Discovery of precursor and mature microRNAs and their putative gene targets using high-throughput sequencing in pineapple (Ananas comosus var. comosus)

Yusuf, Noor Hydayaty Md; Ong, Wen Dee; Redwan, Raimi Mohamed; Latip, Mariam Abd.; Subbiah, Vijay Kumar

doi:10.1016/j.gene.2015.06.050

Cited by 19 publications

(12 citation statements)

References 67 publications

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“…A characteristic of miR444 in grasses is its genomic antisense configuration relative to the target gene (Lu et al, 2008); we observed the same configuration in pineapple, indicating that this arrangement may reflect its ancestral state and even its evolutionary origins (Supplemental Figure 7). miR530 and miR1432 were also described previously in pineapple (Md Yusuf et al, 2015), and we also found that they were detected in other sister species within the commelinids, but not earlier in the monocots. Therefore, our analysis of annotated miRNAs demonstrated a combination of patterns of conservation and divergence within the monocots, with at least three monocot-specific miRNAs that emerged coincident with the commelinids.…”

Section: Resultssupporting

confidence: 87%

“…We next examined the set of monocot-specific miRNAs represented by miR444, miR530, and miR1432. miR444 has been previously characterized in several grass species (Lu et al, 2008), and it was identified without further analysis in pineapple (Md Yusuf et al, 2015). We found miR444 in several other monocots including the palms, but no earlier diverging lineages ( Figure 3B ).…”

Section: Resultsmentioning

confidence: 99%

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Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants

Patel

Mathioni

Hammond

et al. 2020

Preprint

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200 words) 1 In monocots other than maize and rice, the repertoire and diversity of microRNAs (miRNAs) and 2 the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly 3 characterized. To remedy this, we sequenced small RNAs from vegetative and dissected 4 inflorescence tissue in 28 phylogenetically diverse monocots and from several early-diverging 5 angiosperm lineages, as well as publicly available data from 10 additional monocot species. We 6 annotated miRNAs, siRNAs and phasiRNAs across the monocot phylogeny, identifying miRNAs 7 apparently lost or gained in the grasses relative to other monocot families, as well as a number 8 of tRNA fragments misannotated as miRNAs. Using our miRNA database cleaned of these 9 misannotations, we identified conservation at the 8 th , 9 th , 19 th and 3' end positions that we 10 hypothesize are signatures of selection for processing, targeting, or Argonaute sorting. We show 11 that 21-nt reproductive phasiRNAs are far more numerous in grass genomes than other 12 monocots. Based on sequenced monocot genomes and transcriptomes, DICER-LIKE5 (DCL5), 13 important to 24-nt phasiRNA biogenesis, likely originated via gene duplication before the 14 diversification of the grasses. This curated database of phylogenetically diverse monocot miRNAs, 15 siRNAs, and phasiRNAs represents a large collection of data that should facilitate continued 16 exploration of small RNA diversification in flowering plants. 17 18 19 20 55 2018). Rice, Brachypodium, and maize are the most studied of the grasses, with miRNAs 56 characterized using varying genotypes, tissue types, growth and stress conditions (Jeong et al., 57 2011; Zhang et al., 2009). With the major goal of assessing the diversity and origins of miRNAs 58 4in monocots, we analyzed sRNA data from 38 phylogenetically diverse monocots, spanning 59 orders from the Acorales to the Zingiberales. We described sRNA size classes, miRNA 60 conservation, divergence, sequence variability, 5' and 3' end nucleotide preferences, and single 61 nucleotide sequence profile characterizing positional biases and providing novel insights within 62 the miRNA sequences. We performed comparative analysis of miR2118 and miR2275 and their 63 long non-coding RNA (lncRNA) targets in monocots relative to other flowering plants, 64 demonstrating their presence and absence in these species. We found that both miR2118 and 65 miR2275 are conserved across diverse monocot species, and are present in vegetative tissues but 66 are found at high abundances predominantly in inflorescence tissues. The 21-and 24-nt PHAS 67 loci are most numerous in the genomes of grasses, relative to other monocots, and are similarly 68 most abundant in inflorescence tissues. Fewer PHAS loci were identified in non-grass monocots. 69 Overall, our study provides a deep comparative analysis of sRNAs in monocots, including a refined 70 database of monocot miRNAs. 71 72 Results 73 74Sequencing from diverse monocots demonstrates atypically abundant 22-nt siRNAs 75 We c...

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Section: Resultssupporting

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants

Patel

Mathioni

Hammond

et al. 2020

Preprint

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“…The raw data produced by Illumina sequencing were analyzed as previously described (Yusuf et al, 2015). After removing the adapter sequences and low-quality reads, unique reads of 18-25 nt were used for further analysis.…”

Section: Analysis Of Mirna High-throughput Sequencing Datamentioning

confidence: 99%

Integrative proteomic and microRNA analysis of the priming phase during rat liver regeneration

Geng

Chang

Zang

et al. 2016

Gene

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“…The raw data generated by Illumina sequencing were analyzed as previously described [25]. The expression abundance of each unique miRNA for each library was normalized to obtain the expression of the transcript per million using the following formula: normalized expression ¼ actual miRNA count/total count of clean reads Â 1,000,000 [26].…”

Section: Preparation Of Partial Hepatectomy Modelmentioning

confidence: 99%

An integrated analysis of the circRNA–miRNA–mRNA network reveals novel insights into potential mechanisms of cell proliferation during liver regeneration

Wang

Guo

Cheng

et al. 2019

Artificial Cells, Nanomedicine, and Biotechnology

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Discovery of precursor and mature microRNAs and their putative gene targets using high-throughput sequencing in pineapple (Ananas comosus var. comosus)

Cited by 19 publications

References 67 publications

Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants

Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants

Integrative proteomic and microRNA analysis of the priming phase during rat liver regeneration

An integrated analysis of the circRNA–miRNA–mRNA network reveals novel insights into potential mechanisms of cell proliferation during liver regeneration

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