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Cataloguing the small RNA content of honey using next generation sequencing. FOOD CHEMISTRY. MOLECULAR SCIENCES 2021; 2:100014. [PMID: 35415639 PMCID: PMC8991712 DOI: 10.1016/j.fochms.2021.100014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 12/02/2022]
Abstract
Plant miRNAs are present in Australian polyfloral and Leptospermum scoparium honey. Sequencing shows that honey contains a diverse range of small, non-coding RNAs. Honey RNA comes from different phylogenies including invertebrates and prokaryotes. Unique small RNA profiles can provide insight into honey production conditions.
Honey adulteration is a problem that effects the global honey industry and specifically, has been discovered in the Australian market. Common methods of adulteration include dilution with sugar syrup substitutes and the mislabelling of the floral and geographic origin(s) of honey. Current authentication tools rely on the molecular variability between different honeys, identifying unique chemical profiles and/or DNA signatures characteristic of a particular honey. Honey is known to contain plant miRNAs derived from its floral source. To explore the composition and variability of honey RNA molecules, this is the first study to catalogue the small RNA content of Australian polyfloral table honey and New Zealand Leptospermum scoparium honey using next generation sequencing. The data shows that in addition to miRNAs, honey contains a variety of small non-coding RNAs including tRNA-derived fragments. Moreover, the honey small RNAs are derived from a range of phylogenetic sources, including from plant, invertebrate, and prokaryotic species. The data indicates that different honeys contain unique small RNA profiles, which suggests a novel avenue in developing molecular-based honey authentication tools.
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Ángel Martín-Rodríguez J, Ariani A, Leija A, Elizondo A, Fuentes SI, Ramirez M, Gepts P, Hernández G, Formey D. Phaseolus vulgaris MIR1511 genotypic variations differentially regulate plant tolerance to aluminum toxicity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1521-1533. [PMID: 33300202 DOI: 10.1111/tpj.15129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/20/2020] [Accepted: 12/03/2020] [Indexed: 05/28/2023]
Abstract
The common-bean (Phaseolus vulgaris), a widely consumed legume, originated in Mesoamerica and expanded to South America, resulting in the development of two geographically distinct gene pools. Poor soil condition, including metal toxicity, are often constraints to common-bean crop production. Several P. vulgaris miRNAs, including miR1511, respond to metal toxicity. The MIR1511 gene sequence from the two P. vulgaris model sequenced genotypes revealed that, as opposed to BAT93 (Mesoamerican), the G19833 (Andean) accession displays a 58-bp deletion, comprising the mature and star miR1511 sequences. Genotyping-By-Sequencing data analysis from 87 non-admixed Phaseolus genotypes, comprising different Phaseolus species and P. vulgaris populations, revealed that all the P. vulgaris Andean genotypes and part of the Mesoamerican (MW1) genotypes analyzed displayed a truncated MIR1511 gene. The geographic origin of genotypes with a complete versus truncated MIR1511 showed a distinct distribution. The P. vulgaris ALS3 (Aluminum Sensitive Protein 3) gene, known to be important for aluminum detoxification in several plants, was experimentally validated as the miR1511 target. Roots from BAT93 plants showed decreased miR1511 and increased ALS3 transcript levels at early stages under aluminum toxicity (AlT), while G19833 plants, lacking mature miR1511, showed higher and earlier ALS3 response. Root architecture analyses evidenced higher tolerance of G19833 plants to AlT. However, G19833 plants engineered for miR1511 overexpression showed lower ALS3 transcript level and increased sensitivity to AlT. Absence of miR1511 in Andean genotypes, resulting in a diminished ALS3 transcript degradation, appears to be an evolutionary advantage to high Al levels in soils with increased drought conditions.
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Affiliation(s)
| | - Andrea Ariani
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Armando Elizondo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara I Fuentes
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramirez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Sun Y, Mui Z, Liu X, Yim AKY, Qin H, Wong FL, Chan TF, Yiu SM, Lam HM, Lim BL. Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages. Int J Mol Sci 2016; 17:E2043. [PMID: 27929436 PMCID: PMC5187843 DOI: 10.3390/ijms17122043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; from PHAS loci), play key roles in plant development. Cultivated soybean, Glycine max, contributes a great deal to food production, but, compared to its wild kin, Glycine soja, it may lose some genetic information during domestication. In this work, we analyzed the sRNA profiles of different tissues in both cultivated (C08) and wild soybeans (W05) at three stages of development. A total of 443 known miRNAs and 15 novel miRNAs showed varying abundances between different samples, but the miRNA profiles were generally similar in both accessions. Based on a sliding window analysis workflow that we developed, 50 PHAS loci generating 55 21-nucleotide phasiRNAs were identified in C08, and 46 phasiRNAs from 41 PHAS loci were identified in W05. In germinated seedlings, phasiRNAs were more abundant in C08 than in W05. Disease resistant TIR-NB-LRR genes constitute a very large family of PHAS loci. PhasiRNAs were also generated from several loci that encode for NAC transcription factors, Dicer-like 2 (DCL2), Pentatricopeptide Repeat (PPR), and Auxin Signaling F-box 3 (AFB3) proteins. To investigate the possible involvement of miRNAs in initiating the PHAS-phasiRNA pathway, miRNA target predictions were performed and 17 C08 miRNAs and 15 W05 miRNAs were predicted to trigger phasiRNAs biogenesis. In summary, we provide a comprehensive description of the sRNA profiles of wild versus cultivated soybeans, and discuss the possible roles of sRNAs during soybean germination.
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Affiliation(s)
- Yuzhe Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Zeta Mui
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Xuan Liu
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Aldrin Kay-Yuen Yim
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Hao Qin
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Fuk-Ling Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Siu-Ming Yiu
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Hon-Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Boon Leong Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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