Identification of Blueberry miRNAs and Their Targets Based on High-Throughput Sequencing and Degradome Analyses

Li, Guangping; Wang, Yun; Lou, Xiaoming; Li, Yong; Zhang, Changqing

doi:10.3390/ijms19040983

Cited by 11 publications

(6 citation statements)

References 38 publications

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“…The complement of miRNAs has been identified in blueberries using high-throughput sequencing. For example, 412 conserved miRNAs belonging to 29 families were identified in fruits from rabbiteye blueberry ( Yue et al, 2017 ); similarly, 127 known and 101 novel miRNAs were identified from flowers, young fruits, and ripe fruits of rabbiteye blueberry ( Li G. et al, 2018 ). In highbush blueberry, 84 known miRNAs and 16 novel miRNAs were identified from fruits, with 10 miRNAs from miR166 family ( Hou et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Conservation and Diversity of miR166 Family Members From Highbush Blueberry (Vaccinium corymbosum) and Their Potential Functions in Abiotic Stress

Wang²,

Guo³

et al. 2022

Front. Genet.

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MicroRNA166 (miR166) is highly conserved and has diverse functions across plant species. The highbush blueberry (Vaccinium corymbosum) genome is thought to harbor 10 miRNA166 loci (Vco-miR166), but the extent of their evolutionary conservation or functional diversification remains unknown. In this study, we identified six additional Vco-miR166 loci based on conserved features of the miR166 family. Phylogenetic analyses showed that mature Vco-miR166s and their precursor cluster in several clades are evolutionary conserved with diverse species. The cis-regulatory elements in the Vco-miR166 promoters indicated functions related to different phytohormones and defense responses. We also identified putative targets of vco-miR166s, which targeted the same gene families, suggesting the functional conservation and diversification of Vco-miR166 family members. Furthermore, we examined the accumulation patterns of six mature Vco-miR166s in response to abiotic stresses by stem-loop reverse RT-qPCR, which revealed their upregulation under freezing, cold, and heat stress, while they were downregulated by drought compared to control growth conditions. However, Vco-miR166 members showed different expression patterns when exposed to salt stress. These results showed that conserved Vco-miR166 family members display functional diversification but also coordinately influence plant responses to abiotic stress.

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Section: Introductionmentioning

confidence: 99%

Conservation and Diversity of miR166 Family Members From Highbush Blueberry (Vaccinium corymbosum) and Their Potential Functions in Abiotic Stress

Wang²,

Guo³

et al. 2022

Front. Genet.

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“…Previous studies have found that the length of sRNA varies among different species. The sRNA length of blueberry [ 37 ], sweet potato [ 38 ], and tea tree [ 39 ] is at most 24 nt, whereas that of poplar [ 40 ], soybeans [ 41 ], and tomato [ 42 ] is at most 21 nt, and high-throughput sequencing data showed that the sRNA length in 12 databases is at most 24 nt, followed by 21 nt ( Figure 1 ), which is similar to that of Ramat Ju [ 43 ]. The reported typical sRNA distribution patterns are extremely similar.…”

Section: Discussionmentioning

confidence: 99%

Identification of Small RNAs Associated with Salt Stress in Chrysanthemums through High-Throughput Sequencing and Bioinformatics Analysis

Nai

Liu

et al. 2023

Genes

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The Chrysanthemum variety “Niu 9717” exhibits excellent characteristics as an ornamental plant and has good salt resistance. In this study, this plant was treated with 200 mM NaCl for 12 h followed by high-throughput sequencing of miRNA and degradome. Subsequently, the regulatory patterns of potential miRNAs and their target genes were searched to elucidate how Chrysanthemum miRNAs respond to salt. From the root and leaf samples, we identified a total of 201 known miRNAs belonging to 40 families; furthermore, we identified 79 new miRNAs, of which 18 were significantly differentially expressed (p < 0.05). The expressed miRNAs, which targeted a total of 144 mRNAs in the leaf and 215 mRNAs in the root, formed 144 and 226 miRNA–target pairs in roots and leaves, respectively. Combined with the miRNA expression profile, degradome and transcriptome data were then analyzed to understand the possible effects of the miRNA target genes and their pathways on salt stress. The identified genes were mostly located in pathways related to hormone signaling during plant growth and development. Overall, these findings suggest that conserved and novel miRNAs may improve salt tolerance through the regulation of hormone signal synthesis or expression of genes involved in hormone synthesis.

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“…Many of them are widely involved in the plant growth and development, metabolism, hormone regulation, and various biological and abiotic stresses (Li et al, 2020 ). Presently, miR828, miR858, miR156, miR159, miR157, miR160, miR172, miR393, miR396, miR824, and miR870 in Litchi chinensis (Liu et al, 2017 ), Punica granatum (Saminathan et al, 2016 ), Hylocereus monacanthus (Chen et al, 2020 ), Raphanus sativus (Gao et al, 2019 ), Lycium ruthenicum (Qi et al, 2020 ), Diospyros kaki (Luo et al, 2015 ), Vaccinium ashei (Li et al, 2018 ), Actinidia arguta (Li et al, 2019 ), and Lonicera edulis (Li et al, 2018 ), respectively, have been found to be involved in the regulation of anthocyanin metabolism. Both miR156h‐3p and miR396a‐3p can target UFGT in L. edulis and significantly negatively correlate with anthocyanin biosynthesis (Cui et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…Lonicera edulis (Li et al, 2018), respectively, have been found to be involved in the regulation of anthocyanin metabolism. Both miR156h-3p and miR396a-3p can target UFGT in L. edulis and significantly negatively correlate with anthocyanin biosynthesis (Cui et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs and their target genes related to the accumulation of anthocyanin in purple potato tubers (Solanum tuberosum)

et al. 2022

Plant Direct

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MicroRNAs (miRNAs) are types of endogenous non‐coding small RNAs found in eukaryotes that are 18–25 nucleotides long. miRNAs are considered to be key regulatory factors of the expression of target mRNA. The roles of miRNAs involved in the regulation of anthocyanin accumulation in pigmented potatoes have not been systematically reported. In this study, the differentially expressed miRNAs and their target genes involved in the accumulation of anthocyanin during different developmental stages in purple potato ( Solanum tuberosum L.) were identified using small RNA (sRNA) and degradome sequencing. A total of 275 differentially expressed miRNAs were identified in the sRNA libraries. A total of 69,387,200 raw reads were obtained from three degradome libraries. The anthocyanin responsive miRNA–mRNA modules were analyzed, and 37 miRNAs and 23 target genes were obtained. Different miRNAs regulate the key enzymes of anthocyanin synthesis in purple potato. The structural genes included phenylalanine ammonia lyase, chalcone isomerase, flavanone 3‐hydroxylase, and anthocyanidin 3‐ O ‐glucosyltransferase. The regulatory genes included WD40, MYB, and SPL9. stu‐miR172e‐5p_L‐1R‐1, stu‐miR828a, stu‐miR29b‐4‐5p, stu‐miR8019‐5p_L‐4R‐3, stu‐miR396b‐5p, stu‐miR5303f_L‐7R + 2, stu‐miR7997a_L‐3, stu‐miR7997b_L‐3, stu‐miR7997c_L + 3R‐5_2ss2TA3AG, stu‐miR156f‐5p_L + 1, stu‐miR156a, stu‐miR156a_R‐1, stu‐miR156e, stu‐miR858, stu‐miR5021, stu‐miR828 and their target genes were validated by qRT‐PCR. They play important roles in the coloration and accumulation of purple potatoes. These results provide new insights into the biosynthesis of anthocyanins in pigmented potatoes.

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Identification of Blueberry miRNAs and Their Targets Based on High-Throughput Sequencing and Degradome Analyses

Cited by 11 publications

References 38 publications

Conservation and Diversity of miR166 Family Members From Highbush Blueberry (Vaccinium corymbosum) and Their Potential Functions in Abiotic Stress

Conservation and Diversity of miR166 Family Members From Highbush Blueberry (Vaccinium corymbosum) and Their Potential Functions in Abiotic Stress

Identification of Small RNAs Associated with Salt Stress in Chrysanthemums through High-Throughput Sequencing and Bioinformatics Analysis

Identification of microRNAs and their target genes related to the accumulation of anthocyanin in purple potato tubers (Solanum tuberosum)

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