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Li C, Nong W, Zhao S, Lin X, Xie Y, Cheung MY, Xiao Z, Wong AYP, Chan TF, Hui JHL, Lam HM. Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean. BMC Genomics 2022; 23:65. [PMID: 35057741 PMCID: PMC8780314 DOI: 10.1186/s12864-022-08308-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Soybean is a major legume crop with high nutritional and environmental values suitable for sustainable agriculture. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are important regulators of gene functions in eukaryotes. However, the interactions between these two types of ncRNAs in the context of plant physiology, especially in response to salinity stress, are poorly understood. RESULTS Here, we challenged a cultivated soybean accession (C08) and a wild one (W05) with salt treatment and obtained their small RNA transcriptomes at six time points from both root and leaf tissues. In addition to thoroughly analyzing the differentially expressed miRNAs, we also documented the first case of miRNA arm-switching (miR166m), the swapping of dominant miRNA arm expression, in soybean in different tissues. Two arms of miR166m target different genes related to salinity stress (chloroplastic beta-amylase 1 targeted by miR166m-5p and calcium-dependent protein kinase 1 targeted by miR166m-3p), suggesting arm-switching of miR166m play roles in soybean in response to salinity stress. Furthermore, two pairs of miRNA:lncRNA interacting partners (miR166i-5p and lncRNA Gmax_MSTRG.35921.1; and miR394a-3p and lncRNA Gmax_MSTRG.18616.1) were also discovered in reaction to salinity stress. CONCLUSIONS This study demonstrates how ncRNA involves in salinity stress responses in soybean by miRNA arm switching and miRNA:lncRNA interactions. The behaviors of ncRNAs revealed in this study will shed new light on molecular regulatory mechanisms of stress responses in plants, and hence provide potential new strategies for crop improvement.
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Affiliation(s)
- Chade Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Wenyan Nong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Shancen Zhao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, P.R. China
| | - Xiao Lin
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Yichun Xie
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ming-Yan Cheung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Zhixia Xiao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Annette Y P Wong
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ting Fung Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Jerome H L Hui
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
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Nong W, Qu Z, Li Y, Barton-Owen T, Wong AYP, Yip HY, Lee HT, Narayana S, Baril T, Swale T, Cao J, Chan TF, Kwan HS, Ngai SM, Panagiotou G, Qian PY, Qiu JW, Yip KY, Ismail N, Pati S, John A, Tobe SS, Bendena WG, Cheung SG, Hayward A, Hui JHL. Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication. Commun Biol 2021; 4:83. [PMID: 33469163 PMCID: PMC7815833 DOI: 10.1038/s42003-020-01637-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/21/2020] [Indexed: 11/08/2022] Open
Abstract
Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7 Gb, N50 = 90.2 Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7 Gb, N50 = 109.7 Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C. rotundicauda and T. tridentatus genomes from populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for improving our understanding of invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both the individual and population level. We also provide improved genomic resources for horseshoe crabs, of applied value for breeding programs and conservation of this fascinating and unusual invertebrate lineage.
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Affiliation(s)
- Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tom Barton-Owen
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Annette Y P Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hoi Ting Lee
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Satya Narayana
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Jianquan Cao
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Fung Chan
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Sai Ming Ngai
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Gianni Panagiotou
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- Leibniz Institute of Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Noraznawati Ismail
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Siddhartha Pati
- Department of Bioscience and Biotechnology, Fakir Mohan University, Balasore, India
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, 20130, Kuala Nerus, Terengganu, Malaysia
- Research Division, Association for Biodiversity Conservation and Research (ABC), Odisha, 756003, India
| | - Akbar John
- Institute of Oceanography and Maritime Studies (INOCEM), Kulliyyah of Science, International Islamic University, Kuantan, Malaysia
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | | | - Siu Gin Cheung
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
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Zhe Q, Yiu WC, Yip HY, Nong W, Yu CWC, Lee IHT, Wong AYP, Wong NWY, Cheung FKM, Chan TF, Lau KF, Zhong S, Chu KH, Tobe SS, Ferrier DEK, Bendena WG, Hui JHL. Micro-RNA Clusters Integrate Evolutionary Constraints on Expression and Target Affinities: The miR-6/5/4/286/3/309 Cluster in Drosophila. Mol Biol Evol 2020; 37:2955-2965. [PMID: 32521021 DOI: 10.1093/molbev/msaa146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A striking feature of micro-RNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a micro-RNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this micro-RNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of micro-RNA cluster members were also constructed. Expression of individual micro-RNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient micro-RNAs together (miR-5/4/286/3/309) or more recently evolved clustered micro-RNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed downregulation of leg-patterning gene cassettes in generation of the leg-shortening phenotype. Furthermore, cell transfection with different combinations of micro-RNA cluster members revealed a suite of downstream genes targeted by all cluster members, as well as complements of targets that are unique for distinct micro-RNAs. Considered together, the micro-RNA targets and the evolutionary ages of each micro-RNA in the cluster demonstrate the importance of micro-RNA clustering, where new members can reinforce and modify the selection forces on both the cluster regulation and the gene regulatory network of existing micro-RNAs. Key words: micro-RNA, cluster, evolution.
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Affiliation(s)
- Qu Zhe
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Wing Chung Yiu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Clare W C Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Ivy H T Lee
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Annette Y P Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Nicola W Y Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Fiona K M Cheung
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Kwok Fai Lau
- School of Life Sciences, The Chinese University of Hong Kong
| | - Silin Zhong
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Ka Hou Chu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, The Chinese University of Hong Kong
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Canada
| | | | | | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
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4
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Qu Z, Nong W, So WL, Barton-Owen T, Li Y, Leung TCN, Li C, Baril T, Wong AYP, Swale T, Chan TF, Hayward A, Ngai SM, Hui JHL. Millipede genomes reveal unique adaptations during myriapod evolution. PLoS Biol 2020; 18:e3000636. [PMID: 32991578 PMCID: PMC7523956 DOI: 10.1371/journal.pbio.3000636] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 08/24/2020] [Indexed: 01/27/2023] Open
Abstract
The Myriapoda, composed of millipedes and centipedes, is a fascinating but poorly understood branch of life, including species with a highly unusual body plan and a range of unique adaptations to their environment. Here, we sequenced and assembled 2 chromosomal-level genomes of the millipedes Helicorthomorpha holstii (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] = 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (assembly size = 449 Mb, N50 = 26.78 Mb mainly on 17 pseudomolecules). Unique genomic features, patterns of gene regulation, and defence systems in millipedes, not observed in other arthropods, are revealed. Both repeat content and intron size are major contributors to the observed differences in millipede genome size. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute (AGO) proteins for loading small RNAs are duplicated in both millipedes, but unlike in insects, an AGO duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs—including species-specific microRNA arm switching—providing differential gene regulation is also obtained. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules found in centipedes. We identify sets of genes associated with the ozadene that play roles in chemical defence as well as antimicrobial activity. Macro-synteny analyses revealed highly conserved genomic blocks between the 2 millipedes and deuterostomes. Collectively, our analyses of millipede genomes reveal that a series of unique adaptations have occurred in this major lineage of arthropod diversity. The 2 high-quality millipede genomes provided here shed new light on the conserved and lineage-specific features of millipedes and centipedes. These findings demonstrate the importance of the consideration of both centipede and millipede genomes—and in particular the reconstruction of the myriapod ancestral situation—for future research to improve understanding of arthropod evolution, and animal evolutionary genomics more widely. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes. This study describes the genome sequences of two millipedes, Helicorthomorpha holstii and Trigoniulus corallinus, revealing unique adaptations not found in other arthropods.
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Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Tom Barton-Owen
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Thomas C. N. Leung
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Chade Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Tobias Baril
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, United Kingdom
| | - Annette Y. P. Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Thomas Swale
- Dovetail Genomics, Scotts Valley, California, United States of America
| | - Ting-Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Alexander Hayward
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, United Kingdom
| | - Sai-Ming Ngai
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Jerome H. L. Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
- * E-mail:
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Huang EYY, Wong AYP, Lee IHT, Qu Z, Yip HY, Leung CW, Yin SM, Hui JHL. Infection patterns of dengue, Zika and endosymbiont Wolbachia in the mosquito Aedes albopictus in Hong Kong. Parasit Vectors 2020; 13:361. [PMID: 32690078 PMCID: PMC7372788 DOI: 10.1186/s13071-020-04231-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/15/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The mosquito Aedes albopictus is a vector of dengue and Zika viruses. Insecticide-resistant mosquito populations have evolved in recent decades, suggesting that new control strategies are needed. Hong Kong has a monsoon-influenced humid subtropical climate, which favours the spread of mosquitoes. However, baseline information on the composition and dynamics of the occurrence of endosymbiont Wolbachia in local Ae. albopictus is lacking, hindering the development of scientifically-informed control measures. This study identifies the presence and absence of dengue and Zika viruses, and Wolbachia infection in Aedes albopictus in Hong Kong. METHODS Oviposition traps were set at 57 areas in Hong Kong, and both immature and adult mosquitoes were collected on a monthly basis between April 2018 and April 2019 as the study sample. Each individual mosquito in this sample was processed and screened for the presence of the dengue and Zika viruses and the endosymbionts Wolbachia wAlbA and wAlbB with PCR. RESULTS Totals of 967 and 984 mosquitoes were tested respectively for the presence of dengue and Zika viruses, and no trace of either infection was found in these samples. The presence of wAlbA and wAlbB was also tested in 1582 individuals. Over 80% of these individuals were found to be stably infected with Wolbachia throughout the thirteen-month collection period (~ 47% singly-infected; ~ 36.8% doubly infected with both wAlbA and wAlbB). CONCLUSIONS The high degree of Wolbachia wAlbA and wAlbB infection in Ae. albopictus mosquitoes in Hong Kong, coupled with the absence of any signs of infection by dengue and Zika viruses, contrasts significantly with the pattern of mosquito infection in other parts of Asia. Further studies of the infection pattern in local mosquitoes are warranted before mosquito control strategies used in other regions are implemented in Hong Kong.
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Affiliation(s)
- Elaine Y. Y. Huang
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Annette Y. P. Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ivy H. T. Lee
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-wah Leung
- Pest Control Advisory Section, Food and Environmental Hygiene Department, The Government of the Hong Kong Special Administrative Region (HKSAR), Hong Kong, China
| | - Shuk-may Yin
- Pest Control Advisory Section, Food and Environmental Hygiene Department, The Government of the Hong Kong Special Administrative Region (HKSAR), Hong Kong, China
| | - Jerome H. L. Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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Nong W, Law STS, Wong AYP, Baril T, Swale T, Chu LM, Hayward A, Lau DTW, Hui JHL. Chromosomal-level reference genome of the incense tree Aquilaria sinensis. Mol Ecol Resour 2020; 20:971-979. [PMID: 32157789 PMCID: PMC7496549 DOI: 10.1111/1755-0998.13154] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/01/2020] [Accepted: 03/04/2020] [Indexed: 11/29/2022]
Abstract
Trees in the genus Aquilaria (Thymelaeaceae) are known as lign aloes, and are native to the forests of southeast Asia. Lign aloes produce agarwood as an antimicrobial defence. Agarwood has a long history of cultural and medicinal use, and is of considerable commercial value. However, due to habitat destruction and over collection, lign aloes are threatened in the wild. We present a chromosomal‐level assembly for Aquilaria sinensis, a lign aloe endemic to China known as the incense tree, based on Illumina short‐read, 10X Genomics linked‐read, and Hi‐C sequencing data. Our 783.8 Mbp A. sinensis genome assembly is of high physical contiguity, with a scaffold N50 of 87.6 Mbp, and high completeness, with a 95.8% BUSCO score for eudicotyledon genes. We include 17 transcriptomes from various plant tissues, providing a total of 35,965 gene models. We reveal the first complete set of genes involved in sesquiterpenoid production, plant defence, and agarwood production for the genus Aquilaria, including genes involved in the biosynthesis of sesquiterpenoids via the mevalonic acid (MVA), 1‐deoxy‐D‐xylulose‐5‐phosphate (DXP), and methylerythritol phosphate (MEP) pathways. We perform a detailed repeat content analysis, revealing that transposable elements account for ~61% of the genome, with major contributions from gypsy‐like and copia‐like LTR retroelements. We also provide a comparative analysis of repeat content across sequenced species in the order Malvales. Our study reveals the first chromosomal‐level genome assembly for a tree in the genus Aquilaria and provides an unprecedented opportunity to address a variety of applied, genomic and evolutionary questions in the Thymelaeaceae more widely.
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Affiliation(s)
- Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Sean T S Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Annette Y P Wong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tobias Baril
- Department of Conservation and Ecology, University of Exeter, Exeter, UK
| | | | - Lee Man Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Alexander Hayward
- Department of Conservation and Ecology, University of Exeter, Exeter, UK
| | - David T W Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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7
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Li C, Wong AYP, Wang S, Jia Q, Chuang WP, Bendena WG, Tobe SS, Yang SH, Chung G, Chan TF, Lam HM, Bede JC, Hui JHL. miRNA-Mediated Interactions in and between Plants and Insects. Int J Mol Sci 2018; 19:E3239. [PMID: 30347694 PMCID: PMC6213987 DOI: 10.3390/ijms19103239] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 01/17/2023] Open
Abstract
Our understanding of microRNA (miRNA) regulation of gene expression and protein translation, as a critical area of cellular regulation, has blossomed in the last two decades. Recently, it has become apparent that in plant-insect interactions, both plants and insects use miRNAs to regulate their biological processes, as well as co-opting each others' miRNA systems. In this review article, we discuss the current paradigms of miRNA-mediated cellular regulation and provide examples of plant-insect interactions that utilize this regulation. Lastly, we discuss the potential biotechnological applications of utilizing miRNAs in agriculture.
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Affiliation(s)
- Chade Li
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Annette Y P Wong
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Shuang Wang
- Key Laboratory of Soil Environment and Plant Nutrition of Heilongjiang Province, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Qi Jia
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wen-Po Chuang
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan.
| | - William G Bendena
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada.
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
| | - Ting-Fung Chan
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hon-Ming Lam
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Jacqueline C Bede
- Department of Plant Science, McGill University, 21,111 Lakeshore, Ste-Anne-de-Bellevue, Montreal, QC H9X 3V9, Canada.
| | - Jerome H L Hui
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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Woo PCY, Teng JLL, Bai R, Wong AYP, Martelli P, Hui SW, Tsang AKL, Lau CCY, Ahmed SS, Yip CCY, Choi GKY, Li KSM, Lam CSF, Lau SKP, Yuen KY. High Diversity of Genogroup I Picobirnaviruses in Mammals. Front Microbiol 2016; 7:1886. [PMID: 27933049 PMCID: PMC5120130 DOI: 10.3389/fmicb.2016.01886] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/09/2016] [Indexed: 12/13/2022] Open
Abstract
In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs) were positive by RT-PCR targeting the partial RdRp gene in specimens from five cattle, six monkeys, 17 horses, nine pigs, one rabbit, one dog, and 12 California sea lions, with 11, 9, 23, 17, 1, 1, and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, sharing 47.4–89.0% nucleotide identities with other genogroup I PBV strains based on the partial RdRp gene. Nine complete segment 1 (viral loads 1.7 × 104 to 5.9 × 106/ml) and 15 segment 2 (viral loads 4.1 × 103 to 1.3 × 106/ml) of otarine PBVs from fecal samples serially collected from California sea lions were sequenced. In the two phylogenetic trees constructed using ORF2 and ORF3 of segment 1, the nine segment 1 sequences were clustered into four distinct clades (C1–C4). In the tree constructed using RdRp gene of segment 2, the 15 segment 2 sequences were clustered into nine distinct clades (R1–R9). In four sea lions, PBVs were detected in two different years, with the same segment 1 clade (C3) present in two consecutive years from one sea lion and different clades present in different years from three sea lions. A high diversity of PBVs was observed in a variety of terrestrial and marine mammals. Multiple sequence types with significant differences, representing multiple strains of PBV, were present in the majority of PBV-positive samples from different kinds of animals.
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Affiliation(s)
- Patrick C Y Woo
- Department of Microbiology, The University of Hong KongHong Kong, China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong KongHong Kong, China; Research Centre of Infection and Immunology, The University of Hong KongHong Kong, China; Carol Yu Centre for Infection, The University of Hong KongHong Kong, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, China
| | - Jade L L Teng
- Department of Microbiology, The University of Hong KongHong Kong, China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong KongHong Kong, China; Research Centre of Infection and Immunology, The University of Hong KongHong Kong, China; Carol Yu Centre for Infection, The University of Hong KongHong Kong, China
| | - Ru Bai
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | - Annette Y P Wong
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | | | | | - Alan K L Tsang
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | - Candy C Y Lau
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | - Syed S Ahmed
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | - Cyril C Y Yip
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | - Garnet K Y Choi
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | - Kenneth S M Li
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | - Carol S F Lam
- Department of Microbiology, The University of Hong Kong Hong Kong, China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong KongHong Kong, China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong KongHong Kong, China; Research Centre of Infection and Immunology, The University of Hong KongHong Kong, China; Carol Yu Centre for Infection, The University of Hong KongHong Kong, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong KongHong Kong, China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong KongHong Kong, China; Research Centre of Infection and Immunology, The University of Hong KongHong Kong, China; Carol Yu Centre for Infection, The University of Hong KongHong Kong, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, China
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Teng JLL, Ho TCC, Yeung RSY, Wong AYP, Wang H, Chen C, Fung KSC, Lau SKP, Woo PCY. Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes. Diagn Microbiol Infect Dis 2013; 78:105-15. [PMID: 24295571 DOI: 10.1016/j.diagmicrobio.2013.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 10/21/2013] [Accepted: 10/27/2013] [Indexed: 02/04/2023]
Abstract
Interpretation of 16S rRNA sequences is a difficult problem faced by clinical microbiologists and technicians. In this study, we evaluated the updated 16SpathDB 2.0 database, using 689 16S rRNA sequences from 689 complete genomes of medically important bacteria. Among these 689 16S rRNA sequences, none was wrongly identified, with 35.8% reported as a single bacterial species having >98% identity with the query sequence (category 1), 63.9% reported as more than 1 bacterial species having >98% identity with the query sequence (category 2), 0.3% reported to the genus level (category 3), and none reported as no match (category 4). For the 16S rRNA sequences of non-duplicated bacterial species reported as category 1 or 2, the percentage of bacterial species reported as category 1 was significantly higher for anaerobic Gram-positive/Gram-negative bacteria than aerobic/facultative anaerobic Gram-positive/Gram-negative bacteria. 16SpathDB 2.0 is a user-friendly and accurate database for 16S rRNA sequence interpretation in clinical laboratories.
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Affiliation(s)
- Jade L L Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
| | - Tom C C Ho
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ronald S Y Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Annette Y P Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Haiyin Wang
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Chen Chen
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Kitty S C Fung
- Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
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10
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Lau SKP, Chow WN, Wong AYP, Yeung JMY, Bao J, Zhang N, Lok S, Woo PCY, Yuen KY. Identification of microRNA-like RNAs in mycelial and yeast phases of the thermal dimorphic fungus Penicillium marneffei. PLoS Negl Trop Dis 2013; 7:e2398. [PMID: 23991243 PMCID: PMC3749987 DOI: 10.1371/journal.pntd.0002398] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/19/2013] [Indexed: 01/16/2023] Open
Abstract
Background Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in China and Southeast Asia. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less well studied and their potential roles in fungal dimorphism were largely unknown. Based on P. marneffei genome sequence, we hypothesize that miRNA-like RNAs (milRNAs) may be expressed in the dimorphic fungus. Methodology/Principal Findings We attempted to identify milRNAs in P. marneffei in both mycelial and yeast phase using high-throughput sequencing technology. Small RNAs were more abundantly expressed in mycelial than yeast phase. Sequence analysis revealed 24 potential milRNA candidates, including 17 candidates in mycelial and seven in yeast phase. Two genes, dcl-1 and dcl-2, encoding putative Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were identified in P. marneffei. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp., suggesting the co-evolution of dcl-2 among the thermal dimorphic fungi. Moreover, dcl-2 demonstrated higher mRNA expression levels in mycelial than yeast phase by 7 folds (P<0.001). Northern blot analysis confirmed the expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase. Using dcl-1KO, dcl-2KO, dclDKO and qde-2KO deletion mutants, we showed that the biogenesis of both milRNAs were dependent on dcl-2 but not dcl-1 or qde-2. The mRNA expression levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1KD, supporting regulatory function of milRNAs. Conclusions/Significance Our findings provided the first evidence for differential expression of milRNAs in different growth phases of thermal dimorphic fungi and shed light on the evolution of fungal proteins involved in milRNA biogenesis and possible role of post-transcriptional control in governing thermal dimorphism. Penicillium marneffei is the most important thermal dimorphic pathogenic fungus in Southeast Asia. Despite findings on diverse genes and mechanisms involved in dimorphic switching, the key to signally pathways governing the switch is still unknown. Since miRNAs are important regulatory molecules in eukaryotes, we attempt to define if miRNAs are expressed in different growth phases of P. marneffei. Using high-throughput sequencing, we identified 24 potential milRNA candidates in P. marneffei, which were more abundantly expressed in mycelial than yeast phase. Two genes, dcl-1 and dcl-2, encoding Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were also identified. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp.. dcl-2 demonstrated higher mRNA levels in mycelial than yeast phase. Northern blot analysis confirmed expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase, whose expression was dependent on dcl-2 but not dcl-1 or qde-2. The mRNA levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1KD, supporting its regulatory function. This study represents the first discovery of milRNAs in thermal dimorphic fungi, with differential expression in different growth phases.
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Affiliation(s)
- Susanna K. P. Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Annette Y. P. Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Julian M. Y. Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jessie Bao
- Genome Research Centre, The University of Hong Kong, Hong Kong, China
| | - Na Zhang
- Genome Research Centre, The University of Hong Kong, Hong Kong, China
| | - Si Lok
- Genome Research Centre, The University of Hong Kong, Hong Kong, China
| | - Patrick C. Y. Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- * E-mail: (PCYW); (KYY)
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- * E-mail: (PCYW); (KYY)
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11
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Lau SKP, Woo PCY, Wu Y, Wong AYP, Wong BHL, Lau CCY, Fan RYY, Cai JP, Tsoi HW, Chan KH, Yuen KY. Identification and characterization of a novel paramyxovirus, porcine parainfluenza virus 1, from deceased pigs. J Gen Virol 2013; 94:2184-2190. [PMID: 23918408 DOI: 10.1099/vir.0.052985-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We describe the discovery and characterization of a novel paramyxovirus, porcine parainfluenza virus 1 (PPIV-1), from swine. The virus was detected in 12 (3.1 %) of 386 nasopharyngeal and two (0.7 %) of 303 rectal swab samples from 386 deceased pigs by reverse transcription-PCR, with viral loads of up to 10(6) copies ml(-1). Complete genome sequencing and phylogenetic analysis showed that PPIV-1 represented a novel paramyxovirus within the genus Respirovirus, being most closely related to human parainfluenza virus 1 (HPIV-1) and Sendai virus (SeV). In contrast to HPIV-1, PPIV-1 possessed a mRNA editing function in the phosphoprotein gene. Moreover, PPIV-1 was unique among respiroviruses in having two G residues instead of three to five G residues following the A6 run at the editing site. Nevertheless, PPIV-1, HPIV-1 and SeV share common genomic features and may belong to a separate group within the genus Respirovirus. The presence of PPIV-1 in mainly respiratory samples suggests a possible association with respiratory disease, similar to HPIV-1 and SeV.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China.,Carol Yu Center for Infection, University of Hong Kong, Hong Kong, PR China.,State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, PR China.,Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, PR China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, PR China.,Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, PR China.,Department of Microbiology, University of Hong Kong, Hong Kong, PR China.,Carol Yu Center for Infection, University of Hong Kong, Hong Kong, PR China
| | - Ying Wu
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China
| | - Annette Y P Wong
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China
| | - Beatrice H L Wong
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China
| | - Candy C Y Lau
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China
| | - Rachel Y Y Fan
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China
| | - Jian-Piao Cai
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China
| | - Hoi-Wah Tsoi
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China
| | - Kwok-Hung Chan
- Department of Microbiology, University of Hong Kong, Hong Kong, PR China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, PR China.,Carol Yu Center for Infection, University of Hong Kong, Hong Kong, PR China.,Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, PR China.,Department of Microbiology, University of Hong Kong, Hong Kong, PR China
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12
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Woo PCY, Tsang AKL, Wong AYP, Chen H, Chu J, Lau SKP, Yuen KY. Analysis of multilocus sequence typing schemes for 35 different bacteria revealed that gene loci of 10 bacteria could be replaced to improve cost-effectiveness. Diagn Microbiol Infect Dis 2011; 70:316-23. [PMID: 21558049 DOI: 10.1016/j.diagmicrobio.2011.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/09/2011] [Accepted: 03/09/2011] [Indexed: 11/17/2022]
Abstract
Although multilocus sequence typing (MLST) has been widely used for bacterial typing, the contribution of the gene loci to the discriminatory power of each MLST scheme is unknown. We analyzed the discriminatory powers of 36 MLST schemes using all combinations of the 7 loci and contributions of each locus to the schemes. In 10 schemes, sequencing 6 loci can achieve the discriminatory powers of 7 loci. For the other 26 schemes, the median marginal increase in discriminatory power when 7 instead of 6 loci were used is 0.0004. Sequencing the 7 loci of 50 strains each of Pseudomonas aeruginosa and Acinetobacter baumannii revealed that the discriminatory power for P. aeruginosa was 0.9861 when either 6 (without trp) or 7 loci were used and that for A. baumannii was 0.9363 when 5, 6, or 7 loci were used. Genes that have no additional or minimal contribution to the overall discriminatory powers should be replaced.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.
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13
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Lau SKP, Woo PCY, Wong BHL, Wong AYP, Tsoi HW, Wang M, Lee P, Xu H, Poon RWS, Guo R, Li KSM, Chan KH, Zheng BJ, Yuen KY. Identification and complete genome analysis of three novel paramyxoviruses, Tuhoko virus 1, 2 and 3, in fruit bats from China. Virology 2010; 404:106-16. [PMID: 20537670 PMCID: PMC7111929 DOI: 10.1016/j.virol.2010.03.049] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/03/2010] [Accepted: 03/31/2010] [Indexed: 11/04/2022]
Abstract
Among 489 bats of 11 species in China, three novel paramyxoviruses [Tuhokovirus 1, 2 and 3 (ThkPV-1, ThkPV-2 and ThkPV-3)] were discovered in 15 Leschenault's rousettes. Phylogenetically, the three viruses are most closely related to Menangle and Tioman virus. Genome analysis showed that their 3'-leader sequences are unique by possessing GA instead of AG at the 5th and 6th positions. Unlike Menangle and Tioman virus, key amino acids for neuraminidase activity characteristic of rubulavirus attachment proteins are present. The genome of ThkPV-1 represents the largest rubulavirus genome. Unique features between the three viruses include perfect complementary 5'-trailer and 3'-leader sequence and a unique cysteine pair in attachment protein of ThkPV-1, G at + 1 position in all predicted mRNA sequences of ThkPV-2, and amino acid substitutions in the conserved N-terminal motif of nucleocapsid of ThkPV-3. Analysis of phosphoprotein gene mRNA products confirmed mRNA editing. Antibodies to the viruses were detected in 48–60% of Leschenault's rousettes.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
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