Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaeaL.)

Zhao, Chuan Zhi; Xia, Han; Frazier, Taylor P.; Yao, Yingyin; Bi, Yu; Li, Ai Qin; Li, Meng Jun; Li, Chang Sheng; Zhang, Baohong; Wang, Xing Jun

doi:10.1186/1471-2229-10-3

Cited by 225 publications

(184 citation statements)

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“…In our data, we found two reads mapping the RNAi-5x insert, in very low abundance, yet, we found consistently low levels of aflatoxin in repeated challenging experiments in one or both transformed lines, particularly in line 288-10. Low copy numbers of sRNAs in peanut has been reported previously [36,37]; where, similar to our study, the majority of the peanut miRNAs had only one copy. Low copy numbers for transgene-derived siRNAs has been reported previously as well: Jahan et al [50] found few and low copy numbers of transgene-derived siRNAs in transgenic potato expressing a hairpin RNA construct targeting the G protein ß-subunit (PiGB1) of Phytophthora infestans, which is an essential gene involved in the pathogenicity of this pathogen.…”

Section: Discussionsupporting

confidence: 92%

“…In this study a large percentage of the sRNAs had read lengths of 20-24 nucleotides, which is typical for DICER-processed sRNA products [24][25][26]. The size distribution of the sRNAs in peanut is also consistent with previous reports [36,37]. Furthermore, the majority of sRNAs had a uracil or adenine as 5 terminal nucleotide, which suggest preferential loading onto AGO1, and AGO2 and AGO4, respectively [27]; these enzymes have a crucial role in the RNAi process.…”

Section: Discussionsupporting

confidence: 90%

“…The miRNAs not detected were miR394, miR3510, miR3512, miR3515, miR3517, miR3518, miR3519, and miR3520. Furthermore, miR162, miR166, miR168, miR169, miR171, miR172, miR390, miR894, miR1507, miR1511, and miR2118 are not reported in miRBase as peanut miRNAs, but have been reported by Chi et al [36] and Zhao et al [37], and these miRNAs were detected in our libraries as well (Tables A1, A2). The miRNA families miR319, miR2592, miR2673, miR2916, miR5072, miR5083, miR5368, miR5538, miR5652, miR5724, miR6025, miR6108, miR6300, miR64788175, and miR9410 have not been reported in peanut before.…”

Section: Abundance and Expression Profiles Of Known Peanut Mirnassupporting

confidence: 63%

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Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

et al. 2017

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Power, Imana L.; Dang, Phat M.; Sobolev, Victor S.; Orner, Valerie; Powell, Joseph L.; Lamb, Marshall C.; and Arias, Renée S., "Characterization of small RNA populations in non-transgenic andaflatoxin-reducing-transformed peanut" (2017 t r a c tAflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumulation of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNA populations in a control line and in two transformed peanut lines that expressed an inverted repeat targeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B 1 than the controls. The objective was to determine the putative involvement of the small RNA populations in aflatoxin reduction. In total, 41 known microRNA (miRNA) families and many novel miRNAs were identified. Among those, 89 known and 10 novel miRNAs were differentially expressed in the transformed lines. We furthermore found two small interfering RNAs derived from the inverted repeat, and 39 sRNAs that mapped without mismatches to the genome of A. flavus and were present only in the transformed lines. This information will increase our understanding of the effectiveness of RNAi and enable the possible improvement of the RNAi technology for the control of aflatoxins.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 90%

Section: Abundance and Expression Profiles Of Known Peanut Mirnassupporting

confidence: 63%

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Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

et al. 2017

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“…Bars = 10 mm. [See online article for color version of this figure. ] nucleotides, while the size of most known miRNAs is 21 nucleotides (Mi et al, 2008;Wu et al, 2009;Zhao et al, 2010). Consistently, small RNAs in our libraries were predominantly 21 and 24 nucleotides ( Fig.…”

Section: Deep-sequencing Analysis Of Small Rna Libraries From M Oryzsupporting

confidence: 85%

Multiple Rice MicroRNAs Are Involved in Immunity against the Blast Fungus Magnaporthe oryzae

et al. 2013

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MicroRNAs (miRNAs) are indispensable regulators for development and defense in eukaryotes. However, the miRNA species have not been explored for rice (Oryza sativa) immunity against the blast fungus Magnaporthe oryzae, the most devastating fungal pathogen in rice production worldwide. Here, by deep sequencing small RNA libraries from susceptible and resistant lines in normal conditions and upon M. oryzae infection, we identified a group of known rice miRNAs that were differentially expressed upon M. oryzae infection. They were further classified into three classes based on their expression patterns in the susceptible japonica line Lijiangxin Tuan Hegu and in the resistant line International Rice Blast Line Pyricularia-Kanto51-m-Tsuyuake that contains a single resistance gene locus, Pyricularia-Kanto 51-m (Pikm), within the Lijiangxin Tuan Hegu background. RNA-blot assay of nine of them confirmed sequencing results. Real-time reverse transcription-polymerase chain reaction assay showed that the expression of some target genes was negatively correlated with the expression of miRNAs. Moreover, transgenic rice plants overexpressing miR160a and miR398b displayed enhanced resistance to M. oryzae, as demonstrated by decreased fungal growth, increased hydrogen peroxide accumulation at the infection site, and up-regulated expression of defense-related genes. Taken together, our data indicate that miRNAs are involved in rice immunity against M. oryzae and that overexpression of miR160a or miR398b can enhance rice resistance to the disease.

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“…The prediction of precursor sequences for about 60% of the conserved miRNAs in our analysis was high when compared to previous reports in other species without an available genome sequence such as Arachis hypogaea L., for which precursors of nine conserved miRNA families out of 75 were identified (Zhao et al 2010). These results suggest that the database used in this analysis adequately covers the transcriptome of the studied tissues.…”

Section: Morais Et Al 2013)mentioning

confidence: 42%

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

Chaves

Lin

Pinto-Ricardo

et al. 2014

Tree Genetics & Genomes

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The differentiation of cork (phellem) cells from the phellogen (cork cambium) is a secondary growth process observed in the cork oak tree conferring a unique ability to produce a thick layer of cork. At present, the molecular regulators of phellem differentiation are unknown. The previously documented involvement of microRNAs in the regulation of developmental processes, including secondary growth, motivated the search for these regulators in cork oak tissues.We performed deep-sequencing of the small-RNA fraction obtained from cork oak leaves and differentiating phellem. RNA sequences with lengths of 19-25 nt derived from the two libraries were analysed, leading to the identification of 41 families of conserved miRNAs, of which the most abundant were miR167, miR165/166, miR396 and miR159. Thirty novel miRNA candidates were also unveiled, 11 of which were unique to leaves and 13 to phellem. Northern blot detection of a set of conserved and novel-miRNAs confirmed their differential expression profile. Prediction and analysis of putative miRNA target genes provided clues regarding processes taking place in leaf and phellem tissues but further experimental work will be needed for functional characterization. In conclusion, we here provide a first characterization of the miRNA population in a Fagacea species and the comparative analysis of miRNA expression in leaf and phellem libraries represents an important step to uncovering specific regulatory networks controlling phellem differentiation.

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Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaeaL.)

Cited by 225 publications

References 57 publications

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

Multiple Rice MicroRNAs Are Involved in Immunity against the Blast Fungus Magnaporthe oryzae

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

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