RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus ¨Heritage¨) revealed several candidate genes involved in fruit development and ripening

Travisany, Dante; Ayala-Raso, Aníbal; Génova, Alex Di; Monsalve, Liliam; Bernales, Maricarmen; Martínez, Juan Pablo; González-Agüero, Mauricio; Defilippi, Bruno G.; Cherian, Sam; Maass, Alejandro; Fuentes, Lida

doi:10.1016/j.scienta.2019.04.018

Cited by 21 publications

(22 citation statements)

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“…Although raspberry fruit has been described as non-climacteric fruit, ethylene can be detected at the onset of ripening and continues to increase until full ripening [3,10,53]. There are no reports regarding other hormones in raspberry, although we could detect the presence of auxin in green stages and our transcriptome analysis has shown differential expression of phytohormone-related genes during fruit development and ripening [204]. More details in the text.…”

Section: Cytokininsmentioning

confidence: 70%

“…Data from several transcriptomic analyses, including our data on raspberry [204], suggest a coordinated role of different phytohormones during fruit development and ripening in non-climacteric fruit such as grape [104,215] and strawberry [31,216]. However, an in-depth analysis is still required to fully elucidate the role of phytohormone crosstalk in non-climacteric fruit ripening.…”

Section: Hormone Crosstalkmentioning

confidence: 88%

“…This study showed that IAA downregulated and MeJA clearly upregulated the expression of the genes encoding for transcription factor MYB10 and anthocyanin synthase (ANS), two genes related to anthocyanin biosynthesis, suggesting an opposite effect of both hormones in the regulation of anthocyanin accumulation in fruits [186]. Although there is still a lot to study in terms of raspberry fruit ripening regulation, our de-novo assembly analysis during different developmental stages showed that the DEGs included transcripts related to synthesis and response to ABA, enzymes with GH3 activity, transmembrane transporter for influx and efflux of auxin, proteins related to response to auxin, proteins related to BR biosynthesis and response, and proteins related to ethylene biosynthesis and perception [204]. All this information suggests a role for different hormones during raspberry development.…”

Section: Raspberrymentioning

confidence: 90%

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Recent Advances in Hormonal Regulation and Cross-Talk during Non-Climacteric Fruit Development and Ripening

2019

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Fleshy fruits are characterized by having a developmentally and genetically controlled, highly intricate ripening process, leading to dramatic modifications in fruit size, texture, color, flavor, and aroma. Climacteric fruits such as tomato, pear, banana, and melon show a ripening-associated increase in respiration and ethylene production and these processes are well-documented. In contrast, the hormonal mechanism of fruit development and ripening in non-climacteric fruit, such as strawberry, grape, raspberry, and citrus, is not well characterized. However, recent studies have shown that non-climacteric fruit development and ripening, involves the coordinated action of different hormones, such as abscisic acid (ABA), auxin, gibberellins, ethylene, and others. In this review, we discuss and evaluate the recent research findings concerning the hormonal regulation of non-climacteric fruit development and ripening and their cross-talk by taking grape, strawberry, and raspberry as reference fruit species.

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Section: Cytokininsmentioning

confidence: 70%

Section: Hormone Crosstalkmentioning

confidence: 88%

Section: Raspberrymentioning

confidence: 90%

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Recent Advances in Hormonal Regulation and Cross-Talk during Non-Climacteric Fruit Development and Ripening

2019

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“…Advances in genomics have led to the development of NGS based trait mapping approaches that have tremendously increased the efficiency of traits selection and mapping in complex genomes 43 . Among the high throughput genotyping approaches, Next Generation RNA Sequencing technology has contributed to a more comprehensive understanding of functional genes and is widely used for characterization of transcriptome profiles of various model and non-model plants 44 . De novo transcriptome analysis is not only providing an excellent platform for finding novel genes, molecular markers development but also cater a base for the construction of networks of gene expressions for various tissues and organs of animals as well as plants.…”

Section: Resultsmentioning

confidence: 99%

“…2 B). Additionally, comparison of the unigenes annotated with homologous sequences of other plant species was also performed 44 . Among the nucleotide sequences, highest similarity was noted for Sesamum indicum (with the highest similarity score of 67.5%).…”

Section: Resultsmentioning

confidence: 99%

De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

Shah

Alharby

Hakeem

et al. 2020

Sci Rep

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Lantana camara L. is an economically important essential oil producing plant belonging to family Verbenaceae. It is used in medication for treating various diseases like cancer, ulcers, tumor, asthma and fever. The plant is a useful source of essential bioactive compounds such as steroids, flavonoids and phenylpropanoid glycosides etc. Nonetheless, very little is known about the genomic or transcriptomic resources of L. camara , and this might be the reason of hindering molecular studies leading to identification of improved lines. Here we used Illumina sequencing platform and performed the L. camara leaf (LCL) and root (LCR) de novo transcriptome analyses . A total of 70,155,594 and 84,263,224 clean reads were obtained and de novo assembly generated 72,877 and 513,985 unigenes from leaf (LCL) and root (LCR) respectively. Furthermore, the pathway analysis revealed the presence of 229 and 943 genes involved in the phenylpropanoid biosynthesis in leaf and root tissues respectively. Similarity search was performed against publically available genome databases and best matches were found with Sesamum indicum (67.5%) that were much higher than that of Arabidopsis thaliana (3.9%). To the best of our knowledge, this is the first comprehensive transcriptomic analysis of leaf and root tissues of this non-model plant from family Verbenaceae and may serve as a baseline for further molecular studies.

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Transcriptome analysis reveals genes related to the synthesis and metabolism of cell wall polysaccharides in goji berry (Lycium barbarum L.) from various regions

Zhang

Yang

et al. 2023

J Sci Food Agric

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BACKGROUNDIn goji berries (Lycium barbarum L.), the cell wall properties and ripening environment affect fruit quality and their economic benefits. However, the mechanism underlying the cell wall remains to be fully elucidated.RESULTSThe results showed that total sugar content was higher in Qinghai berries (13.87%, P < 0.01), whereas cellulose content peaked in Zhongning berries (28%, P < 0.05). Arabinose, galactose, and galacturonic acid were the principal components of the cell wall polysaccharides in goji berries. Among them, the content of galactose in Zhongning was significantly the highest (P < 0.05). Interestingly, we found that highly expressed β‐glucosidase and lowly expressed endoglucanase led to cellulose accumulation by RNA‐sequencing analysis. The expression analysis results suggested that pectate lyase and pectinesterase enzymes could be major factors related to higher galactose and galacturonic acid contents in Zhongning compared to in Qinghai and Gansu. The starch and sucrose metabolism pathway, pentose and glucuronate interconversions pathway, and galactose metabolism pathway played a significant role in cell wall polysaccharide synthesis and metabolism.CONCLUSIONIn the present study, we aimed to provide some insights into the cell wall on polysaccharide composition, structural features, and gene analysis in goji berries from Zhongning, Qinghai, and Gansu in China. These results might help to clarify the molecular function of the major genes in the cell wall polysaccharides of goji berries and provide a solid foundation for further study. © 2023 Society of Chemical Industry.

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RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus ¨Heritage¨) revealed several candidate genes involved in fruit development and ripening

Cited by 21 publications

References 58 publications

Recent Advances in Hormonal Regulation and Cross-Talk during Non-Climacteric Fruit Development and Ripening

Recent Advances in Hormonal Regulation and Cross-Talk during Non-Climacteric Fruit Development and Ripening

De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

Transcriptome analysis reveals genes related to the synthesis and metabolism of cell wall polysaccharides in goji berry (Lycium barbarum L.) from various regions

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