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Hyder Z, Hafeez Rizwani G, Shareef H, Azhar I, Zehra M. Authentication of important medicinal herbal species through DNA-based molecular characterization. Saudi J Biol Sci 2024; 31:103985. [PMID: 38681226 PMCID: PMC11047781 DOI: 10.1016/j.sjbs.2024.103985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 03/22/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024] Open
Abstract
DNA-based molecular markers have great importance among other methods used for the authentication, detection, and identification of medicinal herbal species. Currently, it is more common to identify the medicinal herbal species (monoherbal or polyherbal forms) morphologically by using sensory, macroscopic, and microscopic methods. DNA-based markers made an easy for accurate detection of herbal species by using the polymerase chain reaction (PCR) which involves in vitro amplification of a particular region of DNA sequence. In the current study, we used heterogenic parts for isolation of DNA from twelve important medicinal herbal species followed by purity determination, and yield calculation. We optimized a PCR reaction using universal primer sets to amplify the target DNA followed by DNA sequencing, and species identification. We also performed phylogenetic analysis for determining the evolutionary relationship between the herbal species, by using MEGAX32 software. Further, we prepared adulterated herbal species samples to validate the method. The method was able to amplify the target gene through PCR in 11 out of 12 herbal species samples (sensitivity 91.66%).The DNA from cinnamon could not yield a truly amplified product. On DNA sequencing, all the amplified products were identified as true herbal species (specificity 100%). In the adulterated samples, non-specific DNA bands were observed after performing the PCR reaction, indicating the mixing of more than one herbal species. To conclude, DNA sequencing-based molecular analysis is advantageous for the correct identification, and detection of adulterated herbal species.
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Affiliation(s)
- Zeeshan Hyder
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, University of Karachi, Sindh, Pakistan
| | - Ghazala Hafeez Rizwani
- Hamdard University, Madinat al-Hikmah, Hakim Mohammed Said Road, Karachi, Sindh, Pakistan
| | - Huma Shareef
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Jinnah Sindh Medical University, JSMU, Karachi, Sindh, Pakistan
| | - Iqbal Azhar
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, University of Karachi, Sindh, Pakistan
| | - Meraj Zehra
- Department: Almajeed College of Eastern Medicine, Hamdard University, Madinat al-Hikmah, Hakim Mohammed Said Road, Karachi, Sindh, Pakistan
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Amosova AV, Gnutikov AA, Rodionov AV, Loskutov IG, Nosov NN, Yurkevich OY, Samatadze TE, Zoshchuk SA, Muravenko OV. Genome Variability in Artificial Allopolyploid Hybrids of Avena sativa L. and Avena macrostachya Balansa ex Coss. et Durieu Based on Marker Sequences of Satellite DNA and the ITS1-5.8S rDNA Region. Int J Mol Sci 2024; 25:5534. [PMID: 38791572 PMCID: PMC11122565 DOI: 10.3390/ijms25105534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena macrostachya and their parental species was carried out based on the chromosome FISH mapping of satellite DNA sequences (satDNAs) and also analysis of intragenomic polymorphism in the 18S-ITS1-5.8S rDNA region, using NGS data. Chromosome distribution patterns of marker satDNAs allowed us to identify all chromosomes in the studied karyotypes, determine their subgenomic affiliation, and detect several chromosome rearrangements. Based on the obtained cytogenomic data, we revealed differences between two A. macrostachya subgenomes and demonstrated that only one of them was inherited in the studied octoploid hybrids. Ribotype analyses showed that the second major ribotype of A. macrostachya was species-specific and was not represented in rDNA pools of the octoploids, which could be related to the allopolyploid origin of this species. Our results indicate that the use of marker satDNAs in cytogenomic studies can provide important data on genomic relationships within Avena allopolyploid species and hybrids, and also expand the potential for interspecific crosses for breeding.
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Affiliation(s)
- Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander A. Gnutikov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
| | - Alexander V. Rodionov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Igor G. Loskutov
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
| | - Nikolai N. Nosov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
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Simon C, Fort A, Jouanneau D, McHale M, Sulpice R. Fast screening method to identify salinity tolerant strains of foliose Ulva species. Low salinity leads to increased organic matter of the biomass. JOURNAL OF APPLIED PHYCOLOGY 2024; 36:2161-2172. [PMID: 39050553 PMCID: PMC11263424 DOI: 10.1007/s10811-024-03222-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/21/2024] [Accepted: 02/25/2024] [Indexed: 07/27/2024]
Abstract
Sea lettuce (Ulva) is recognised for its potential in food, pharmaceutical, nutraceutical, biorefinery and bioremediation industries and is increasingly being cultivated. The requirements of those industries vary widely in terms of biomass composition. Ulva biomass composition and growth is known to be directly influenced by environmental factors, e.g., temperature, light, salinity, nutrient availability as well as by genetic factors and likely by microbiome composition. In order to select for the highest yielding strains in a given environment, we tested the suitability of common-garden experiments, i.e., the co-cultivation of different strains grown under shared conditions. Fifteen strains from six different foliose Ulva species were grown together under two different salinities, 35 ppt and 15 ppt. After 32 days, only U. australis strains remained at both salinities. If selection at low salinity was mostly based on survival, the selection process at seawater salinity was driven by competition, largely based on growth performance. Growth rates after a month were very similar at both salinities, suggesting the U. australis strains cope equally well in either condition. However, the composition of the biomass produced in both environments varied, with the content of all organic compounds being higher at low salinity, and the ash content being reduced in average by 66%. To summarize, this study provides an established bulk-selection protocol for efficiently screening large numbers of locally-sourced strains and highlights the potential of low salinity treatments for increased organic matter content, particularly in carbohydrates. Supplementary Information The online version contains supplementary material available at 10.1007/s10811-024-03222-0.
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Affiliation(s)
- Clara Simon
- School, Plant Systems Biology Lab, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, Galway, Ireland
| | - Antoine Fort
- School, Plant Systems Biology Lab, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, Galway, Ireland
- Department of Veterinary and Microbial Sciences, Technological University of The Shannon: Midlands, Athlone, Ireland
| | - Diane Jouanneau
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Roscoff, France
| | - Marcus McHale
- School, Plant Systems Biology Lab, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, Galway, Ireland
| | - Ronan Sulpice
- School, Plant Systems Biology Lab, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, Galway, Ireland
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Wu HY, Wong KL, Law STS, Nong W, Chan KT, Hui JHL, Lin G, Chan WH, Shaw PC. Determination of ITS1 haplotypes of Fritillariae Cirrhosae Bulbus by amplicon sequencing. Chin Med 2024; 19:33. [PMID: 38419104 PMCID: PMC10900738 DOI: 10.1186/s13020-024-00911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Fritillariae Cirrhosae Bulbus is an antitussive and expectorant Chinese medicinal material derived from the dried bulbs of six Fritillaria species. In the 2015 edition of the Chinese Pharmacopoeia, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is the officially listed method for their authenfication. Specifically, the ~ 300-bp ITS1 amplicon of only Fritillariae Cirrhosae Bulbus but not other Fritillaria species can be cleaved into two smaller fragments with restriction enzyme SmaI. Considering repeated reported cases of incomplete digestion of ITS1 amplicon, this study aims to investigate the possibility of heterogeneous ITS1 sequences contained in the Fritillariae Cirrhosae Bulbus. METHODS In this study, ITS1 amplicons of Fritillaria Cirrhosae Bulbus and four other Fritillaria species were sequenced on Illumina platform. We utilised high-throughout amplicon sequencing to determine ITS1 haplotypes and their frequencies in Fritillaria genomes. RESULTS Our results showed that all six botanical sources of Fritillariae Cirrhosae Bulbus indeed possess ITS1 haplotypes with no SmaI restriction site, and the average percentages of ITS1 reads containing SmaI restriction site ranged from 63.60% to 91.81%. CONCLUSION Our findings suggest that the incomplete digestion in PCR-RFLP analysis of Fritillariae Cirrhosae Bulbus is caused by the presence of ITS1 haplotypes without SmaI restriction site due to intragenomic heterogeneity.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ka-Lok Wong
- Government Chinese Medicines Testing Institute, Chinese Medicine Regulatory Office, Department of Health, Shatin, N.T., Hong Kong, China
| | - Sean Tsz-Sum Law
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wenyang Nong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Kwun-Tin Chan
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jerome Ho-Lam Hui
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ge Lin
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wing-Han Chan
- Government Chinese Medicines Testing Institute, Chinese Medicine Regulatory Office, Department of Health, Shatin, N.T., Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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Ambra R, Marcelli M, D’Orso F. Development of a Sensitive, Easy and High-Throughput Compliant Protocol for Maize and Soybean DNA Extraction and Quantitation Using a Plant-Specific Universal Taqman Minor Groove Binder Probe. Genes (Basel) 2023; 14:1797. [PMID: 37761937 PMCID: PMC10530873 DOI: 10.3390/genes14091797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
We report the optimization of a high-throughput, compliant DNA extraction method that uses standard format 96-well plates and a commercial automated DNA purification system (ABI PRISM® 6100 Nucleic Acid PrepStation). The procedure was set up for maize and soybean, the most common GMO crops and the main ingredients of several foodstuffs, and compared with an EU-validated CTAB-based method. Optimization of the DNA extraction was achieved by applying self-prepared buffers (for DNA extraction, binding, and washing) on the PrepStation loaded with proprietary glass-fiber-coated purification plates. Quantification of extracted DNA was performed by real-time PCR using previously reported endogenous soybean lectin and maize starch synthase genes and a novel plant-specific universal TaqMan MGB probe that targets the 18S rRNA multiple copy gene. Using serial dilutions of both maize and soybean genomic DNAs, we show low PCR sensitivity and efficiency for the official TransPrep DNA extraction protocol compared to the CTAB-based one. On the other hand, using serial dilutions of a standard reference plasmid containing a 137 bp sequence cloned from the 18S rRNA plant-specific ribosomal gene, we demonstrate the high PCR sensitivity and efficiency of the optimized DNA extraction protocol setup with self-prepared buffers. The limits of detection and quantification of the 18S rDNA reiteration were consistent with the calculated values, supporting the suitability of the DNA extraction procedure for high-throughput analyses of large populations and small amounts of tissue.
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Affiliation(s)
- Roberto Ambra
- Council for Agricultural Research and Economics, Research Centre for Food and Nutrition (CREA-AN), 00178 Rome, Italy
| | - Marco Marcelli
- Volta Institute, MIUR (Italian Ministry of Education, University and Research), 09036 Guspini, Italy;
| | - Fabio D’Orso
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy;
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The Curious Case of Fritillaria sonnikovae (Liliaceae) in South Siberia: New Insights into Its Origin and Phylogeny. DIVERSITY 2023. [DOI: 10.3390/d15020193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fritillaria Tourn. ex L. is a genus of Liliaceae including a little more than 150 species occurring in the temperate Holarctic. Fritillaria sonnikovae Shaulo & Erst is the most recently described Siberian species in the genus. In the affinity section of the F. sonnikovae diagnosis, only F. dagana Turcz. and F. roylei Hook. are mentioned. Our study is an original attempt to shed light on the F. sonnikovae origin and its evolutionary relationships with other Fritillaria using nuclear (ITS) and plastid (matK + rps16 + trnH-psbA) DNA markers. Our results showed that F. sonnikovae together with F. dagana and F. maximowiczii Freyn belongs to the North Asian lineage of the Liliorhiza subgenus and produced no evidence supporting relationship between F. sonnikovae and F. roylei. Monophyly of Fritillaria sonnikovae was not reliably confirmed in our study since its close affinity with F. maximowiczii was demonstrated by phylogenetic analysis and morphology. Fritillaria dagana was shown to be a sister to the F. maximowiczii + F. sonnikovae group. Most authors of the present study suggest considering F. sonnikovae as a synonym for F. maximowiczii. In this view, F. sonnikovae may be considered a narrow endemic and one of the light-perianth morphs of F. maximowiczii, which has emerged in the Western Sayan and remained there as a tertiary relict.
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Yücel G, Senderowicz M, Kolano B. The Use of Ribosomal DNA for Comparative Cytogenetics. Methods Mol Biol 2023; 2672:265-284. [PMID: 37335483 DOI: 10.1007/978-1-0716-3226-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) sequences provides excellent chromosome markers for comparative cytogenetic analyses, especially in non-model plant species. The tandem repeat nature of a sequence and the presence of a highly conserved genic region make rDNA sequences relatively easy to isolate and clone. In this chapter, we describe the use of rDNA as markers for comparative cytogenetics studies. Traditionally, cloned probes labeled with Nick-translation have been used to detect rDNA loci. Recently, pre-labeled oligonucleotides are also employed quite frequently to detect both 35S and 5S rDNA loci. Ribosomal DNA sequences, together with other DNA probes in FISH/GISH or with fluorochromes such as CMA3 banding or silver staining, are very useful tools in comparative analyses of plant karyotypes.
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Affiliation(s)
- Gülru Yücel
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
| | - Magdalena Senderowicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bożena Kolano
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland.
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Point-of-care suitable identification of the adulterants Carthamus tinctorius and Curcuma longa in Crocus sativus based on loop-mediated isothermal amplification (LAMP) and lateral-flow-assay (LFA). Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Belyakov EA, Mikhaylova YV, Machs EM, Zhurbenko PM, Rodionov AV. Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing. Sci Rep 2022; 12:21610. [PMID: 36517537 PMCID: PMC9750990 DOI: 10.1038/s41598-022-25954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Sparganium is an emergent aquatic macrophyte widely spread in temperate and subtropical zones. Taxa of this genus feature high phenotypic plasticity and can produce interspecific hybrids. By means of high-throughput sequencing of the internal transcribed spacer (ITS1) of 35S rDNA, the status of 15 Eurasian Sparganium species and subspecies was clarified and the role of hybridization events in the recent evolution of the genus was investigated. It has been shown that a number of species such as S. angustifolium, S. fallax and S. subglobosum have homogenized rDNA represented by one major ribotype. The rDNA of other taxa is represented by two or more major ribotypes. Species with high rDNA heterogeneity are apparently of hybrid origin. Based on the differences in rDNA patterns, intraspecific diversity was identified in S. probatovae and S. emersum. Thus, we have concluded that Sparganium has extensive interspecific hybridization at the subgenus level, and there may also be occasional hybridization between species from different subgenera.
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Affiliation(s)
- Evgeny A. Belyakov
- grid.464570.40000 0001 1092 3616Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl Region, Nekouz District, 109, Borok, Russia 152742 ,grid.446199.70000 0000 8543 3323Cherepovets State University, Lunacharsky Ave., 5, Cherepovets, Russia 162600
| | - Yulia V. Mikhaylova
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376
| | - Eduard M. Machs
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376
| | - Peter M. Zhurbenko
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376 ,grid.15447.330000 0001 2289 6897St. Petersburg State University, Universitetskaya Embankment, 7-9, St. Petersburg, Russia 199034
| | - Aleksandr V. Rodionov
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376 ,grid.15447.330000 0001 2289 6897St. Petersburg State University, Universitetskaya Embankment, 7-9, St. Petersburg, Russia 199034
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Mlinarec J, Boštjančić LL, Malenica N, Jurković A, Boland T, Yakovlev SS, Besendorfer V. Structure and Methylation of 35S rDNA in Allopolyploids Anemone multifida (2 n = 4 x = 32, BBDD) and Anemone baldensis (2 n = 6 x = 48, AABBDD) and Their Parental Species Show Evidence of Nucleolar Dominance. FRONTIERS IN PLANT SCIENCE 2022; 13:908218. [PMID: 35874014 PMCID: PMC9296772 DOI: 10.3389/fpls.2022.908218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/07/2022] [Indexed: 05/26/2023]
Abstract
Transcriptional silencing of 35S rDNA loci inherited from one parental species is occurring relatively frequently in allopolyploids. However, molecular mechanisms by which it is selected for transcriptional silencing remain unclear. We applied NGS, silver staining and bisulfite sequencing to study the structure, expression and methylation landscape of 35S rDNA in two allopolyploids of common origin, allotetraploid Anemone multifida (2n = 4x = 32, genome composition BBDD) and allohexaploid A. baldensis (2n = 6x = 48, AABBDD), and their genome donors, A. sylvestris (2n = 16, AA), A. cylindrica (2n = 16, BB) and A. parviflora (2n = 16, DD). The size of the recovered 35S rDNA units varied from 10,489 bp in A. cylindrica to 12,084 bp in A. sylvestris. Anemone showed an organization typical of most ribosomal 35S rDNA composed of NTS, ETS, rRNA genes, TTS and TIS with structural features of plant IGS sequences and all functional elements needed for rRNA gene activity. The NTS was more variable than the ETS and consisted of SRs which are highly variable among Anemone. Five to six CpG-rich islands were found within the ETS. CpG island located adjacent to the transcription initiation site (TIS) was highly variable regarding the sequence size and methylation level and exhibited in most of the species lower levels of methylation than CpG islands located adjacent to the 18S rRNA gene. Our results uncover hypomethylation of A. sylvestris- and A. parviflora-derived 35S rDNA units in allopolyploids A. multifida and A. baldensis. Hypomethylation of A. parviflora-derived 35S rDNA was more prominent in A. baldensis than in A. multifida. We showed that A. baldensis underwent coupled A. sylvestris-derived 35S rDNA array expansion and A. parviflora-derived 35S rDNA copy number decrease that was accompanied by lower methylation level of A. sylvestris-derived 35S rDNA units in comparison to A. parviflora-derived 35S rDNA units. These observations suggest that in A. baldensis nucleolar dominance is directed toward A. sylvestris-derived chromosomes. This work broadens our current knowledge of the 35S rDNA organization in Anemone and provides evidence of the progenitor-specific 35S rDNA methylation in nucleolar dominance.
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Affiliation(s)
| | - Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
- Department of Computer Science, ICube, UMR 7357, CNRS, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, Strasbourg, France
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Todd Boland
- Memorial University of Newfoundland’s Botanical Gardens, St. John’s, NL, Canada
| | - Sonja Siljak Yakovlev
- CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
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Gnutikov AA, Nosov NN, Loskutov IG, Blinova EV, Shneyer VS, Probatova NS, Rodionov AV. New Insights into the Genomic Structure of Avena L.: Comparison of the Divergence of A-Genome and One C-Genome Oat Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:1103. [PMID: 35567104 PMCID: PMC9102028 DOI: 10.3390/plants11091103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
We used next-generation sequencing analysis of the 3′-part of 18S rDNA, ITS1, and a 5′-part of the 5.8S rDNA region to understand genetic variation among seven diploid A-genome Avena species. We used 4−49 accessions per species that represented the As genome (A. atlantica, A. hirtula, and wiestii), Ac genome (A. canariensis), Ad genome (A. damascena), Al genome (A. longiglumis), and Ap genome (A. prostrata). We also took into our analysis one C-genome species, A. clauda, which previously was found to be related to A-genome species. The sequences of 169 accessions revealed 156 haplotypes of which seven haplotypes were shared by two to five species. We found 16 ribotypes that consisted of a unique sequence with a characteristic pattern of single nucleotide polymorphisms and deletions. The number of ribotypes per species varied from one in A. longiglumis to four in A. wiestii. Although most ribotypes were species-specific, we found two ribotypes shared by three species (one for A. damascena, A. hirtula, and A. wiestii, and the second for A. longiglumis, A. atlantica, and A. wiestii), and a third ribotype shared between A. atlantica and A. wiestii. A characteristic feature of the A. clauda ribotype, a diploid C-genome species, is that two different families of ribotypes have been found in this species. Some of these ribotypes are characteristic of Cc-genome species, whereas others are closely related to As-genome ribotypes. This means that A. clauda can be a hybrid between As- and C-genome oats.
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Affiliation(s)
- Alexander A. Gnutikov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Nikolai N. Nosov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Igor G. Loskutov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Elena V. Blinova
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Viktoria S. Shneyer
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Nina S. Probatova
- Laboratory of Botany, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
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12
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Wu HY, Shaw PC. Strategies for molecular authentication of herbal products: from experimental design to data analysis. Chin Med 2022; 17:38. [PMID: 35317843 PMCID: PMC8939074 DOI: 10.1186/s13020-022-00590-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/02/2022] [Indexed: 12/22/2022] Open
Abstract
Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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13
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Gauthier MEA, Lelwala RV, Elliott CE, Windell C, Fiorito S, Dinsdale A, Whattam M, Pattemore J, Barrero RA. Side-by-Side Comparison of Post-Entry Quarantine and High Throughput Sequencing Methods for Virus and Viroid Diagnosis. BIOLOGY 2022; 11:biology11020263. [PMID: 35205129 PMCID: PMC8868628 DOI: 10.3390/biology11020263] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/27/2023]
Abstract
Rapid and safe access to new plant genetic stocks is crucial for primary plant industries to remain profitable, sustainable, and internationally competitive. Imported plant species may spend several years in Post Entry Quarantine (PEQ) facilities, undergoing pathogen testing which can impact the ability of plant industries to quickly adapt to new global market opportunities by accessing new varieties. Advances in high throughput sequencing (HTS) technologies provide new opportunities for a broad range of fields, including phytosanitary diagnostics. In this study, we compare the performance of two HTS methods (RNA-Seq and sRNA-Seq) with that of existing PEQ molecular assays in detecting and identifying viruses and viroids from various plant commodities. To analyze the data, we tested several bioinformatics tools which rely on different approaches, including direct-read, de novo, and reference-guided assembly. We implemented VirusReport, a new portable, scalable, and reproducible nextflow pipeline that analyses sRNA datasets to detect and identify viruses and viroids. We raise awareness of the need to evaluate cross-sample contamination when analyzing HTS data routinely and of using methods to mitigate index cross-talk. Overall, our results suggest that sRNA analyzed using VirReport provides opportunities to improve quarantine testing at PEQ by detecting all regulated exotic viruses from imported plants in a single assay.
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Affiliation(s)
- Marie-Emilie A. Gauthier
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (M.-E.A.G.); (R.V.L.); (C.W.)
| | - Ruvini V. Lelwala
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (M.-E.A.G.); (R.V.L.); (C.W.)
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Water and the Environment, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Candace E. Elliott
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Water and the Environment, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Craig Windell
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (M.-E.A.G.); (R.V.L.); (C.W.)
| | - Sonia Fiorito
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Water and the Environment, Mickleham, VIC 3064, Australia; (S.F.); (A.D.); (M.W.)
| | - Adrian Dinsdale
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Water and the Environment, Mickleham, VIC 3064, Australia; (S.F.); (A.D.); (M.W.)
| | - Mark Whattam
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Water and the Environment, Mickleham, VIC 3064, Australia; (S.F.); (A.D.); (M.W.)
| | - Julie Pattemore
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Water and the Environment, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Roberto A. Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (M.-E.A.G.); (R.V.L.); (C.W.)
- Correspondence:
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14
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Polling M, Sin M, de Weger LA, Speksnijder AGCL, Koenders MJF, de Boer H, Gravendeel B. DNA metabarcoding using nrITS2 provides highly qualitative and quantitative results for airborne pollen monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150468. [PMID: 34583071 PMCID: PMC8651626 DOI: 10.1016/j.scitotenv.2021.150468] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/28/2021] [Accepted: 09/16/2021] [Indexed: 05/30/2023]
Abstract
Airborne pollen monitoring is of global socio-economic importance as it provides information on presence and prevalence of allergenic pollen in ambient air. Traditionally, this task has been performed by microscopic investigation, but novel techniques are being developed to automate this process. Among these, DNA metabarcoding has the highest potential of increasing the taxonomic resolution, but uncertainty exists about whether the results can be used to quantify pollen abundance. In this study, it is shown that DNA metabarcoding using trnL and nrITS2 provides highly improved taxonomic resolution for pollen from aerobiological samples from the Netherlands. A total of 168 species from 143 genera and 56 plant families were detected, while using a microscope only 23 genera and 22 plant families were identified. NrITS2 produced almost double the number of OTUs and a much higher percentage of identifications to species level (80.1%) than trnL (27.6%). Furthermore, regressing relative read abundances against the relative abundances of microscopically obtained pollen concentrations showed a better correlation for nrITS2 (R2 = 0.821) than for trnL (R2 = 0.620). Using three target taxa commonly encountered in early spring and fall in the Netherlands (Alnus sp., Cupressaceae/Taxaceae and Urticaceae) the nrITS2 results showed that all three taxa were dominated by one or two species (Alnus glutinosa/incana, Taxus baccata and Urtica dioica). Highly allergenic as well as artificial hybrid species were found using nrITS2 that could not be identified using trnL or microscopic investigation (Alnus × spaethii, Cupressus arizonica, Parietaria spp.). Furthermore, perMANOVA analysis indicated spatiotemporal patterns in airborne pollen trends that could be more clearly distinguished for all taxa using nrITS2 rather than trnL. All results indicate that nrITS2 should be the preferred marker of choice for molecular airborne pollen monitoring.
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Affiliation(s)
- Marcel Polling
- Naturalis Biodiversity Center, Leiden, the Netherlands; Natural History Museum, University of Oslo, Norway.
| | - Melati Sin
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Letty A de Weger
- Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arjen G C L Speksnijder
- Naturalis Biodiversity Center, Leiden, the Netherlands; Leiden University of Applied Sciences, Leiden, the Netherlands
| | | | - Hugo de Boer
- Naturalis Biodiversity Center, Leiden, the Netherlands; Natural History Museum, University of Oslo, Norway
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden, the Netherlands; Radboud Institute for Biological and Environmental Sciences, Nijmegen, the Netherlands
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15
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Hemleben V, Grierson D, Borisjuk N, Volkov RA, Kovarik A. Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:797348. [PMID: 34992624 PMCID: PMC8724763 DOI: 10.3389/fpls.2021.797348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
The history of rDNA research started almost 90 years ago when the geneticist, Barbara McClintock observed that in interphase nuclei of maize the nucleolus was formed in association with a specific region normally located near the end of a chromosome, which she called the nucleolar organizer region (NOR). Cytologists in the twentieth century recognized the nucleolus as a common structure in all eukaryotic cells, using both light and electron microscopy and biochemical and genetic studies identified ribosomes as the subcellular sites of protein synthesis. In the mid- to late 1960s, the synthesis of nuclear-encoded rRNA was the only system in multicellular organisms where transcripts of known function could be isolated, and their synthesis and processing could be studied. Cytogenetic observations of NOR regions with altered structure in plant interspecific hybrids and detailed knowledge of structure and function of rDNA were prerequisites for studies of nucleolar dominance, epistatic interactions of rDNA loci, and epigenetic silencing. In this article, we focus on the early rDNA research in plants, performed mainly at the dawn of molecular biology in the 60 to 80-ties of the last century which presented a prequel to the modern genomic era. We discuss - from a personal view - the topics such as synthesis of rRNA precursor (35S pre-rRNA in plants), processing, and the organization of 35S and 5S rDNA. Cloning and sequencing led to the observation that the transcribed and processed regions of the rRNA genes vary enormously, even between populations and species, in comparison with the more conserved regions coding for the mature rRNAs. Epigenetic phenomena and the impact of hybridization and allopolyploidy on rDNA expression and homogenization are discussed. This historical view of scientific progress and achievements sets the scene for the other articles highlighting the immense progress in rDNA research published in this special issue of Frontiers in Plant Science on "Molecular organization, evolution, and function of ribosomal DNA."
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Affiliation(s)
- Vera Hemleben
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Donald Grierson
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nikolai Borisjuk
- School of Life Sciences, Huaiyin Normal University, Huai'an, China
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Ales Kovarik
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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16
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Ebrahimzadegan R, Orooji F, Ma P, Mirzaghaderi G. Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes. FRONTIERS IN PLANT SCIENCE 2021; 12:716750. [PMID: 34490015 PMCID: PMC8417419 DOI: 10.3389/fpls.2021.716750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn't detect differences between subspecies, although (GAA)10 signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Fatemeh Orooji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, China
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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17
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Faller AC, Shanmughanandhan D, Ragupathy S, Zhang Y, Lu Z, Chang P, Swanson G, Newmaster SG. Validation of a Triplex Quantitative Polymerase Chain Reaction Assay for Detection and Quantification of Traditional Protein Sources, Pisum sativum L. and Glycine max (L.) Merr., in Protein Powder Mixtures. FRONTIERS IN PLANT SCIENCE 2021; 12:661770. [PMID: 34108980 PMCID: PMC8183462 DOI: 10.3389/fpls.2021.661770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Several botanicals have been traditionally used as protein sources, including the leguminous Pisum sativum L. and Glycine max (L.) Merr. While a rich history exists of cultivating these plants for their whole, protein-rich grain, modern use as powdered supplements present a new challenge in material authentication. The absence of clear morphological identifiers of an intact plant and the existence of long, complex supply chains behoove industry to create quick, reliable analytical tools to identify the botanical source of a protein product (many of which contain multiple sources). The utility of molecular tools for plant-based protein powder authentication is gaining traction, but few validated tools exist. Multiplex quantitative polymerase chain reaction (qPCR) can provide an economical means by which sources can be identified and relative proportions quantified. We followed established guidelines for the design, optimization, and validation of qPCR assay, and developed a triplex qPCR assay that can amplify and quantify pea and soy DNA targets, normalized by a calibrator. The assay was evaluated for analytical specificity, analytical sensitivity, efficiency, precision, dynamic range, repeatability, and reproducibility. We tested the quantitative ability of the assay using pea and soy DNA mixtures, finding exceptional quantitative linearity for both targets - 0.9983 (p < 0.0001) for soy and 0.9915 (p < 0.0001) for pea. Ratios based on mass of protein powder were also tested, resulting in non-linear patterns in data that suggested the requirement of further sample preparation optimization or algorithmic correction. Variation in fragment size within different lots of commercial protein powder samples was also analyzed, revealing low SD among lots. Ultimately, this study demonstrated the utility of qPCR in the context of protein powder mixtures and highlighted key considerations to take into account for commercial implementation.
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Affiliation(s)
- Adam C. Faller
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
| | - Dhivya Shanmughanandhan
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
| | - Subramanyam Ragupathy
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
| | - Yanjun Zhang
- Herbalife International, Torrance, CA, United States
| | - Zhengfei Lu
- Herbalife International, Torrance, CA, United States
| | - Peter Chang
- Herbalife International, Torrance, CA, United States
| | - Gary Swanson
- Herbalife International, Torrance, CA, United States
| | - Steven G. Newmaster
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
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18
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Fort A, Linderhof C, Coca-Tagarro I, Inaba M, McHale M, Cascella K, Potin P, Guiry MD, Sulpice R. A sequencing-free assay for foliose Ulva species identification, hybrid detection and bulk biomass characterisation. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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Fehrer J, Slavíková R, Paštová L, Josefiová J, Mráz P, Chrtek J, Bertrand YJK. Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae). FRONTIERS IN PLANT SCIENCE 2021; 12:647375. [PMID: 33777082 PMCID: PMC7994888 DOI: 10.3389/fpls.2021.647375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 05/14/2023]
Abstract
Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Here we investigate non-coding rDNA sequences (ITS/ETS, 5S-NTS) along with the chromosomal organization of their respective loci (45S and 5S rDNA) in diploids of the Hieraciinae. The subtribe consists of genera Hieracium, Pilosella, Andryala, and Hispidella and has a complex evolutionary history characterized by ancient intergeneric hybridization, allele sharing among species, and incomplete lineage sorting. Direct or cloned Sanger sequences and phased alleles derived from Illumina genome sequencing were subjected to phylogenetic analyses. Patterns of homogenization and tree topologies based on the three regions were compared. In contrast to most other plant groups, 5S-NTS sequences were generally better homogenized than ITS and ETS sequences. A novel case of ancient intergeneric hybridization between Hispidella and Hieracium was inferred, and some further incongruences between the trees were found, suggesting independent evolution of these regions. In some species, homogenization of ITS/ETS and 5S-NTS sequences proceeded in different directions although the 5S rDNA locus always occurred on the same chromosome with one 45S rDNA locus. The ancestral rDNA organization in the Hieraciinae comprised 4 loci of 45S rDNA in terminal positions and 2 loci of 5S rDNA in interstitial positions per diploid genome. In Hieracium, some deviations from this general pattern were found (3, 6, or 7 loci of 45S rDNA; three loci of 5S rDNA). Some of these deviations concerned intraspecific variation, and most of them occurred at the tips of the tree or independently in different lineages. This indicates that the organization of rDNA loci is more dynamic than the evolution of sequences contained in them and that locus number is therefore largely unsuitable to inform about species relationships in Hieracium. No consistent differences in the degree of sequence homogenization and the number of 45S rDNA loci were found, suggesting interlocus concerted evolution.
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Affiliation(s)
- Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- *Correspondence: Judith Fehrer,
| | - Renáta Slavíková
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | | | - Jiřina Josefiová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Patrik Mráz
- Department of Botany, Charles University, Prague, Czechia
| | - Jindřich Chrtek
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Charles University, Prague, Czechia
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20
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Abstract
Despite possible drawbacks (intraspecific polymorphisms and possible fungal contamination), sequencing of the ITS region of the ribosomal RNA genes remains one of the most popular nuclear sequences used for plant taxonomy and phylogeny. A protocol for PCR amplification and sequencing of this region using universal plant primers is provided.
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21
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Setiawan AB, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T. Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species. Cytogenet Genome Res 2020; 160:554-564. [DOI: 10.1159/000511119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
Mobile elements are major regulators of genome evolution through their effects on genome size and chromosome structure in higher organisms. Non-long terminal repeat (non-LTR) retrotransposons, one of the subclasses of transposons, are specifically inserted into repetitive DNA sequences. While studies on the insertion of non-LTR retrotransposons into ribosomal RNA genes and other repetitive DNA sequences have been reported in the animal kingdom, studies in the plant kingdom are limited. Here, using FISH, we confirmed that <i>Menolird18</i>, a member of LINE (long interspersed nuclear element) in non-LTR retrotransposons and found in <i>Cucumis melo</i>, was inserted into ITS and ETS (internal and external transcribed spacers) regions of 18S rDNA in melon and cucumber. Beside the 18S rDNA regions, <i>Menolird18</i> was also detected in all centromeric regions of melon, while it was located at pericentromeric and sub-telomeric regions in cucumber. The fact that FISH signals of <i>Menolird18</i> were found in centromeric and rDNA regions of mitotic chromosomes suggests that <i>Menolird18</i> is a rDNA and centromere-specific non-LTR retrotransposon in melon. Our findings are the first report on a non-LTR retrotransposon that is highly conserved in 2 different plant species, melon and cucumber. The clear distinction of chromosomal localization of <i>Menolird18</i> in melon and cucumber implies that it might have been involved in the evolutionary processes of the melon (<i>C. melo</i>) and cucumber (<i>C. sativus</i>) genomes.
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22
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Amosova AV, Samatadze TE, Mozgova GV, Kipen VN, Dubovskaya AG, Artemyeva AM, Yurkevich OY, Zoshchuk SA, Lemesh VA, Muravenko OV. Genomic Markers Associated with Cold-Hardiness in Brassica rapa L. Mol Biol 2020. [DOI: 10.1134/s0026893320040032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Abstract
Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.
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24
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Georgiev O, Mishev K, Krasnikova M, Kitanova M, Dimitrova A, Karagyozov L. The Hordeum bulbosum 25S-18S rDNA region: comparison with Hordeum vulgare and other Triticeae. ACTA ACUST UNITED AC 2019; 74:319-328. [PMID: 31421048 DOI: 10.1515/znc-2018-0109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 07/18/2019] [Indexed: 11/15/2022]
Abstract
Hordeum vulgare and Hordeum bulbosum are two closely related barley species, which share a common H genome. H. vulgare has two nucleolar organizer regions (NORs), while the NOR of H. bulbosum is only one. We sequenced the 2.5 kb 25S-18S region in the rDNA of H. bulbosum and compared it to the same region in H. vulgare as well as to the other Triticeae. The region includes an intergenic spacer (IGS) with a number of subrepeats, a promoter, and an external transcribed spacer (5'ETS). The IGS of H. bulbosum downstream of 25S rRNA contains two 143-bp repeats and six 128-bp repeats. In contrast, the IGS in H. vulgare contains an array of seven 79-bp repeats and a varying number of 135-bp repeats. The 135-bp repeats in H. vulgare and the 128-bp repeats in H. bulbosum show similarity. Compared to H. vulgare, the 5'ETS of H. bulbosum is shorter. Additionally, the 5'ETS regions in H. bulbosum and H. vulgare diverged faster than in other Triticeae genera. Alignment of the Triticeae promoter sequences suggests that in Hordeum, as in diploid Triticum, transcription starts with guanine and not with adenine as it is in many other plants.
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Affiliation(s)
- Oleg Georgiev
- Institute of Molecular Life Sciences, University Zurich-Irchel, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Kiril Mishev
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Maria Krasnikova
- Department of Genetics, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
| | - Meglena Kitanova
- Department of Genetics, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
| | - Anna Dimitrova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria, Phone: +359 2 9792677, Fax: +359 2 9785516, E-mail:
| | - Luchezar Karagyozov
- Department of Genetics, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
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Ballin NZ, Onaindia JO, Jawad H, Fernandez-Carazo R, Maquet A. High-resolution melting of multiple barcode amplicons for plant species authentication. Food Control 2019; 105:141-150. [PMID: 31680728 PMCID: PMC6686639 DOI: 10.1016/j.foodcont.2019.05.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In recent years, species identification in herbs has attracted considerable attention due to several cases of fraud; hence inexpensive high-throughput authentication methods are highly welcomed. Species authentication is often performed through DNA analysis and several specific regions (barcodes) are considered suitable. Each barcode (Bar) possesses different qualities in terms of universality and discrimination power. A multiplexed format where information can be extracted simultaneously from several barcode regions is seemingly appropriate to ensure the power of both universality and discrimination. In this approach, we amplified DNA from five different barcode regions in a multiplexed PCR format followed by high-resolution melting (HRM). This multiplexed Bar-HRM approach was first applied to plants spanning the plant kingdom and then gradually narrowing down the genetic variability within the Lamiaceae and the Solanaceae families to finally reach closely related cultivars. Universality was demonstrated through distinct melting profiles obtained for species originating from 29 different families spanning the angiosperms, gymnosperm, mosses, and liverwort (Marchantiophyta). Discrimination power was retained for species, sub-species, and a few cultivars through the application of multivariate statistics to the high-resolution melting profiles. This preliminary investigation has shown the potential to discriminate a vast amount of species within the whole plant kingdom. It requires no a priori knowledge of the species' DNA sequence and occurs in a closed system within 2.5 h at a reduced cost per sample compared to other DNA based approaches. A DNA profiling platform for species authentication throughout the plant kingdom. Distinct and reproducible melting profiles were obtained for all tested species. Universality was demonstrated across 29 families spanning the plant kingdom. Specificity was demonstrated for related species, sub-species, and cultivars.
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Affiliation(s)
| | | | - Hadeel Jawad
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | | | - Alain Maquet
- European Commission, Joint Research Centre (JRC), Geel, Belgium
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Rogers SO. Integrated evolution of ribosomal RNAs, introns, and intron nurseries. Genetica 2018; 147:103-119. [PMID: 30578455 DOI: 10.1007/s10709-018-0050-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
The initial components of ribosomes first appeared more than 3.8 billion years ago during a time when many types of RNAs were evolving. While modern ribosomes are complex molecular machines consisting of rRNAs and proteins, they were assembled during early evolution by the association and joining of small functional RNA units. Introns may have provided the means to ligate many of these pieces together. All four classes of introns (group I, group II, spliceosomal, and archaeal) are present in many rRNA gene loci over a broad phylogenetic range. A survey of rRNA intron sequences across the three major life domains suggests that some of the classes of introns may have diverged from one another within rRNA gene loci. Analyses of rRNA sequences revealed self-splicing group I and group II introns are present in ancestral regions of the SSU (small subunit) and LSU (large subunit), whereas spliceosomal and archaeal introns appeared in sections of the rRNA that evolved later. Most classes of introns increased in number for approximately 1 billion years. However, their frequencies are low in the most recently evolved regions added to the SSU and LSU rRNAs. Furthermore, many of the introns appear to have been in the same locations for billions of years, suggesting an ancient origin for these sequences. In this Perspectives paper, I reviewed and analyzed rRNA intron sequences, locations, structural characteristics, and splicing mechanisms; and suggest that rRNA gene loci may have served as evolutionary nurseries for intron formation and diversification.
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Affiliation(s)
- Scott O Rogers
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
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Li B, Kremling KAG, Wu P, Bukowski R, Romay MC, Xie E, Buckler ES, Chen M. Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation. Genome Res 2018; 28:1555-1565. [PMID: 30166407 PMCID: PMC6169892 DOI: 10.1101/gr.229716.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 08/29/2018] [Indexed: 12/16/2022]
Abstract
Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variation present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA (rDNA) copy number and ribosomal RNA (rRNA) expression for a population of maize inbred lines and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variation was found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We have not found that the rDNA gene dosage has a regulatory role in gene expression; however, thousands of genes are identified to be coregulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We further investigated the potential roles of copy number and the expression level of rDNA on agronomic traits and found that both correlated with flowering time but through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is a valuable source of functional diversity that affects gene expression variation and field-based phenotypic changes.
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Affiliation(s)
- Bo Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Karl A G Kremling
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Penghao Wu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- College of Agronomy, Xinjiang Agriculture University, Urumqi, China 830052
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York 14853, USA
| | - Maria C Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - En Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
- US Department of Agriculture-Agricultural Research Service (USDA-ARS), Ithaca, New York 14853, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 100101
- University of Chinese Academy of Sciences, Beijing, China 100049
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Yan ZH, Rogers SO, Wang CJK. Assessment of Phialophora species based on ribosomal DNA internal transcribed spacers and morphology. Mycologia 2018. [DOI: 10.1080/00275514.1995.12026505] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Zhong Hua Yan
- Faculty of Environmental and Forest Biology, State University of New York, College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York 13210-2788
| | - Scott O. Rogers
- Faculty of Environmental and Forest Biology, State University of New York, College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York 13210-2788
| | - C. J. K. Wang
- Faculty of Environmental and Forest Biology, State University of New York, College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, New York 13210-2788
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Albee SR, Mueller GM, Kropp BR. Polymorphisms in the large intergenic spacer of the nuclear ribosomal repeat identify Laccaria proxima strains. Mycologia 2018. [DOI: 10.1080/00275514.1996.12026738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Steven R. Albee
- Biology Department, Utah State University, Logan, Utah 84322-5305
| | - Gregory M. Mueller
- Department of Botany, Field Museum of Natural History, Chicago, Illinois 60605-2496
| | - Bradley R. Kropp
- Biology Department, Utah State University, Logan, Utah 84322-5305
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Redkar RJ, Lemke PA, Singh NK. Altered gene expression inAspergillus nidulansin response to salt stress. Mycologia 2018. [DOI: 10.1080/00275514.1996.12026651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Rajendra J. Redkar
- Department of Botany and Microbiology, 101 Life Sciences Building, Auburn University, Auburn AL 36849-5407
| | - Paul A. Lemke
- Department of Botany and Microbiology, 101 Life Sciences Building, Auburn University, Auburn AL 36849-5407
| | - Narendra K. Singh
- Department of Botany and Microbiology, 101 Life Sciences Building, Auburn University, Auburn AL 36849-5407
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Molecular Diversity of Tidal Swamp Rice (Oryza sativa L.) in South Kalimantan, Indonesia. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Environmental DNA detection of aquatic invasive plants in lab mesocosm and natural field conditions. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1718-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Doganay-Knapp K, Orland A, König GM, Knöss W. The potential of three different PCR-related approaches for the authentication of mixtures of herbal substances and finished herbal medicinal products. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2018; 43:60-67. [PMID: 29747755 DOI: 10.1016/j.phymed.2018.03.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 02/08/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Herbal substances and preparations thereof play an important role in healthcare systems worldwide. Due to the variety of these products regarding origin, composition and processing procedures, appropriate methodologies for quality assessment need to be considered. A majority of herbal substances is administered as multicomponent mixtures, especially in the field of Traditional Chinese Medicine and ayurvedic medicine, but also in finished medicinal products. Quality assessment of complex mixtures of herbal substances with conventional methods is challenging. Thus, emphasis of the present work was directed on the development of complementary methods to elucidate the composition of mixtures of herbal substances and finished herbal medicinal products. HYPOTHESIS/PURPOSE An indispensable prerequisite for the safe and effective use of herbal medicines is the unequivocal authentication of the medicinal plants used therein. In this context, we investigated the potential of three different PCR-related methods in the characterization and authentication of herbal substances. METHODS A multiplex PCR assay and a quantitative PCR (qPCR) assay were established to analyze defined mixtures of the herbal substances Quercus cortex, Juglandis folium, Aristolochiae herba, Matricariae flos and Salviae miltiorrhizae radix et rhizoma and a finished herbal medicinal product. Furthermore, a standard cloning approach using universal primers targeting the ITS region was established in order to allow the investigation of herbal mixtures with unknown content. RESULTS The cloning approach had some limitations regarding the detection/recovery of the components in defined mixtures of herbal substances, but the complementary use of two sets of universal primer pairs increased the detection of components out of the mixture. While the multiplex PCR did not retrace all components in the defined mixtures of herbal substances, the established qPCR resulted in simultaneous and specific detection of the five target sequences in all defined mixtures. CONCLUSION These data indicate that for authentication purposes, complementary PCR-related methods are highly recommendable for the analysis of herbal mixtures in parallel.
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Affiliation(s)
- Kirsten Doganay-Knapp
- Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany; Federal Institute for Drugs and Medical Devices, Kurt-Georg-Kiesinger-Allee 3, Bonn 53175, Germany
| | - Annika Orland
- Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany; Federal Institute for Drugs and Medical Devices, Kurt-Georg-Kiesinger-Allee 3, Bonn 53175, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Werner Knöss
- Federal Institute for Drugs and Medical Devices, Kurt-Georg-Kiesinger-Allee 3, Bonn 53175, Germany.
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Pisupati R, Vergara D, Kane NC. Diversity and evolution of the repetitive genomic content in Cannabis sativa. BMC Genomics 2018; 19:156. [PMID: 29466945 PMCID: PMC5822635 DOI: 10.1186/s12864-018-4494-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 01/24/2018] [Indexed: 01/13/2023] Open
Abstract
Background The repetitive content of the genome, once considered to be “junk DNA”, is in fact an essential component of genomic architecture and evolution. In this study, we used the genomes of three varieties of Cannabis sativa, three varieties of Humulus lupulus and one genotype of Morus notabilis to explore their repetitive content using a graph-based clustering method, designed to explore and compare repeat content in genomes that have not been fully assembled. Results The repetitive content in the C. sativa genome is mainly composed of the retrotransposons LTR/Copia and LTR/Gypsy (14% and 14.8%, respectively), ribosomal DNA (2%), and low-complexity sequences (29%). We observed a recent copy number expansion in some transposable element families. Simple repeats and low complexity regions of the genome show higher intra and inter species variation. Conclusions As with other sequenced genomes, the repetitive content of C. sativa’s genome exhibits a wide range of evolutionary patterns. Some repeat types have patterns of diversity consistent with expansions followed by losses in copy number, while others may have expanded more slowly and reached a steady state. Still, other repetitive sequences, particularly ribosomal DNA (rDNA), show signs of concerted evolution playing a major role in homogenizing sequence variation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4494-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rahul Pisupati
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721302, India.,Present address: Gregor Mendel Institute, Dr. Bohr-gasse 3, Vienna, 1030, Austria
| | - Daniela Vergara
- Ecology and Evolutionary Biology, University of Colorado, Boulder, 80302, USA
| | - Nolan C Kane
- Ecology and Evolutionary Biology, University of Colorado, Boulder, 80302, USA.
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Kudoh T, Takahashi M, Osabe T, Toyoda A, Hirakawa H, Suzuki Y, Ohmido N, Onodera Y. Molecular insights into the non-recombining nature of the spinach male-determining region. Mol Genet Genomics 2017; 293:557-568. [PMID: 29222702 DOI: 10.1007/s00438-017-1405-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/04/2017] [Indexed: 11/30/2022]
Abstract
Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species' sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars. These observations suggest that, in spinach, a Y-chromosomal region around the male-determining locus does not (or almost not) recombine with a counterpart region on the X chromosome. Using five of the seven DNA markers, five bacterial artificial chromosome (BAC) clone contigs with a total length of approximately 690 kbp were constructed. Full sequencing of six representative BAC clones (total insert length 504 kbp) from the five contigs and a transcriptome analysis by RNA-seq revealed that the Y-chromosomal region around the male-determining locus contains large amounts of repetitive elements, suggesting that the region might be poor in gene content. Most of the repeats found in this region are novel Ty1-copia-like and its derivative elements that accumulate predominantly in heterochromatic regions. Our findings may provide valuable insight into spinach genome structure and clues for future research into the evolution of the sex determining locus.
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Affiliation(s)
- Tomohiro Kudoh
- The Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo, 060-8589, Japan
| | - Mitsuhiko Takahashi
- The Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo, 060-8589, Japan
| | - Takayuki Osabe
- The Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo, 060-8589, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Hideki Hirakawa
- The Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yutaka Suzuki
- The Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Yasuyuki Onodera
- The Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo, 060-8589, Japan.
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Szlachetko DL, Kolanowska M, Naczk A, Górniak M, Dudek M, Rutkowski P, Chiron G. Taxonomy of Cyrtochilum-alliance (Orchidaceae) in the light of molecular and morphological data. BOTANICAL STUDIES 2017; 58:8. [PMID: 28510191 PMCID: PMC5430592 DOI: 10.1186/s40529-017-0164-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 01/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The generic separateness and specific composition of the orchid genus Cyrtochilum was discussed for almost two centuries. Over the years several smaller taxa were segregated from this taxon, but their separateness was recently questioned based on molecular studies outcomes. The aim of our study was to revise concepts of morphological-based generic delimitation in Cyrtochilum-alliance and to compare it with the results of genetic analysis. We used phylogenetic framework in combination with phenetical analysis to provide proposal of the generic delimitation within Cyrtochilum-alliance. Two molecular markers, ITS and matK were used to construct phylogenetic tree. A total of over 5000 herbarium specimens were included in the morphological examination and the phenetical analysis included 29 generative and vegetative characters. RESULTS Comparative morphology of the previously recognized genera: Buesiella, Dasyglossum, Neodryas, Rusbyella, Siederella and Trigonochilum is presented. A new species within the the latter genus is described. Fourteen new combinations are proposed. The key to the identification of the genera of the Cyrtochilum-alliance and morphological characteristics of each genus are provided. CONCLUSIONS A total of six separated genera are recognized within Cyrtochilum-alliance. The reasons of the incompatibility between morphological differences observed within studied taxa and phylogenetic tree are argued and the taxonomic implications of such inconsistency, resulting in fragmentation or lumping of taxonomic units, are discussed.
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Affiliation(s)
- Dariusz L. Szlachetko
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Marta Kolanowska
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
- Department of Biodiversity Research, Global Change Research Institute AS CR, Bělidla 4a., 603 00 Brno, Czech Republic
| | - Aleksandra Naczk
- Department of Molecular Evolution, The University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Marcin Górniak
- Department of Molecular Evolution, The University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Magdalena Dudek
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Piotr Rutkowski
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Guy Chiron
- Herbiers, Université de Lyon I, 69622 Villeurbanne Cedex, France
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Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2734960. [PMID: 29181391 PMCID: PMC5664236 DOI: 10.1155/2017/2734960] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/17/2017] [Accepted: 09/13/2017] [Indexed: 11/17/2022]
Abstract
Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.
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Martínez-González CR, Ramírez-Mendoza R, Jiménez-Ramírez J, Gallegos-Vázquez C, Luna-Vega I. Improved method for genomic DNA extraction for Opuntia Mill. (Cactaceae). PLANT METHODS 2017; 13:82. [PMID: 29046708 PMCID: PMC5637266 DOI: 10.1186/s13007-017-0234-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/03/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Genomic DNA extracted from species of Cactaceae is often contaminated with significant amounts of mucilage and pectin. Pectin is one of the main components of cellular walls, whereas mucilage is a complex polysaccharide with a ramified structure. Thus, pectin- and mucilage-free extraction of DNA is a key step for further downstream PCR-based analyses. RESULTS We tested our DNA extraction method on cladode tissue (juvenile, adult, and herbaria exemplars) of 17 species of Opuntia Mill., which are characterized by a large quantity of pectin and mucilage. CONCLUSION We developed a method for the extraction of gDNA free of inhibitory compounds common in species of Opuntia Mill., such as pectin and mucilage. Compared to previously extraction protocols, our method produced higher yields of high-quality genomic DNA.
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Affiliation(s)
- César Ramiro Martínez-González
- Laboratorio de Biogeografía y Sistemática, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510 Mexico City, México
| | - Rosario Ramírez-Mendoza
- Laboratorio de Biotecnología de Semillas, Colegio de Postgraduados, Carretera México-Texcoco, 56230 Estado de México, México
| | - Jaime Jiménez-Ramírez
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510 Mexico City, México
| | - Clemente Gallegos-Vázquez
- Centro Regional Universitario Centro Norte, Universidad Autónoma Chapingo, Cruz del Sur núm. 100, Colonia Constelación, El Orito, 98085 Zacatecas, Zacatecas México
| | - Isolda Luna-Vega
- Laboratorio de Biogeografía y Sistemática, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510 Mexico City, México
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Krawczyk K, Nobis M, Nowak A, Szczecińska M, Sawicki J. Phylogenetic implications of nuclear rRNA IGS variation in Stipa L. (Poaceae). Sci Rep 2017; 7:11506. [PMID: 28912548 PMCID: PMC5599551 DOI: 10.1038/s41598-017-11804-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/25/2017] [Indexed: 01/03/2023] Open
Abstract
The article takes up the problem of deficiency of molecular marker, which could illustrate molecular variability as well as phylogenetic relation within the genus of Stipa L. (Poaceae). Researches made so far hadn’t delivered sufficient information about relationships between particular taxa from the genus of Stipa. In the present study, we analyzed variability and phylogenetic informativeness of nuclear ribosomal DNA in six species from the genus against five other species from Poaceae including a division of this region into functional elements and domains. Our results showed that the intergenic spacer region, and especially its part adjacent to 26 S nrDNA, is a molecular marker giving a real chance for a phylogeny reconstruction of Stipa. The region seems to be the most phylogenetically informative for Stipa from all the chloroplast and nuclear markers tested so far. Comparative analysis of nrDNA repeat units from Stipa to other representatives of Poaceae showed that their structure does not deviate from the general scheme. However, the rate of evolution within the inter-repeats in the IGS region is extremely high and therefore it predestines the region for phylogenetic analyses of Stipa at genus level or in shallower taxonomic scale.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden - Center for Biological Diversity Conservation in Powsin, Warsaw, Poland
| | - Monika Szczecińska
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Fu R, Gong J. Single Cell Analysis Linking Ribosomal (r)DNA and rRNA Copy Numbers to Cell Size and Growth Rate Provides Insights into Molecular Protistan Ecology. J Eukaryot Microbiol 2017; 64:885-896. [PMID: 28499076 PMCID: PMC5697653 DOI: 10.1111/jeu.12425] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/03/2017] [Accepted: 05/02/2017] [Indexed: 11/30/2022]
Abstract
Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)‐based characteristics are linked with diversity, abundance, and activity of protist populations and communities observed at organismal levels. Here, we applied a single‐cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per‐cell rDNA and rRNA CNs scaled with cell volume (CV) to 0.44 and 0.58 powers, respectively. The modeled rDNA and rRNA concentrations thus appear to be much higher in smaller than in larger cells. The observed rRNA:rDNA ratio scaled with CV0.14. The maximum growth rate could be well predicted by a combination of per‐cell ribotype CN and temperature. Our empirical data and modeling on single‐cell ribotype scaling are in agreement with both the metabolic theory of ecology and the growth rate hypothesis, providing a quantitative framework for linking cellular rDNA and rRNA CNs with body size, growth (activity), and biomass stoichiometry. This study also demonstrates that the expression rate of rRNA genes is constrained by cell size, and favors biomass rather than abundance‐based interpretation of quantitative ribotype data in population and community ecology of protists.
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Affiliation(s)
- Rao Fu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Gong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Laboratory of Microbial Ecology and Matter Cycles, School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
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41
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Soltis DE, Kuzoff RK. DISCORDANCE BETWEEN NUCLEAR AND CHLOROPLAST PHYLOGENIES IN THE
HEUCHERA
GROUP (SAXIFRAGACEAE). Evolution 2017; 49:727-742. [DOI: 10.1111/j.1558-5646.1995.tb02309.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/1993] [Accepted: 10/04/1994] [Indexed: 11/26/2022]
Affiliation(s)
- Douglas E. Soltis
- Department of Botany Washington State University Pullman Washington 99164‐4238
| | - Robert K. Kuzoff
- Department of Botany Washington State University Pullman Washington 99164‐4238
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42
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King LM, Schaal BA. RIBOSOMAL‐DNA VARIATION AND DISTRIBUTION IN
RUDBECKIA MISSOURIENSIS. Evolution 2017; 43:1117-1119. [DOI: 10.1111/j.1558-5646.1989.tb02557.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/1988] [Accepted: 03/15/1989] [Indexed: 12/01/2022]
Affiliation(s)
- Lynn M. King
- Department of Biology Washington University St. Louis MO 63130
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43
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Xu B, Zeng XM, Gao XF, Jin DP, Zhang LB. ITS non-concerted evolution and rampant hybridization in the legume genus Lespedeza (Fabaceae). Sci Rep 2017; 7:40057. [PMID: 28051161 PMCID: PMC5209741 DOI: 10.1038/srep40057] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/30/2016] [Indexed: 12/27/2022] Open
Abstract
The internal transcribed spacer (ITS) as one part of nuclear ribosomal DNA is one of the most extensively sequenced molecular markers in plant systematics. The ITS repeats generally exhibit high-level within-individual homogeneity, while relatively small-scale polymorphism of ITS copies within individuals has often been reported in literature. Here, we identified large-scale polymorphism of ITS copies within individuals in the legume genus Lespedeza (Fabaceae). Divergent paralogs of ITS sequences, including putative pseudogenes, recombinants, and multiple functional ITS copies were sometimes detected in the same individual. Thirty-seven ITS pseudogenes could be easily detected according to nucleotide changes in conserved 5.8S motives, the significantly lower GC contents in at least one of three regions, and the lost ability of 5.8S rDNA sequence to fold into a conserved secondary structure. The distribution patterns of the putative functional clones were highly different between the traditionally recognized two subgenera, suggesting different rates of concerted evolution in two subgenera which could be attributable to their different extents/frequencies of hybridization, confirmed by our analysis of the single-copy nuclear gene PGK. These findings have significant implications in using ITS marker for reconstructing phylogeny and studying hybridization.
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MESH Headings
- Base Composition
- Cluster Analysis
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Evolution, Molecular
- Lespedeza/classification
- Lespedeza/genetics
- Nucleic Acid Hybridization
- Phylogeny
- Polymorphism, Genetic
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Xiao-Mao Zeng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Dong-Pil Jin
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Li-Bing Zhang
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166, USA
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44
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Zhang W, Yang S, Zhao H, Huang L. Using the ITS2 sequence-structure as a DNA mini-barcode: A case study in authenticating the traditional medicine“Fang Feng”. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Scaldaferro MA, da Cruz MVR, Cecchini NM, Moscone EA. FISH and AgNor mapping of the 45S and 5S rRNA genes in wild and cultivated species of Capsicum (Solananceae). Genome 2016; 59:95-113. [PMID: 26853884 DOI: 10.1139/gen-2015-0099] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chromosome number and position of rDNA were studied in 12 wild and cultivated species of the genus Capsicum with chromosome numbers x = 12 and x = 13 (22 samples). For the first time in these species, the 5S and 45S rRNA loci were localized and physically mapped using two-color fluorescence in situ hybridization and AgNOR banding. We focused on the comparison of the results obtained with both methods with the aim of accurately revealing the real functional rRNA genes. The analyzes were based on a previous work that reported that the 18S-5.8S-25S loci mostly coincide with GC-rich heterochromatic regions and likely have given rise to satellite DNAs, which are not active genes. These data show the variability of rDNA within karyotypes of the genus Capsicum, providing anchor points for (comparative) genetic maps. In addition, the obtained information might be useful for studies on evolution of repetitive DNA.
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Affiliation(s)
- Marisel A Scaldaferro
- a Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina.,b Facultad de Ciencias Exactas, Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba, Av. Vélez Sarsfield 299, CP 5000, Córdoba, Argentina
| | | | - Nicolás M Cecchini
- d Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS Room W519P, Chicago, USA
| | - Eduardo A Moscone
- a Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
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46
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Dimitrova AD, Georgiev O, Mishev K, Tzvetkov S, Ananiev ED, Karagyozov L. Mapping of unmethylated sites in rDNA repeats in barley NOR deletion line. JOURNAL OF PLANT PHYSIOLOGY 2016; 205:97-104. [PMID: 27649325 DOI: 10.1016/j.jplph.2016.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Extensive cytosine methylation is characteristic of plant rDNA. Evidence exists, however, that the active rRNA genes are less methylated. In this work we report on the mapping of unmethylated CCGG sites in Hordeum vulgare rDNA repeats by digestion with methylation sensitive restriction enzyme HpaII and indirect end-labeling of the generated fragments. For mapping we used genomic DNA from barley deletion line with a single NOR on chromosome 5H. This NOR is more active in order to compensate for the missing NOR 6H. The enhanced NOR 5H activity in the deletion mutant is not due to higher multiplicity of the rRNA genes or, as sequencing showed, to changes in the subunit structure of the intergenic spacer. The HpaII sites in barley rDNA are heavily methylated. Nevertheless, a fraction of the rDNA repeats is hypomethylated with unmethylated CCGG sites at various positions. One unmethylated CCGG sequence is close to the transcription start site, downstream of the 135bp subrepeats. Unmethylated sites are also present in the external transcribed spacer and in the genes coding mature rRNAs. The patterns of unmethylated sites in the barley deletion line and in lines with two NORs were compared. It is hypothesized that the occurrence of unmethylated sites on a fixed subset of rDNA repeats correlates with their transcriptional activity.
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Affiliation(s)
- Anna D Dimitrova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria.
| | - Oleg Georgiev
- Institute of Molecular Life Sciences, University Zurich-Irchel, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Kiril Mishev
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Stefan Tzvetkov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Evgueni D Ananiev
- Department of Plant Physiology, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
| | - Luchezar Karagyozov
- Department of Plant Physiology, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
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47
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ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae). Genetica 2016; 144:639-650. [DOI: 10.1007/s10709-016-9931-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
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48
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Chen Y, Yang X, Yao J, Kyaw EP, Zhang AF, Li YF, Gu CY, Zang HY, Gao TC. Simple and rapid detection of Tilletia horrida causing rice kernel smut in rice seeds. Sci Rep 2016; 6:33258. [PMID: 27624858 PMCID: PMC5021929 DOI: 10.1038/srep33258] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 08/23/2016] [Indexed: 11/30/2022] Open
Abstract
A simple and rapid method for the detection of Tilletia horrida, the causal agent of rice kernel smut, in rice seeds is developed based on specific polymerase chain reaction (PCR). To design the specific primers for the detection of T. horrida, partial sequences of internal transcribed spacer (ITS) DNA region of T. horrida, T. controversa, T. walkeri, T. ehrhartae, T. indica and T. caries were analyzed and compared. A 503-bp fragment was amplified with the designed primers from the T. horrida genomic DNA. However, no PCR product was obtained from the DNA of other five Tilletia species and 22 fungal plant pathogens tested in the present work indicating the specificity of the primers for the detection of T. horrida. The PCR was performed by directly using the spores, isolated from the 21 different rice seed samples, as template DNA. The T. horrida was detected in 6 of the samples, indicating that 28.6% of the rice samples were contaminated with the kernel smut pathogen. This simple PCR based diagnostic assay can be applied for the direct and rapid detection and identification of T. horrida to screen large numbers of rice seed samples.
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Affiliation(s)
- Yu Chen
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Xue Yang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Jian Yao
- Anhui Entry-Exit Inspection and Quarantine Bureau, Hefei 230022, China
| | - Ei Phyu Kyaw
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
- Department of Biotechnology, Mandalay Technological University, Mandalay, Republic of the Union of Myanmar
| | - Ai-Fang Zhang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Yun-Fei Li
- Anhui Entry-Exit Inspection and Quarantine Bureau, Hefei 230022, China
| | - Chun-Yan Gu
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Hao-Yu Zang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Tong-Chun Gao
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
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49
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Bell KL, de Vere N, Keller A, Richardson RT, Gous A, Burgess KS, Brosi BJ. Pollen DNA barcoding: current applications and future prospects. Genome 2016; 59:629-40. [DOI: 10.1139/gen-2015-0200] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.
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Affiliation(s)
- Karen L. Bell
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, United Kingdom
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
| | | | - Annemarie Gous
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Berry J. Brosi
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
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50
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Transcriptional Activity of rRNA Genes in Barley Cells after Mutagenic Treatment. PLoS One 2016; 11:e0156865. [PMID: 27257817 PMCID: PMC4892555 DOI: 10.1371/journal.pone.0156865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/01/2016] [Indexed: 12/02/2022] Open
Abstract
In the present study, the combination of the micronucleus test with analysis of the activity of the rRNA genes in mutagen-treated Hordeum vulgare (barley) by maleic hydrazide (MH) cells was performed. Simultaneously fluorescence in situ hybridization (FISH) with 25S rDNA as probes and an analysis of the transcriptional activity of 35S rRNA genes with silver staining were performed. The results showed that transcriptional activity is always maintained in the micronuclei although they are eliminated during the next cell cycle. The analysis of the transcriptional activity was extended to barley nuclei. MH influenced the fusion of the nucleoli in barley nuclei. The silver staining enabled detection of the nuclear bodies which arose after MH treatment. The results confirmed the usefulness of cytogenetic techniques in the characterization of micronuclei. Similar analyses can be now extended to other abiotic stresses to study the response of plant cells to the environment.
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