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Hellferscee O, Treurnicht F, Gaelejwe L, Moerdyk A, Reubenson G, McMorrow M, Tempia S, McAnerney J, Walaza S, Wolter N, von Gottberg A, Cohen C. Detection of Victoria lineage influenza B viruses with K162 and N163 deletions in the hemagglutinin gene, South Africa, 2018. Health Sci Rep 2021; 4:e367. [PMID: 34557595 PMCID: PMC8448392 DOI: 10.1002/hsr2.367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 07/29/2021] [Accepted: 08/08/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND A group of Victoria lineage influenza B viruses with a two amino acid deletion in the hemagglutinin (HA) at residues K162 and N163, was detected during the 2016 to 2017 Northern Hemisphere influenza season and continues to spread geographically. We describe the first identification of viruses with these deletions from South Africa in 2018. METHODS Nasopharyngeal samples were obtained from the syndromic surveillance programs. Real-time reverse transcription-polymerase chain reaction was used for virus detection and lineage determination. Influenza genetic characterization was done using next-generation sequencing on the MiSeq platform. The duration of virus circulation was determined using thresholds calculated using the Moving Epidemic Method; duration was used as an indicator of disease transmissibility and impact. RESULTS In 2018, 42% (426/1015) of influenza-positive specimens were influenza B viruses. Of 426 influenza B-positive samples, 376 (88%) had the lineage determined of which 75% (283/376) were Victoria lineage. The transmissibility of the 2018 South African influenza season was high for a few weeks, although the severity remained moderate through most of the season. The sequenced 2018 South African Victoria lineage influenza B viruses clustered in sub-clade V1A.1 with the 162-163 deletions. CONCLUSIONS We report the first detection of the 162-163 deletion variant of influenza B/Victoria viruses from South Africa in 2018, and suggest that this deletion variant replaced the previous circulating influenza B/Victoria viruses. These deletions putatively affect the antigenic properties of the viruses because they border an immune-dominant region at the tip of the HA. Therefore, close monitoring of these newly emerging viruses is essential.
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Affiliation(s)
- Orienka Hellferscee
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- Department of Medical Virology, School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Florette Treurnicht
- Department of Medical Virology, School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Lucinda Gaelejwe
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| | - Alexandra Moerdyk
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| | - Gary Reubenson
- Department of Paediatrics & Child Health, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Meredith McMorrow
- Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
- Influenza ProgramCenters for Disease Control and PreventionPretoriaSouth Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
- Influenza ProgramCenters for Disease Control and PreventionPretoriaSouth Africa
- MassGenicsDuluthGeorgiaUSA
- School of Public Health, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Johanna McAnerney
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- School of Public Health, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and MeningitisNational Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- School of Public Health, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
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Anton BP, Fomenkov A, Wu V, Roberts RJ. Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments. PLoS One 2021; 16:e0247541. [PMID: 33974631 PMCID: PMC8112702 DOI: 10.1371/journal.pone.0247541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022] Open
Abstract
Single-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that "write" these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.
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Affiliation(s)
- Brian P. Anton
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
| | - Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Victoria Wu
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- Wellesley College, Wellesley, Massachusetts, United States of America
| | - Richard J. Roberts
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
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Braich S, Baillie RC, Spangenberg GC, Cogan NOI. A new and improved genome sequence of Cannabis sativa. GIGABYTE 2020; 2020:gigabyte10. [PMID: 36824593 PMCID: PMC9632002 DOI: 10.46471/gigabyte.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/18/2020] [Indexed: 11/09/2022] Open
Abstract
Cannabis is a diploid species (2n = 20), the estimated haploid genome sizes of the female and male plants using flow cytometry are 818 and 843 Mb respectively. Although the genome of Cannabis has been sequenced (from hemp, wild and high-THC strains), all assemblies have significant gaps. In addition, there are inconsistencies in the chromosome numbering which limits their use. A new comprehensive draft genome sequence assembly (∼900 Mb) has been generated from the medicinal cannabis strain Cannbio-2, that produces a balanced ratio of cannabidiol and delta-9-tetrahydrocannabinol using long-read sequencing. The assembly was subsequently analysed for completeness by ordering the contigs into chromosome-scale pseudomolecules using a reference genome assembly approach, annotated and compared to other existing reference genome assemblies. The Cannbio-2 genome sequence assembly was found to be the most complete genome sequence available based on nucleotides assembled and BUSCO evaluation in Cannabis sativa with a comprehensive genome annotation. The new draft genome sequence is an advancement in Cannabis genomics permitting pan-genome analysis, genomic selection as well as genome editing.
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Affiliation(s)
- Shivraj Braich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Rebecca C. Baillie
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia, Corresponding author. E-mail:
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Valley-Omar Z, Cloete A, Pieterse R, Walaza S, Salie-Bassier Y, Smith M, Govender N, Seleka M, Hellferscee O, Mtshali PS, Allam M, Ismail A, Anthony T, Seutloali M, McCarthy K, van Helden L, Cohen C, Treurnicht FK. Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017. Influenza Other Respir Viruses 2020; 14:266-273. [PMID: 32058677 PMCID: PMC7182598 DOI: 10.1111/irv.12724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/19/2019] [Accepted: 01/15/2020] [Indexed: 12/14/2022] Open
Abstract
Background In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces. Objectives We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak. Methods Influenza A(H5N8)‐positive veterinary specimens were used to evaluate the ability of real‐time PCR‐based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next‐generation sequencing for phylogenetic characterization and screening for mammalian‐adaptive mutations. Results Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real‐time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation. Conclusions Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression of molecular adaptation for mammalian infection suggest that this avian pathogen continues to be low‐risk human pathogen.
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Affiliation(s)
- Ziyaad Valley-Omar
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Department of Pathology, Division of Medical Virology, University of Cape Town, South Africa
| | - Alicia Cloete
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Reneé Pieterse
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Sibongile Walaza
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Yusrah Salie-Bassier
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mikhail Smith
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mpho Seleka
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Orienka Hellferscee
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Phillip Senzo Mtshali
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Tasneem Anthony
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Michelle Seutloali
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Kerrigan McCarthy
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Lesley van Helden
- Veterinary Services, Western Cape Department of Agriculture, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Florette Kathleen Treurnicht
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Malmberg MM, Shi F, Spangenberg GC, Daetwyler HD, Cogan NOI. Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:508. [PMID: 29725344 PMCID: PMC5917405 DOI: 10.3389/fpls.2018.00508] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.
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Affiliation(s)
- M. Michelle Malmberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Fan Shi
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
| | - German C. Spangenberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- *Correspondence: Noel O. I. Cogan,
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Shinozuka H, Hettiarachchige IK, Shinozuka M, Cogan NOI, Spangenberg GC, Cocks BG, Forster JW, Sawbridge TI. Horizontal transfer of a ß-1,6-glucanase gene from an ancestral species of fungal endophyte to a cool-season grass host. Sci Rep 2017; 7:9024. [PMID: 28831055 PMCID: PMC5567365 DOI: 10.1038/s41598-017-07886-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/10/2017] [Indexed: 11/22/2022] Open
Abstract
Molecular characterisation has convincingly demonstrated some types of horizontal gene transfer in eukaryotes, but nuclear gene transfer between distantly related eukaryotic groups appears to have been rare. For angiosperms (flowering plants), nuclear gene transfer events identified to date have been confined to genes originating from prokaryotes or other plant species. In this report, evidence for ancient horizontal transfer of a fungal nuclear gene, encoding a ß-1,6-glucanase enzyme for fungal cell wall degradation, into an angiosperm lineage is presented for the first time. The gene was identified from de novo sequencing and assembly of the genome and transcriptome of perennial ryegrass, a cool-season grass species. Molecular analysis confirmed the presence of the complete gene in the genome of perennial ryegrass. No corresponding sequence was found in other plant species, apart from members of the Poeae sub-tribes Loliinae and Dactylidinae. Evidence suggests that a common ancestor of the two sub-tribes acquired the gene from a species ancestral to contemporary grass-associated fungal endophytes around 9-13 million years ago. This first report of horizontal transfer of a nuclear gene from a taxonomically distant eukaryote to modern flowering plants provides evidence for a novel adaptation mechanism in angiosperms.
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Affiliation(s)
- Hiroshi Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia.
- Dairy Futures Cooperative Research Centre, Bundoora, Australia.
| | - Inoka K Hettiarachchige
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
| | - Maiko Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
| | - Noel O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - German C Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Benjamin G Cocks
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - John W Forster
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Timothy I Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
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Zha L, Liu S, Liu J, Jiang C, Yu S, Yuan Y, Yang J, Wang Y, Huang L. DNA Methylation Influences Chlorogenic Acid Biosynthesis in Lonicera japonica by Mediating LjbZIP8 to Regulate Phenylalanine Ammonia-Lyase 2 Expression. FRONTIERS IN PLANT SCIENCE 2017; 8:1178. [PMID: 28740500 PMCID: PMC5502268 DOI: 10.3389/fpls.2017.01178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/20/2017] [Indexed: 05/10/2023]
Abstract
The content of active compounds differ in buds and flowers of Lonicera japonica (FLJ) and L. japonica var. chinensis (rFLJ). Chlorogenic acid (CGAs) were major active compounds of L. japonica and regarded as measurements for quality evaluation. However, little is known concerning the formation of active compounds at the molecular level. We quantified the major CGAs in FLJ and rFLJ, and found the concentrations of CGAs were higher in the buds of rFLJ than those of FLJ. Further analysis of CpG methylation of CGAs biosynthesis genes showed differences between FLJ and rFLJ in the 5'-UTR of phenylalanine ammonia-lyase 2 (PAL2). We identified 11 LjbZIP proteins and 24 rLjbZIP proteins with conserved basic leucine zipper domains, subcellular localization, and electrophoretic mobility shift assay showed that the transcription factor LjbZIP8 is a nuclear-localized protein that specifically binds to the G-box element of the LjPAL2 5'-UTR. Additionally, a transactivation assay and LjbZIP8 overexpression in transgenic tobacco indicated that LjbZIP8 could function as a repressor of transcription. Finally, treatment with 5-azacytidine decreased the transcription level of LjPAL2 and CGAs content in FLJ leaves. These results raise the possibility that DNA methylation might influence the recruitment of LjbZIP8, regulating PAL2 expression level and CGAs content in L. japonica.
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Affiliation(s)
- Liangping Zha
- College of Pharmacy, Anhui University of Chinese MedicineHefei, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese MedicineHefei, China
| | - Shuang Liu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- School of Chinese Materia Medica, Beijing University of Chinese MedicineBeijing, China
| | - Juan Liu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Chao Jiang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Shulin Yu
- College of Pharmacy, Anhui University of Chinese MedicineHefei, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yuan Yuan
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Jian Yang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yaolong Wang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
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Shinozuka H, Forster JW. Use of the melting curve assay as a means for high-throughput quantification of Illumina sequencing libraries. PeerJ 2016; 4:e2281. [PMID: 27602269 PMCID: PMC4991867 DOI: 10.7717/peerj.2281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/02/2016] [Indexed: 11/30/2022] Open
Abstract
Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to issues of cost and/or processing time. Methods. An inexpensive and high-throughput library quantification method has been developed, based on an adaptation of the melting curve assay. Sequencing libraries were subjected to the assay using the Bio-Rad Laboratories CFX ConnectTM Real-Time PCR Detection System. The library quantity was calculated through summation of reduction of relative fluorescence units between 86 and 95 °C. Results.PCR-enriched sequencing libraries are suitable for this quantification without pre-purification of DNA. Short DNA molecules, which ideally should be eliminated from the library for subsequent processing, were differentiated from the target DNA in a mixture on the basis of differences in melting temperature. Quantification results for long sequences targeted using the melting curve assay were correlated with those from existing methods (R2 > 0.77), and that observed from MiSeq sequencing (R2 = 0.82). Discussion.The results of multiplexed sequencing suggested that the normalisation performance of the described method is equivalent to that of another recently reported high-throughput bead-based method, BeNUS. However, costs for the melting curve assay are considerably lower and processing times shorter than those of other existing methods, suggesting greater suitability for highly multiplexed sequencing applications.
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Affiliation(s)
- Hiroshi Shinozuka
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia; Dairy Futures Cooperative Research Centre, Australia
| | - John W Forster
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia; Dairy Futures Cooperative Research Centre, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
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