Mining transcriptome data to identify genes and pathways related to lemon taste using supervised and unsupervised data learning methods

Zinati, Zahra; Sazegari, Sima; Amin, Hossein; Tahmasebi, Ahmad

doi:10.1007/s13580-021-00337-y

Cited by 10 publications

(3 citation statements)

References 29 publications

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“…However, a malate dehydrogenase gene overexpressed in wild mandarin was identified in this region in our work. MDH has been previously associated with Citrus pulp acidity [ 65 ] and might have been a target of the domestication process. The start of chromosome 8 has been also associated with fruit weight [ 66 ], and a correlation between fruit size and the amount of pummelo introgression has been suggested [ 1 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression

et al. 2022

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Background Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break. Results Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions. Conclusion In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.

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Section: Discussionmentioning

confidence: 99%

Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression

et al. 2022

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“…Gene expression analysis in lemon genotypes with varying acidity facilitated the identification of genes contributing to the sweet or acidic taste. Putative genes such as citrate synthase, malate dehydrogenase, proton-pumping ATPase and flavanone 3-hydroxylase were positively correlated with acidity in citrus [ 150 ]. Moreover, natural variations in the promoter region of flavanone 3-hydroxylase ( CitF3H ) contributed to a change in dihydrokaempferol levels, leading to alteration in flavonoid content in different progenies in citrus.…”

Section: Fruit Ripeningmentioning

confidence: 99%

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

Mathiazhagan

Chidambara

Laxman

et al. 2021

Genes

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The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.

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“…Cheng et al [23] used RapidMiner to preform four machine learning weighting models on gene expression datasets related to Huntington's disease, including decision tree, rule induction, random forest, and generalized linear algorithms, in order to identify contributing genes to this disorder. In another study, Zinati et al [24] used ten different weighting algorithms to identify the genes that differentiate between sour and acidic lemon taste.…”

Section: Introductionmentioning

confidence: 99%

Mining transcriptomic data to identifySaccharomyces cerevisiaesignatures related to improved and repressed ethanol production under fermentation

Sazegari

Niazi‎

Zinati

et al. 2021

Preprint

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Saccharomyces cerevisiae is known for its outstanding ability to produce ethanol in industry. Identifying the dynamic of gene expression in S. cerevisiae in response to fermentation is required for the establishment of any ethanol production improvement program. The goal of this study was to identify the discriminative genes between improved and repressed ethanol production as well as clarifying the molecular responses to this process through mining the transcriptomic data. Through 11 machine learning based algorithms from RapidMiner employed on available microarray datasets related to yeast fermentation performance under Mg 2+ and Cu 2+ supplementation, 172 probe sets were identified by at least 5 AWAs. Some have been identified as being involved in carbohydrate metabolism, oxidative phosphorylation, and ethanol fermentation. Principal component analysis (PCA) and heatmap clustering were also validated the top-ranked selective probe sets. According to decision tree models, 17 roots with 100% performance were identified. OLI1 and CYC3 were identified as the roots with the best performance, demonstrated by the most weighting algorithms and linked to top two significant enriched pathways including porphyrin biosynthesis and oxidative phosphorylation. ADH5 and PDA1 are also recognized as differential top-ranked genes that contribute to ethanol production. According to the regulatory clustering analysis, Tup1 has a significant effect on the top-ranked target genes CYC3 and ADH5 genes. This study provides a basic understanding of the S. cerevisiae cell molecular mechanism and responses to two different medium conditions (Mg 2+ and Cu 2+ ) during the fermentation process.

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Mining transcriptome data to identify genes and pathways related to lemon taste using supervised and unsupervised data learning methods

Cited by 10 publications

References 29 publications

Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression

Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

Mining transcriptomic data to identifySaccharomyces cerevisiaesignatures related to improved and repressed ethanol production under fermentation

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