Correction: Expansion of Capsicum annum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles

Taller, Dénes; Bálint, Jeannette; Gyula, Péter; Nagy, Tibor; Barta, Endre; Baksa, Ivett; Szittya, György; Taller, János; Havelda, Zoltán

doi:10.1371/journal.pone.0203582

Cited by 5 publications

(1 citation statement)

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“…We also uncovered a substantial expansion of predicted miRNAs in pepper (330), which is congruent with previous miRNA predictions for this species (Seo et al, 2018;Taller et al, 2018). In contrast, we predicted relatively few miRNAs for both of the petunia genomes (124 -P. inflata and 126 -P. axillaris).…”

Section: Microrna Predictions Indicate An Expansion Of Novel Mirnas In Nicotiana Speciessupporting

confidence: 89%

The Evolutionary History of Small RNAs in the Solanaceae

Baldrich

Bélanger

Kong

et al. 2021

Preprint

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The Solanaceae or "nightshade" family is an economically important group that harbors a remarkable amount of diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's small RNA genomic landscape, we downloaded over 255 publicly available small RNA datasets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major small RNA classes: (1) microRNAs (miRNAs), typically 20-22 nt RNAs generated from a hairpin precursor and functioning in gene silencing, and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs (hc-siRNAs) typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs (phasiRNAs) and trans-acting siRNAs (tasiRNAs) generated via miRNA-directed cleavage of a Pol II-derived RNA precursor. Our analyses described thousands of small RNA loci, including poorly-understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these small RNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar small RNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.

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Section: Microrna Predictions Indicate An Expansion Of Novel Mirnas In Nicotiana Speciessupporting

confidence: 89%

The Evolutionary History of Small RNAs in the Solanaceae

Baldrich

Bélanger

Kong

et al. 2021

Preprint

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Genetic, Epigenetic, and Hormonal Regulation of Fruit Development and Ripening inCapsicumL. Species

Kumar

Kumar²,

Anju

et al. 2021

Annual Plant Reviews Online

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Fruits are not only important for the plants but also for ensuring sustainable food security of the burgeoning global population. Considering the huge nutritional and ecological importance of fruits, investigation of mechanisms, and factors governing their development and ripening is crucial. The investigation of fruit development in several economically important crops such as tomato, strawberry, grape, and banana includingCapsicumsuggest that early fruit development is largely dependent on auxins and gibberellins (GAs) whereas later ripening is dependent on ethylene or abscisic acid (ABA). The initial development is relatively conserved whereas the ripening of fruits can be either climacteric or non‐climacteric depending on the presence or absence of respiratory burst and ethylene production respectively. Climacteric fruit ripening is mediated by ethylene, and it is well studied in tomato and banana, whereas non‐climacteric fruit ripening requires ABA and much of the information on it comes from strawberry and grape. The genusCapsicumL. shows rich diversity in fruit traits such as shape, colour, size, and even in its ripening behaviour. Early fruit development in different species ofCapsicumappears similar to other fruit crops, whereas later fruit ripening behaviour in different species ofCapsicumcan be either climacteric or non‐climacteric depending upon evolution of ethylene and respiratory burst. It has been found that, even different cultivars of the same species ofCapsicumshow variation in ripening behaviour suggesting interspecific and intraspecific complexities in fruit ripening responses. Until a few years, a majority of the papers have focussed on the non‐climacteric nature of fruit ripening inCapsicum. However, recent studies have shown substantial involvement of ethylene and ethylene related genes in fruit ripening ofCapsicumsuggesting the existence of extensive common regulons between climacteric and non‐climacteric fruits. Recent studies have also suggested the involvement of several epigenetic mechanisms such as non‐coding RNAs (ncRNAs) and cytosine methylation in regulating fruit development and ripening. With the advent of new tools in the omics field such as genomics, transcriptomics, metabolomics, and epigenomics, there is considerable progress in understanding the fruit development and complex nature of ripening inCapsicum. Nevertheless, consolidated information onCapsicumfruit development and its complex nature of ripening is not available. In this article, an attempt is made to present up to date consolidated information on the development and ripening ofCapsicumfruit with an emphasis on its genetic, epigenetic, and hormonal regulation.

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Small RNA-omics: Decoding the regulatory networks associated with horticultural traits

Mohanty

Parida

2022

Omics in Horticultural Crops

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Correction: Expansion of Capsicum annum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles

Cited by 5 publications

References 1 publication

The Evolutionary History of Small RNAs in the Solanaceae

The Evolutionary History of Small RNAs in the Solanaceae

Genetic, Epigenetic, and Hormonal Regulation of Fruit Development and Ripening inCapsicumL. Species

Small RNA-omics: Decoding the regulatory networks associated with horticultural traits

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