement of the plant species. However, the differences in metabolic components and the key genes responsible for the difference in metabolic components between somaclonal variation and the original parent are still largely unknown. In this study, a mutant named ‘Mixue’ was identified with somaclonal variation of the ‘Sachinoka’ strawberry. The contents of pelargonidin-3-O-glucoside and cyanidin-3-O-glucoside in the red fruit of ‘Mixue’ were significantly decreased compared with ‘Sachinoka’. In comparison with ‘Sachinoka’, the expression levels of FaMYB10, FaMYB11.2, FaWD40 and FaTT19 in the turning fruit of ‘Mixue’ were significantly down-regulated, while the expression of FaMYB1 was significantly up-regulated in the red fruit. ‘Sachinoka’ and ‘Mixue’ fruits were found to have 110 volatile components. Among them, 15 volatile components in the red fruit of ‘Mixue’ were significantly increased compared with ‘Sachinoka’, such as nerolidol, benzaldehyde, ethyl hexanoate, ethyl isovalerate, which led to an enhanced aroma in ‘Mixue’ and might result from the up-regulated expression of FaNES1, FaCNL and FaAATs in ‘Mixue’. These results provide useful information on the effect of somaclonal variation on metabolic components of strawberry fruit and lay the foundation for the improvement in quality of strawberry.

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Cited by 86 publications

References 27 publications

RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit

RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit

The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands

An Integrated Metabolomic and Gene Expression Analysis of ‘Sachinoka’ Strawberry and Its Somaclonal Mutant Reveals Fruit Color and Volatiles Differences

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