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Li C, Nong W, Boncan DAT, So WL, Yip HY, Swale T, Jia Q, Vicentin IG, Chung G, Bendena WG, Ngo JCK, Chan TF, Lam HM, Hui JHL. Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis. BMC Genomics 2024; 25:327. [PMID: 38565997 PMCID: PMC10985886 DOI: 10.1186/s12864-024-10232-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of food, protein and oil. Hence, it is imperative to maintain or to increase its yield under different conditions including challenges caused by abiotic and biotic stresses. In recent years, the soybean pod-sucking stinkbug Riptortus pedestris has emerged as an important agricultural insect pest in East, South and Southeast Asia. Here, we present a genomics resource for R. pedestris including its genome assembly, messenger RNA (mRNA) and microRNA (miRNA) transcriptomes at different developmental stages and from different organs. As insect hormone biosynthesis genes (genes involved in metamorphosis) and their regulators such as miRNAs are potential targets for pest control, we analyzed the sesquiterpenoid (juvenile) and ecdysteroid (molting) hormone biosynthesis pathway genes including their miRNAs and relevant neuropeptides. Temporal gene expression changes of these insect hormone biosynthesis pathways were observed at different developmental stages. Similarly, a diet-specific response in gene expression was also observed in both head and salivary glands. Furthermore, we observed that microRNAs (bantam, miR-14, miR-316, and miR-263) of R. pedestris fed with different types of soybeans were differentially expressed in the salivary glands indicating a diet-specific response. Interestingly, the opposite arms of miR-281 (-5p and -3p), a miRNA involved in regulating development, were predicted to target Hmgs genes of R. pedestris and soybean, respectively. These observations among others highlight stinkbug's responses as a function of its interaction with soybean. In brief, the results of this study not only present salient findings that could be of potential use in pest management and mitigation but also provide an invaluable resource for R. pedestris as an insect model to facilitate studies on plant-pest interactions.
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Affiliation(s)
- Chade Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Wenyan Nong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Delbert Almerick T Boncan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
| | - Wai Lok So
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Ho Yin Yip
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, 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, PR China
| | - Ignacio G Vicentin
- Instituto Nacional de Tecnologia Agropecuaria, Avenida Rivadavia, Ciudad de Buenos, 1439, Argentina
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, 59626, Korea
| | - William G Bendena
- Department of Biology, Queen's University, 116 Barrie St, Kingston, ON K7L 3N6, Canada
| | - Jacky C K Ngo
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Ting Fung Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Jerome H L Hui
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
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Law STS, Yu Y, Nong W, So WL, Li Y, Swale T, Ferrier DEK, Qiu J, Qian P, Hui JHL. The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes. Proc Biol Sci 2023; 290:20231563. [PMID: 37876192 PMCID: PMC10598428 DOI: 10.1098/rspb.2023.1563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Members of the phylum Cnidaria include sea anemones, corals and jellyfish, and have successfully colonized both marine and freshwater habitats throughout the world. The understanding of how cnidarians adapt to extreme environments such as the dark, high-pressure deep-sea habitat has been hindered by the lack of genomic information. Here, we report the first chromosome-level deep-sea cnidarian genome, of the anemone Actinernus sp., which was 1.39 Gbp in length and contained 44 970 gene models including 14 806 tRNA genes and 30 164 protein-coding genes. Analyses of homeobox genes revealed the longest chromosome hosts a mega-array of Hox cluster, HoxL, NK cluster and NKL homeobox genes; until now, such an array has only been hypothesized to have existed in ancient ancestral genomes. In addition to this striking arrangement of homeobox genes, analyses of microRNAs revealed cnidarian-specific complements that are distinctive for nested clades of these animals, presumably reflecting the progressive evolution of the gene regulatory networks in which they are embedded. Also, compared with other sea anemones, circadian rhythm genes were lost in Actinernus sp., which likely reflects adaptation to living in the dark. This high-quality genome of a deep-sea cnidarian thus reveals some of the likely molecular adaptations of this ecologically important group of metazoans to the extreme deep-sea environment. It also deepens our understanding of the evolution of genome content and organization of animals in general and cnidarians in particular, specifically from the viewpoint of key developmental control genes like the homeobox-encoding genes, where we find an array of genes that until now has only been hypothesized to have existed in the ancient ancestor that pre-dated both the cnidarians and bilaterians.
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Affiliation(s)
- Sean Tsz Sum Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yifei Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Thomas Swale
- Dovetail Genomics, LLC, Scotts Valley, CA 95066, USA
| | - David E. K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Jianwen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Biology, Hong Kong Baptist University, Hong Kong, People's Republic of China
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
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Lee IHT, Nong W, So WL, Cheung CKH, Xie Y, Baril T, Yip HY, Swale T, Chan SKF, Wei Y, Lo N, Hayward A, Chan TF, Lam HM, Hui JHL. The genome and sex-dependent responses to temperature in the common yellow butterfly, Eurema hecabe. BMC Biol 2023; 21:200. [PMID: 37749565 PMCID: PMC10521528 DOI: 10.1186/s12915-023-01703-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Lepidoptera (butterflies and moths) is one of the most geographically widespread insect orders in the world, and its species play important and diverse ecological and applied roles. Climate change is one of the biggest challenges to biodiversity this century, and lepidopterans are vulnerable to climate change. Temperature-dependent gene expression differences are of relevance under the ongoing climate crisis. However, little is known about how climate affects gene expression in lepidopterans and the ecological consequences of this, particularly with respect to genes with biased expression in one of the sexes. The common yellow butterfly, Eurema hecabe (Family Pieridae), is one of the most geographically widespread lepidopterans that can be found in Asia, Africa, and Australia. Nevertheless, what temperature-dependent effects there may be and whether the effects differ between the sexes remain largely unexplored. RESULTS Here, we generated high-quality genomic resources for E. hecabe along with transcriptomes from eight developmental stages. Male and female butterflies were subjected to varying temperatures to assess sex-specific gene expression responses through mRNA and microRNA transcriptomics. We find that there are more temperature-dependent sex-biased genes in females than males, including genes that are involved in a range of biologically important functions, highlighting potential ecological impacts of increased temperatures. Further, by considering available butterfly data on sex-biased gene expression in a comparative genomic framework, we find that the pattern of sex-biased gene expression identified in E. hecabe is highly species-specific, rather than conserved across butterfly species, suggesting that sex-biased gene expression responses to climate change are complex in butterflies. CONCLUSIONS Our study lays the foundation for further understanding of differential responses to environmental stress in a widespread lepidopteran model and demonstrates the potential complexity of sex-specific responses of lepidopterans to climate change.
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Affiliation(s)
- Ivy H T Lee
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Chris K H Cheung
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Yichun Xie
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, 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, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Simon K F Chan
- Agriculture, Fisheries and Conservation Department, Hong Kong, China
| | - Yingying Wei
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong, China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, 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, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China.
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Huang EYY, Law STS, Nong W, Yip HY, Uea-Anuwong T, Magouras I, Hui JHL. The screening for anticoagulant rodenticide gene VKORC1 polymorphism in the rat Rattus norvegicus, Rattus tanezumi and Rattus losea in Hong Kong. Sci Rep 2022; 12:12545. [PMID: 35869096 PMCID: PMC9307595 DOI: 10.1038/s41598-022-16550-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Anticoagulants are a major component of rodenticides used worldwide, which function by effectively blocking the vitamin K cycle in rodents. The rat Vitamin K epoxide Reductase Complex (VKORC) subunit 1 is the enzyme responsible for recycling vitamin K, and five substitution mutations (Tyr139Cys, Tyr139Ser, Tyr139Phe and Leu128Gln and Leu120Gln) located in the VKORC1 could result in resistance to anticoagulant rodenticides. This study carried out a VKORC1-based survey to estimate the anticoagulant rodenticide resistance in three Rattus species (R. losea, R. norvegicus, and R. tanezumi) collected in Hong Kong. A total of 202 rats captured in Hong Kong between 2017 and 2021 were analysed. Sequencing of molecular marker cytochrome c oxidase subunit 1 (COX1) was carried out to assist the species identification, and the identities of 52 lesser ricefield rats (R. losea), 81 common rats (R. norvegicus) and 69 house rats (R. tanezumi) were confirmed. Three VKORC1 exons were amplified from individuals by PCR followed by Sanger sequencing. A total of 47 R. tanezumi (68.1%) contained Tyr139Cys mutation in VKORC1 gene, and half of them were homozygous. None of the collected R. losea and R. norvegicus were detected with the five known substitutions leading to anticoagulant rodenticides resistance, and previously undescribed missense mutations were revealed in each species. Whole genome sequencing was further carried out on some individuals, and single nucleotide polymorphisms (SNPs) were also identified in the introns. This is the first study investigating the situation of anticoagulant rodenticide resistance in the rats collected in Hong Kong. Given that the efficacy of rodenticides is crucial for effective rodent management, regular genetic testing as well as population genomic analyses will be required to both monitor the situation and understand the adaption of different rat haplotypes for integrated pest management. Susceptibility tests for individual rodenticides should also be conducted regularly to assess their effectiveness on local species.
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So WL, Ting KW, Lai SY, Huang EYY, Ma Y, Chong TK, Yip HY, Lee HT, Cheung BCT, Chan MK, Consortium HKSB, Nong W, Law MMS, Lai DYF, Hui JHL. Revealing the millipede and other soil-macrofaunal biodiversity in Hong Kong using a citizen science approach. Biodivers Data J 2022; 10:e82518. [PMID: 36761556 PMCID: PMC9836596 DOI: 10.3897/bdj.10.e82518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 08/16/2022] [Indexed: 11/12/2022] Open
Abstract
Background Soil biodiversity plays important roles in nutrient recycling in both the environment and agriculture. However, they are generally understudied worldwide. To reveal the diversity of soil macrofauna in Hong Kong, here we initiated a citizen science project involving university, non-governmental organisations and secondary school students and teachers. It is envisioned that the citizen science approach used in this study could be used as a demonstration to future biodiversity sampling and monitoring studies. New information Throughout a year of monitoring and species sampling across different localities in Hong Kong, 150 soil macrofaunal morphospecies were collected. Eighty five of them were further identified by morphology and DNA barcoding was assigned to each identified morphospecies, yielding a total of 646 DNA barcodes, with new millipede sequences deposited to the GenBank. The soil macrofauna morphospecies in Hong Kong found in this study are mainly dominated by millipedes (23 out of 150) and oligochaetes (15 out of 150). Amongst the twenty three identified millipedes, two polyxenid millipedes, Monographisqueenslandica Huynh & Veenstra, 2013 and Alloproctoidesremyi Marquet and Condé, 1950 are first recorded in Hong Kong. Information has been curated on an online platform and database (http://biodiversity.sls.cuhk.edu.hk/millipedes). A postcard summarising the findings of millipedes in Hong Kong has also been made as a souvenir and distributed to citizen participants. The identified macrofauna morphospecies and their 646 DNA barcodes in this study established a solid foundation for further research in soil biodiversity.
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Affiliation(s)
- 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, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - Ka Wai Ting
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - Sheung Yee Lai
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - Elaine Yi Ying Huang
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - Yue Ma
- Department of Geography and Resource Management, The Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Geography and Resource Management, The Chinese University of Hong KongHong KongChina
| | - Tze Kiu Chong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - 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, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - 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, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - Billy Chun Ting Cheung
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - Man Ka Chan
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | | | - 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, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
| | - Michelle Man Suet Law
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, ChinaSchool of Life Sciences, The Chinese University of Hong KongHong KongChina
| | - Derrick Yuk Fo Lai
- Department of Geography and Resource Management, The Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Geography and Resource Management, The Chinese University of Hong KongHong KongChina
| | - Jerome Ho Lam 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, ChinaSchool of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongHong KongChina
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Wang L, Xiong Q, Saelim N, Wang L, Nong W, Wan ATY, Shi M, Liu X, Cao Q, Hui JHL, Sookrung N, Leung TF, Tungtrongchitr A, Tsui SKW. Genome assembly and annotation of Periplaneta americana reveal a comprehensive cockroach allergen profile. Allergy 2022; 78:1088-1103. [PMID: 36153808 DOI: 10.1111/all.15531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/12/2021] [Revised: 07/30/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND One of the most common cockroach types in urban areas, the American cockroach (Periplaneta americana) has been reported to impose an increased risk of allergies and asthma. Limited groups of allergens (Per a 1-13) have been identified in this species due to the lack of genome-related information. METHODS To expand the allergen profile of P. americana, genomic, transcriptomic, and proteomic approaches were applied. With the support of a high-quality genome assembled using nanopore, Illumina, and Hi-C sequencing techniques, potential allergens were identified based on protein homology. Then, using enzyme-linked immunosorbent assay, selected allergens were tested in Thai patients allergic to P. americana. RESULTS A chromosomal-level genome of P. americana (3.06 Gb) has been assembled with 94.6% BUSCO completeness, and its contiguity has been significantly improved (N50 = 151 Mb). A comprehensive allergen profile has been characterized, with seven novel groups of allergens, including enolase (Per a 14), cytochrome C (Per a 15), cofilin (Per a 16), alpha-tubulin (Per a 17), cyclophilin (Per a 18), porin3 (Per a 19), and peroxiredoxin-6 (Per a 20), showing IgE-sensitivity in enzyme-linked immunosorbent assay. A new isoallergen of tropomyosin (Per a 7.02) and multiple potential isoallergens of Per a 5 were revealed using bioinformatics and proteomic approaches. Additionally, comparative analysis of P. americana with the closely related Blattodea species revealed the possibility of cross-reaction. CONCLUSION The high-quality genome and proteome of P. americana are beneficial in studying cockroach allergens at the molecular level. Seven novel allergen groups and one isoallergen in Per a 7 were identified.
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Affiliation(s)
- Lingyi Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Nawannaporn Saelim
- Biodesign Innovation Center, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Lin Wang
- School of Biomedical Sciences, 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
| | - Angel Tsz-Yau Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Xiaoyu Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Qin Cao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Jerome Ho Lam 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
| | - Nitat Sookrung
- Biodesign Innovation Center, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ting-Fan Leung
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong
| | - Anchalee Tungtrongchitr
- Biodesign Innovation Center, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Stephen Kwok Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
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7
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Shum CW, Nong W, So WL, Li Y, Qu Z, Yip HY, Swale T, Ang PO, Chan KM, Chan TF, Chu KH, Chui AP, Lau KF, Ngai SM, Xu F, Hui JH. Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration. Front Cell Dev Biol 2022; 10:900321. [PMID: 36072338 PMCID: PMC9444052 DOI: 10.3389/fcell.2022.900321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/08/2022] [Indexed: 12/19/2022] Open
Abstract
Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that are shown to be likely involved in tissue regeneration as in other cnidarians, we have shown that GLWamide neuropeptides, and for the first time sesquiterpenoid pathway genes could potentially be involved in the late phase of cnidarian tissue regeneration. The established sea anemone model will be useful for further investigation of biology and evolution in, and the effect of climate change on this important group of animals.
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Affiliation(s)
- Cheryl W.Y. Shum
- 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
| | - 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
| | - 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, 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
| | - 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
| | - 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
| | - Thomas Swale
- Dovetail Genomics, Scotts Valley, CA, United States
| | - Put O. Ang
- Institute of Space and Earth Information Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - King Ming Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Apple P.Y. Chui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwok Fai Lau
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Sai Ming Ngai
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fei Xu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 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
- *Correspondence: Jerome H.L. Hui,
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8
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Law STS, Nong W, So WL, Baril T, Swale T, Chan CB, Tobe SS, Kai ZP, Bendena WG, Hayward A, Hui JHL. Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees. Genomics 2022; 114:110440. [PMID: 35905835 DOI: 10.1016/j.ygeno.2022.110440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/20/2022] [Revised: 07/13/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
The moth Heortia vitessoides Moore (Lepidoptera: Crambidae) is a major pest of ecologically, commercially and culturally important agarwood-producing trees in the genus Aquilaria. In particular, H. vitessoides is one of the most destructive defoliating pests of the incense tree Aquilaria sinesis, which produces a valuable fragrant wood used as incense and in traditional Chinese medicine [33]. Nevertheless, a genomic resource for H. vitessoides is lacking. Here, we present a chromosomal-level assembly for H. vitessoides, consisting of a 517 megabase (Mb) genome assembly with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). To aid gene annotation, 8 messenger RNA transcriptomes from different developmental stages were generated, and a total of 16,421 gene models were predicted. Expansion of gene families involved in xenobiotic metabolism and development were detected, including duplications of cytosolic sulfotransferase (SULT) genes shared among lepidopterans. In addition, small RNA sequencing of 5 developmental stages of H. vitessoides facilitated the identification of 85 lepidopteran conserved microRNAs, 94 lineage-specific microRNAs, as well as several microRNA clusters. A large proportion of the H. vitessoides genome consists of repeats, with a 29.12% total genomic contribution from transposable elements, of which long interspersed nuclear elements (LINEs) are the dominant component (17.41%). A sharp decrease in the genome-wide percentage of LINEs with lower levels of genetic distance to family consensus sequences suggests that LINE activity has peaked in H. vitessoides. In contrast, opposing patterns suggest a substantial recent increase in DNA and LTR element activity. Together with annotations of essential sesquiterpenoid hormonal pathways, neuropeptides, microRNAs and transposable elements, the high-quality genomic and transcriptomic resources we provide for the economically important moth H. vitessoides provide a platform for the development of genomic approaches to pest management, and contribute to addressing fundamental research questions in Lepidoptera.
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Affiliation(s)
- 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.
| | - 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
| | - 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, China
| | | | | | - Chi Bun Chan
- School of Biological Science, The University of Hong Kong, Hong Kong, China
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Canada
| | - Zhen-Peng Kai
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 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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9
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Chan PL, Lauw S, Ma KL, Kei N, Ma KL, Wong YO, Lam HY, Ting YY, Yau TK, Nong W, Huang D, Xie Y, Cheung PCK, Kwan HS. ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics. Database (Oxford) 2022; 2022:6645125. [PMID: 35849028 PMCID: PMC9290863 DOI: 10.1093/database/baac059] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022]
Abstract
The use of probiotics to improve health via the modulation of gut microbiota has gained wide attention. The growing volume of investigations of probiotic microorganisms and commercialized probiotic products has created the need for a database to organize the health-promoting functions driven by probiotics reported in academic articles, clinical trials and patents. We constructed ProBioQuest to collect up-to-date literature related to probiotics from PubMed.gov, ClinicalTrials.gov and PatentsView. More than 2.8 million articles have been collected. Automated information technology-assisted procedures enabled us to collect the data continuously, providing the most up-to-date information. Statistical functions and semantic analyses are provided on the website as an advanced search engine, which contributes to the semantic tool of this database for information search and analyses. The semantic analytical output provides categorized search results and functions to enhance further analysis. A keyword bank is included which can display multiple tables of contents. Users can select keywords from different displayed categories to achieve easily filtered searches. Additional information on the searched items can be browsed via the link-out function. ProBioQuest is not only useful to scientists and health professionals but also to dietary supplement manufacturers and the general public. In this paper, the method we used to build this database-web system is described. Applications of ProBioQuest for several literature-based analyses of probiotics are included as examples of the various uses of this search engine. ProBioQuest can be accessed free of charge at http://kwanlab.bio.cuhk.edu.hk/PBQ/.
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Affiliation(s)
- Po Lam Chan
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
- HSK GeneTech Limited, Hong Kong Science Park , Shatin, New Territories, Hong Kong
- Food Research Centre, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Susana Lauw
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Ka Lee Ma
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Nelson Kei
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Ka Leong Ma
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
- HSK GeneTech Limited, Hong Kong Science Park , Shatin, New Territories, Hong Kong
| | - Yiu On Wong
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
- HSK GeneTech Limited, Hong Kong Science Park , Shatin, New Territories, Hong Kong
| | - Ho Yan Lam
- HSK GeneTech Limited, Hong Kong Science Park , Shatin, New Territories, Hong Kong
| | - Yee Yung Ting
- Food Research Centre, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Tsz Kwan Yau
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Dandan Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University , Tianjin 300070, China
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Centre for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University , Tianjin 300070, China
| | - Yichun Xie
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Peter Chi Keung Cheung
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
- Food Research Centre, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
- HSK GeneTech Limited, Hong Kong Science Park , Shatin, New Territories, Hong Kong
- Food Research Centre, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
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10
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Xiong Q, Wan ATY, Liu X, Fung CSH, Xiao X, Malainual N, Hou J, Wang L, Wang M, Yang KY, Cui Y, Leung ELH, Nong W, Shin SK, Au SWN, Jeong KY, Chew FT, Hui JHL, Leung TF, Tungtrongchitr A, Zhong N, Liu Z, Tsui SKW. Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations. Mol Biol Evol 2022; 39:6582989. [PMID: 35535514 PMCID: PMC9113151 DOI: 10.1093/molbev/msac097] [Citation(s) in RCA: 7] [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] [Indexed: 11/24/2022] Open
Abstract
Highly diversified astigmatic mites comprise many medically important human household pests such as house dust mites causing ∼1–2% of all allergic diseases globally; however, their evolutionary origin and diverse lifestyles including reversible parasitism have not been illustrated at the genomic level, which hampers allergy prevention and our exploration of these household pests. Using six high-quality assembled and annotated genomes, this study not only refuted the monophyly of mites and ticks, but also thoroughly explored the divergence of Acariformes and the diversification of astigmatic mites. In monophyletic Acariformes, Prostigmata known as notorious plant pests first evolved, and then rapidly evolving Astigmata diverged from soil oribatid mites. Within astigmatic mites, a wide range of gene families rapidly expanded via tandem gene duplications, including ionotropic glutamate receptors, triacylglycerol lipases, serine proteases and UDP glucuronosyltransferases. Gene diversification after tandem duplications provides many genetic resources for adaptation to sensing environmental signals, digestion, and detoxification in rapidly changing household environments. Many gene decay events only occurred in the skin-burrowing parasitic mite Sarcoptes scabiei. Throughout the evolution of Acariformes, massive horizontal gene transfer events occurred in gene families such as UDP glucuronosyltransferases and several important fungal cell wall lytic enzymes, which enable detoxification and digestive functions and provide perfect drug targets for pest control. This comparative study sheds light on the divergent evolution and quick adaptation to human household environments of astigmatic mites and provides insights into the genetic adaptations and even control of human household pests.
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Affiliation(s)
- Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Angel Tsz-Yau Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Xiaoyu Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Cathy Sin-Hang Fung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Xiaojun Xiao
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Nat Malainual
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jinpao Hou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
| | - Lingyi Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Yubao Cui
- Department of Clinical Laboratory, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Elaine Lai-Han Leung
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Soo-Kyung Shin
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | | | - Kyoung Yong Jeong
- Institute of Allergy, Department of Internal Medicine, College of Medicine, Yonsei University, Seoul, Korea
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jerome Ho-Lam Hui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Ting-Fan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong
| | - Anchalee Tungtrongchitr
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhigang Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
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11
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Kong BLH, Nong W, Wong KH, Law STS, So WL, Chan JJS, Zhang J, Lau TWD, Hui JHL, Shaw PC. Chromosomal level genome of Ilex asprella and insight into antiviral triterpenoid pathway. Genomics 2022; 114:110366. [PMID: 35413434 DOI: 10.1016/j.ygeno.2022.110366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 10/14/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
Abstract
Ilex asprella is a widely used herbs in Traditional Chinese Medicine for treating viral infection and relieving inflammation. Due to the earlier fruiting period of I. asprella, it is the major food source for frugivores in summer. Despite its pharmacological and ecological importance, a reference genome for I. asprella is lacking. By using Illumina, stLFR and Omni-C sequencing data, we present the first chromosomal-level assembly for I. asprella. The genome assembly size is 804 Mbp, with Benchmarking Universal Single-Copy Orthologs (BUSCO) score 94.4% for eudicotyledon single copy genes. Transcriptomes of leaves, stems, flowers, premature fruits and roots were analyzed, providing 39,215 gene models. The complete set of genes involved in the triterpenoids production is disclosed for the first time. We have also found the oxidosqualene cyclases (OSCs), CYP716s and UDP-glycosyltransferases (UGTs), which are responsible for the modification of triterpenoid backbones, resulting in the high variety of triterpenoid saponins.
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Affiliation(s)
- Bobby Lim-Ho Kong
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - 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
| | - Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Sean Tsz-Sum 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
| | - 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, China
| | - Johnson Jor-Shing Chan
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jordan Zhang
- Dovetail Genomics, Scotts Valley, CA, United States
| | - Tai-Wai David Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jerome Ho-Lam 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
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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12
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Nong W, Yu Y, Aase-Remedios ME, Xie Y, So WL, Li Y, Wong CF, Baril T, Law STS, Lai SY, Haimovitz J, Swale T, Chen SS, Kai ZP, Sun X, Wu Z, Hayward A, Ferrier DEK, Hui JHL. Genome of the ramshorn snail Biomphalaria straminea-an obligate intermediate host of schistosomiasis. Gigascience 2022; 11:6528774. [PMID: 35166339 PMCID: PMC8848322 DOI: 10.1093/gigascience/giac012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/02/2022] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Schistosomiasis, or bilharzia, is a parasitic disease caused by trematode flatworms of the genus Schistosoma. Infection by Schistosoma mansoni in humans results when cercariae emerge into water from freshwater snails in the genus Biomphalaria and seek out and penetrate human skin. The snail Biomphalaria straminea is native to South America and is now also present in Central America and China, and represents a potential vector host for spreading schistosomiasis. To date, genomic information for the genus is restricted to the neotropical species Biomphalaria glabrata. This limits understanding of the biology and management of other schistosomiasis vectors, such as B. straminea. FINDINGS Using a combination of Illumina short-read, 10X Genomics linked-read, and Hi-C sequencing data, our 1.005 Gb B. straminea genome assembly is of high contiguity, with a scaffold N50 of 25.3 Mb. Transcriptomes from adults were also obtained. Developmental homeobox genes, hormonal genes, and stress-response genes were identified, and repeat content was annotated (40.68% of genomic content). Comparisons with other mollusc genomes (including Gastropoda, Bivalvia, and Cephalopoda) revealed syntenic conservation, patterns of homeobox gene linkage indicative of evolutionary changes to gene clusters, expansion of heat shock protein genes, and the presence of sesquiterpenoid and cholesterol metabolic pathway genes in Gastropoda. In addition, hormone treatment together with RT-qPCR assay reveal a sesquiterpenoid hormone responsive system in B. straminea, illustrating that this renowned insect hormonal system is also present in the lophotrochozoan lineage. CONCLUSION This study provides the first genome assembly for the snail B. straminea and offers an unprecedented opportunity to address a variety of phenomena related to snail vectors of schistosomiasis, as well as evolutionary and genomics questions related to molluscs more widely.
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Affiliation(s)
- Wenyan Nong
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yifei Yu
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Madeleine E Aase-Remedios
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Yichun Xie
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Science, 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 Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Cheuk Fung Wong
- School of Life Science, 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 Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Sheung Yee Lai
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | - Shan-Shan Chen
- Institute of Agro-food Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhen-Peng Kai
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Xi Sun
- Sun Yat-sen University, Guangdong, China
| | | | | | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Jerome H L Hui
- School of Life Science, 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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13
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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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14
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Zhong Z, Nong W, Xie Y, Hui JHL, Chu LM. Long-term effect of plastic feeding on growth and transcriptomic response of mealworms (Tenebrio molitor L.). Chemosphere 2022; 287:132063. [PMID: 34523442 DOI: 10.1016/j.chemosphere.2021.132063] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 05/23/2023]
Abstract
Plastic waste has been considered a serious global environmental problem for decades. Despite the high recalcitrance of synthetic plastics, the biodegradation of polyethylene (PE), polystyrene (PS), polypropylene (PP), and polyvinyl chloride (PVC) by some insect larvae has been reported; however, the mechanism of degradation remains largely unknown. We investigated the effects of plastics on the growth of mealworms (larvae of Tenebrio molitor) and their role in PS and PE degradation. Mealworms were capable of ingesting high-impact polystyrene (HIPS), expanded polystyrene (EPS) and low-density polyethylene (LDPE) but not linear low-density polyethylene (LLDPE) or polypropylene (PP). Plastic consumption was negatively dependent on plastic crystallinity. Transcriptome analysis and KEGG mapping revealed that mealworms act as downstream decomposers in plastic depolymerization and that fatty acid degradation pathways may play important roles in the digestion of plastic degradation intermediates produced by gut bacteria. In addition, PS and PE degradation was achieved via the diffusion of extracellular depolymerases, which probably acted on the distal backbone and produce shorter linear chains that containing ≤16 C atoms instead of branched chains. Additionally, the intermediates of PS degradation are expected to be further decomposed by mealworms as xenobiotics. This study provided a preliminary understanding of plastic degradation mechanism by mealworms.
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Affiliation(s)
- Zheng Zhong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yichun Xie
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Jerome Ho Lam Hui
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Lee Man Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
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15
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So WL, Leung TCN, Nong W, Bendena WG, Ngai SM, Hui JHL. Transcriptomic and proteomic analyses of venom glands from scorpions Liocheles australasiae, Mesobuthus martensii, and Scorpio maurus palmatus. Peptides 2021; 146:170643. [PMID: 34461138 DOI: 10.1016/j.peptides.2021.170643] [Citation(s) in RCA: 3] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022]
Abstract
Scorpion venom contains a cocktail of differing peptides and proteins. Previous studies focused on the identification of species-specific components in scorpion venoms, and whether there could be peptides and/or proteins conserved in the venom gland of a scorpion ancestor has been rarely investigated. Here, using a combination of transcriptomic and proteomic approaches, putative conserved toxins from the venom glands of scorpions Liocheles australasiae, Mesobuthus martensii, and Scorpio maurus palmatus were identified and compared. Similar to other studies, more than half of the conserved toxins are predominantly proteins including proteases. On the other hand, unique venom peptides, including ion channel toxins were revealed specifically in the M. martensii. The sodium channel toxin peptides revealed in M. martensii consolidated that scorpions in the Buthidae are able to envenomate their prey wih highly neurotoxic venom. This study suggested that these conserved proteins had already formed part of the arsenal in the venom gland of the common ancestor of scorpions, and likely perform important functional roles in envenomation during scorpion evolution.
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Affiliation(s)
- 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, China
| | - Thomas C N Leung
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - 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
| | | | - Sai Ming Ngai
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, 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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16
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Lin Z, Xie Y, Nong W, Ren X, Li R, Zhao Z, Hui JHL, Yuen KWY. Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization. Nucleic Acids Res 2021; 49:9174-9193. [PMID: 34417622 PMCID: PMC8450109 DOI: 10.1093/nar/gkab690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 02/21/2020] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 11/14/2022] Open
Abstract
To investigate how exogenous DNA concatemerizes to form episomal artificial chromosomes (ACs), acquire equal segregation ability and maintain stable holocentromeres, we injected DNA sequences with different features, including sequences that are repetitive or complex, and sequences with different AT-contents, into the gonad of Caenorhabditis elegans to form ACs in embryos, and monitored AC mitotic segregation. We demonstrated that AT-poor sequences (26% AT-content) delayed the acquisition of segregation competency of newly formed ACs. We also co-injected fragmented Saccharomyces cerevisiae genomic DNA, differentially expressed fluorescent markers and ubiquitously expressed selectable marker to construct a less repetitive, more complex AC. We sequenced the whole genome of a strain which propagates this AC through multiple generations, and de novo assembled the AC sequences. We discovered CENP-AHCP-3 domains/peaks are distributed along the AC, as in endogenous chromosomes, suggesting a holocentric architecture. We found that CENP-AHCP-3 binds to the unexpressed marker genes and many fragmented yeast sequences, but is excluded in the yeast extremely high-AT-content centromeric and mitochondrial DNA (> 83% AT-content) on the AC. We identified A-rich motifs in CENP-AHCP-3 domains/peaks on the AC and on endogenous chromosomes, which have some similarity with each other and similarity to some non-germline transcription factor binding sites.
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Affiliation(s)
- Zhongyang Lin
- School of Biological Sciences, the University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Yichun Xie
- 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
| | - Xiaoliang Ren
- Department of Biology, Baptist University of Hong Kong, Sir Run Run Shaw Building, Ho Sin Hang Campus, Kowloon Tong, Hong Kong
| | - Runsheng Li
- Department of Biology, Baptist University of Hong Kong, Sir Run Run Shaw Building, Ho Sin Hang Campus, Kowloon Tong, Hong Kong
| | - Zhongying Zhao
- Department of Biology, Baptist University of Hong Kong, Sir Run Run Shaw Building, Ho Sin Hang Campus, Kowloon Tong, Hong Kong
| | - Jerome Ho Lam 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
| | - Karen Wing Yee Yuen
- School of Biological Sciences, the University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
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17
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Vong KI, Ma TC, Li B, Leung TCN, Nong W, Ngai SM, Hui JHL, Jiang L, Kwan KM. SOX9-COL9A3-dependent regulation of choroid plexus epithelial polarity governs blood-cerebrospinal fluid barrier integrity. Proc Natl Acad Sci U S A 2021; 118:e2009568118. [PMID: 33526661 PMCID: PMC8017668 DOI: 10.1073/pnas.2009568118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Indexed: 01/15/2023] Open
Abstract
The choroid plexus (CP) is an extensively vascularized neuroepithelial tissue that projects into the brain ventricles. The restriction of transepithelial transport across the CP establishes the blood-cerebrospinal fluid (CSF) barrier that is fundamental to the homeostatic regulation of the central nervous system microenvironment. However, the molecular mechanisms that control this process remain elusive. Here we show that the genetic ablation of Sox9 in the hindbrain CP results in a hyperpermeable blood-CSF barrier that ultimately upsets the CSF electrolyte balance and alters CSF protein composition. Mechanistically, SOX9 is required for the transcriptional up-regulation of Col9a3 in the CP epithelium. The reduction of Col9a3 expression dramatically recapitulates the blood-CSF barrier defects of Sox9 mutants. Loss of collagen IX severely disrupts the structural integrity of the epithelial basement membrane in the CP, leading to progressive loss of extracellular matrix components. Consequently, this perturbs the polarized microtubule dynamics required for correct orientation of apicobasal polarity and thereby impedes tight junction assembly in the CP epithelium. Our findings reveal a pivotal cascade of SOX9-dependent molecular events that is critical for construction of the blood-CSF barrier.
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Affiliation(s)
- Keng Ioi Vong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Tsz Ching Ma
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Baiying Li
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Thomas Chun Ning Leung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Sai Ming Ngai
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Jerome Ho Lam Hui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Liwen Jiang
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
- Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Kin Ming Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China;
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
- Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
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18
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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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19
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Leung TCN, Qu Z, Nong W, Hui JHL, Ngai SM. Proteomic Analysis of the Venom of Jellyfishes Rhopilema esculentum and Sanderia malayensis. Mar Drugs 2020; 18:md18120655. [PMID: 33371176 PMCID: PMC7766711 DOI: 10.3390/md18120655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 11/27/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
Venomics, the study of biological venoms, could potentially provide a new source of therapeutic compounds, yet information on the venoms from marine organisms, including cnidarians (sea anemones, corals, and jellyfish), is limited. This study identified the putative toxins of two species of jellyfish—edible jellyfish Rhopilema esculentum Kishinouye, 1891, also known as flame jellyfish, and Amuska jellyfish Sanderia malayensis Goette, 1886. Utilizing nano-flow liquid chromatography tandem mass spectrometry (nLC–MS/MS), 3000 proteins were identified from the nematocysts in each of the above two jellyfish species. Forty and fifty-one putative toxins were identified in R. esculentum and S. malayensis, respectively, which were further classified into eight toxin families according to their predicted functions. Amongst the identified putative toxins, hemostasis-impairing toxins and proteases were found to be the most dominant members (>60%). The present study demonstrates the first proteomes of nematocysts from two jellyfish species with economic and environmental importance, and expands the foundation and understanding of cnidarian toxins.
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Affiliation(s)
- Thomas C. N. Leung
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
| | - Zhe Qu
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (Z.Q.); (W.N.)
| | - Wenyan Nong
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (Z.Q.); (W.N.)
| | - Jerome H. L. Hui
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (Z.Q.); (W.N.)
- Correspondence: (J.H.L.H.); (S.M.N.)
| | - Sai Ming Ngai
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
- Correspondence: (J.H.L.H.); (S.M.N.)
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20
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Qu Z, Nong W, Yu Y, Baril T, Yip HY, Hayward A, Hui JHL. Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae). BMC Genomics 2020; 21:726. [PMID: 33076831 PMCID: PMC7574432 DOI: 10.1186/s12864-020-07145-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/06/2020] [Accepted: 10/12/2020] [Indexed: 12/02/2022] Open
Abstract
Background Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Additionally, the four-finger threadfin Eleutheronema tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is classified as endangered. However, no genomic resources are currently available for the threadfin family Polynemidae. Results We sequenced and assembled the first threadfin fish genome, the four-finger threadfin E. tetradactylum. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date. Just 9.07–10.91% of the genome sequence was found to consist of repetitive elements (standard RepeatMasker analysis vs custom analysis), making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, and we include analyses of developmental transcription factors, including the Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs. Conclusions The four-finger threadfin E. tetradactylum genome presented here represents the first available genome sequence for the ecologically, biologically, and commercially important clade of threadfin fish. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this valuable group of food fish. Supplementary information Supplementary information accompanies this paper at 10.1186/s12864-020-07145-1.
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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, China.
| | - 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
| | - Yifei Yu
- 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 Campus, Penryn, Cornwall, Exeter, TR10 9FE, UK
| | - 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
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, Exeter, TR10 9FE, 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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21
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Huang D, Yi X, Zhou Y, Yao H, Xu H, Wang J, Zhang S, Nong W, Wang P, Shi L, Xuan C, Li M, Wang J, Li W, Kwan HS, Sham PC, Wang K, Li MJ. Ultrafast and scalable variant annotation and prioritization with big functional genomics data. Genome Res 2020; 30:1789-1801. [PMID: 33060171 PMCID: PMC7706736 DOI: 10.1101/gr.267997.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 06/28/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
The advances of large-scale genomics studies have enabled compilation of cell type–specific, genome-wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole-genome sequencing variants against a huge database with billions of genomic features. Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex functional annotation resources. Equipped with a novel index system and a parallel random-sweep searching algorithm, VarNote shows substantial performance improvements (two to three orders of magnitude) over existing algorithms at different scales. It supports both region-based and allele-specific annotations and introduces advanced functions for the flexible extraction of annotations. By integrating massive base-wise and context-dependent annotations in the VarNote framework, we introduce three efficient and accurate pipelines to prioritize the causal regulatory variants for common diseases, Mendelian disorders, and cancers.
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Affiliation(s)
- Dandan Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Hang Xu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jianhua Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Shijie Zhang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Panwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona 85259, USA
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chenghao Xuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Miaoxin Li
- Center for Genome Research, Center for Precision Medicine, Zhongshan School of Medicine, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Junwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona 85259, USA
| | - Weidong Li
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Pak Chung Sham
- Centre of Genomics Sciences, Departments of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Mulin Jun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
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22
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Li Y, Nong W, Baril T, Yip HY, Swale T, Hayward A, Ferrier DEK, Hui JHL. Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome. BMC Genomics 2020; 21:713. [PMID: 33059600 PMCID: PMC7566022 DOI: 10.1186/s12864-020-07027-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 05/01/2020] [Accepted: 08/25/2020] [Indexed: 12/31/2022] Open
Abstract
Background Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians. Results Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~ 758 Mb, scaffold N50 = 72.3 Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al. (Mol Ecol Resources, 2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages. Conclusions The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.
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Affiliation(s)
- Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, 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, Shatin, Hong Kong
| | - Tobias Baril
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, UK
| | - 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, Shatin, Hong Kong
| | | | - Alexander Hayward
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, UK.
| | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Martine Laboratory, University of St. Andrews, St Andrews, 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, Shatin, Hong Kong.
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23
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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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24
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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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25
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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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26
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Ng HM, Ho JCH, Nong W, Hui JHL, Lai KP, Wong CKC. Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica. BMC Genomics 2020; 21:208. [PMID: 32131732 PMCID: PMC7057501 DOI: 10.1186/s12864-020-6630-0] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 12/28/2022] Open
Abstract
Background Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-establishment of fluid and electrolyte homeostasis. The osmoregulatory plasticity of gills provides an excellent model to study the role of microRNAs (miRs) in adaptive osmotic responses. The present study is to characterize an ex-vivo gill filament culture and using omics approach, to decipher the interaction between tonicity-responsive miRs and gene targets, in orchestrating the osmotic stress-induced responses. Results Ex-vivo gill filament culture was exposed to Leibovitz’s L-15 medium (300 mOsmol l− 1) or the medium with an adjusted osmolality of 600 mOsmol l− 1 for 4, 8 and 24 h. Hypertonic responsive genes, including osmotic stress transcriptional factor, Na+/Cl−-taurine transporter, Na+/H+ exchange regulatory cofactor, cystic fibrosis transmembrane regulator, inward rectifying K+ channel, Na+/K+-ATPase, and calcium-transporting ATPase were significantly upregulated, while the hypo-osmotic gene, V-type proton ATPase was downregulated. The data illustrated that the ex-vivo gill filament culture exhibited distinctive responses to hyperosmotic challenge. In the hyperosmotic treatment, four key factors (i.e. drosha RNase III endonuclease, exportin-5, dicer ribonuclease III and argonaute-2) involved in miR biogenesis were dysregulated (P < 0.05). Transcriptome and miR-sequencing of gill filament samples at 4 and 8 h were conducted and two downregulated miRs, miR-29b-3p and miR-200b-3p were identified. An inhibition of miR-29b-3p and miR-200b-3p in primary gill cell culture led to an upregulation of 100 and 93 gene transcripts, respectively. Commonly upregulated gene transcripts from the hyperosmotic experiments and miR-inhibition studies, were overlaid, in which two miR-29b-3p target-genes [Krueppel-like factor 4 (klf4), Homeobox protein Meis2] and one miR-200b-3p target-gene (slc17a5) were identified. Integrated miR-mRNA-omics analysis revealed the specific binding of miR-29b-3p on Klf4 and miR-200b-3p on slc17a5. The target-genes are known to regulate differentiation of gill ionocytes and cellular osmolality. Conclusions In this study, we have characterized the hypo-osmoregulatory responses and unraveled the modulation of miR-biogenesis factors/the dysregulation of miRs, using ex-vivo gill filament culture. MicroRNA-messenger RNA interactome analysis of miR-29b-3p and miR-200b-3p revealed the gene targets are essential for osmotic stress responses.
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Affiliation(s)
- Hoi Man Ng
- Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon Tong, HKSAR, Hong Kong
| | - Jeff Cheuk Hin Ho
- Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon Tong, HKSAR, 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, Shatin, HKSAR, Hong Kong
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Keng Po Lai
- Guanxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, 541004, People's Republic of China.
| | - Chris Kong Chu Wong
- Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon Tong, HKSAR, Hong Kong.
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Nong W, Chai ZYH, Jiang X, Qin J, Ma KY, Chan KM, Chan TF, Chow BKC, Kwan HS, Wong CKC, Qiu JW, Hui JHL, Chu KH. A crustacean annotated transcriptome (CAT) database. BMC Genomics 2020; 21:32. [PMID: 31918660 PMCID: PMC6953184 DOI: 10.1186/s12864-019-6433-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 10/03/2019] [Accepted: 12/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Decapods are an order of crustaceans which includes shrimps, crabs, lobsters and crayfish. They occur worldwide and are of great scientific interest as well as being of ecological and economic importance in fisheries and aquaculture. However, our knowledge of their biology mainly comes from the group which is most closely related to crustaceans - insects. Here we produce a de novo transcriptome database, crustacean annotated transcriptome (CAT) database, spanning multiple tissues and the life stages of seven crustaceans. DESCRIPTION A total of 71 transcriptome assemblies from six decapod species and a stomatopod species, including the coral shrimp Stenopus hispidus, the cherry shrimp Neocaridina davidi, the redclaw crayfish Cherax quadricarinatus, the spiny lobster Panulirus ornatus, the red king crab Paralithodes camtschaticus, the coconut crab Birgus latro, and the zebra mantis shrimp Lysiosquillina maculata, were generated. Differential gene expression analyses within species were generated as a reference and included in a graphical user interface database at http://cat.sls.cuhk.edu.hk/. Users can carry out gene name searches and also access gene sequences based on a sequence query using the BLAST search function. CONCLUSIONS The data generated and deposited in this database offers a valuable resource for the further study of these crustaceans, as well as being of use in aquaculture development.
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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
| | - Zacary Y H Chai
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaosen Jiang
- School of Future Technology, University of Chinese Academy of Sciences, Hong Kong, China
| | - Jing Qin
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Ka Yan Ma
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, The Chinese University of Hong Kong, Hong Kong, China
| | - King Ming Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Billy K C Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chris K C Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, 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.
| | - Ka Hou Chu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, The Chinese University of Hong Kong, Hong Kong, China
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28
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Yang X, Brobst D, Chan WS, Tse MCL, Herlea-Pana O, Ahuja P, Bi X, Zaw AM, Kwong ZSW, Jia WH, Zhang ZG, Zhang N, Chow SKH, Cheung WH, Louie JCY, Griffin TM, Nong W, Hui JHL, Du GH, Noh HL, Saengnipanthkul S, Chow BKC, Kim JK, Lee CW, Chan CB. Muscle-generated BDNF is a sexually dimorphic myokine that controls metabolic flexibility. Sci Signal 2019; 12:12/594/eaau1468. [PMID: 31409756 DOI: 10.1126/scisignal.aau1468] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability of skeletal muscle to switch between lipid and glucose oxidation for ATP production during metabolic stress is pivotal for maintaining systemic energy homeostasis, and dysregulation of this metabolic flexibility is a dominant cause of several metabolic disorders. However, the molecular mechanism that governs fuel selection in muscle is not well understood. Here, we report that brain-derived neurotrophic factor (BDNF) is a fasting-induced myokine that controls metabolic reprograming through the AMPK/CREB/PGC-1α pathway in female mice. Female mice with a muscle-specific deficiency in BDNF (MBKO mice) were unable to switch the predominant fuel source from carbohydrates to fatty acids during fasting, which reduced ATP production in muscle. Fasting-induced muscle atrophy was also compromised in female MBKO mice, likely a result of autophagy inhibition. These mutant mice displayed myofiber necrosis, weaker muscle strength, reduced locomotion, and muscle-specific insulin resistance. Together, our results show that muscle-derived BDNF facilitates metabolic adaption during nutrient scarcity in a gender-specific manner and that insufficient BDNF production in skeletal muscle promotes the development of metabolic myopathies and insulin resistance.
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Affiliation(s)
- Xiuying Yang
- Department of Physiology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., BMSB 634, Oklahoma City, OK 73104, USA.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, Beijing 100050, China
| | - Daniel Brobst
- Department of Physiology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., BMSB 634, Oklahoma City, OK 73104, USA
| | - Wing Suen Chan
- School of Biological Sciences, The University of Hong Kong, 6N01 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Margaret Chui Ling Tse
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Oana Herlea-Pana
- Department of Physiology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., BMSB 634, Oklahoma City, OK 73104, USA
| | - Palak Ahuja
- School of Biological Sciences, The University of Hong Kong, 6N01 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Xinyi Bi
- School of Biological Sciences, The University of Hong Kong, 6N01 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Aung Moe Zaw
- School of Biological Sciences, The University of Hong Kong, 6N01 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong.,Department of Chemical Engineering, University of Waterloo, ON N2L 3G1, Canada
| | - Zara Sau Wa Kwong
- School of Biological Sciences, The University of Hong Kong, 6N01 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Wei-Hua Jia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, Beijing 100050, China
| | - Zhong-Gou Zhang
- Department of Colorectal Cancer Oncological Surgery, Large-Scale Data Analysis Center of Cancer Precision Medicine, Cancer Hospital of Chinese Medical University, Liaoning Provincial Cancer Institute and Hospital, Shenyang 110042, China
| | - Ning Zhang
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, 5/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Shatin, Hong Kong
| | - Simon Kwoon Ho Chow
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, 5/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Shatin, Hong Kong
| | - Wing Hoi Cheung
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, 5/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Shatin, Hong Kong
| | - Jimmy Chun Yu Louie
- School of Biological Sciences, The University of Hong Kong, 6N01 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Timothy M Griffin
- Department of Physiology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., BMSB 634, Oklahoma City, OK 73104, USA.,Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Wenyan Nong
- School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jerome Ho Lam Hui
- School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Guan-Hua Du
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, Beijing 100050, China
| | - Hye Lim Noh
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Suchaorn Saengnipanthkul
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Billy K C Chow
- School of Biological Sciences, The University of Hong Kong, 6N01 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Jason K Kim
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Chi Wai Lee
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.
| | - Chi Bun Chan
- School of Biological Sciences, The University of Hong Kong, 6N01 Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong. .,State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong
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29
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Wang Q, Zhang J, Li C, Wang B, Nong W, Bian Y, Xiao Y. Phenotypic and Genetic Diversity of the Culinary-Medicinal Winter Mushroom Flammulina velutipes (Agaricomycetes) in China. Int J Med Mushrooms 2018; 20:517-536. [PMID: 29953349 DOI: 10.1615/intjmedmushrooms.2018026253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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]
Abstract
Flammulina velutipes is one of the mushrooms produced most widely in East Asia. In this study we investigated phenotypic variations of 7 agronomic traits in 37 F. velutipes strains from China, and we analyzed their genetic diversity with 70 simple sequence repeat markers. The Shannon information index and gene diversity were 0.894 and 0.478, respectively, demonstrating high genetic variation among the tested strains. Poor genetic variation was found among white strains, in contrast to yellow ones. Analysis of population structure resolved 2 unambiguous genetic groups in the tested F. velutipes strains, with little differentiation between them (FST = 0.016). Yellow cultivars possibly originated from indigenous wild strains in southwest China. Phenotypic correlations were identified among the 7 traits. In particular, stipe length (SL) was significantly positively correlated with yield, indicating that SL could be used as an index for breeding high-yield strains. The 2 genetic groups, and white strains and yellow ones, showed significant differences between SL, yield, and the time interval (days) from mycelial scratch to formation of the first fruiting body. These results indicate that these 3 traits were stratified by population structure. Detection of genetic and phenotypic variations would lay the groundwork for further breeding of elite F. velutipes strains.
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Affiliation(s)
- Qiuying Wang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jingcheng Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Bo Wang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, People's Republic of China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, People's Republic of China
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30
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Qu Z, Bendena WG, Nong W, Siggens KW, Noriega FG, Kai ZP, Zang YY, Koon AC, Chan HYE, Chan TF, Chu KH, Lam HM, Akam M, Tobe SS, Lam Hui JH. MicroRNAs regulate the sesquiterpenoid hormonal pathway in Drosophila and other arthropods. Proc Biol Sci 2018; 284:rspb.2017.1827. [PMID: 29237851 DOI: 10.1098/rspb.2017.1827] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 08/16/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022] Open
Abstract
Arthropods comprise the majority of all described animal species, and understanding their evolution is a central question in biology. Their developmental processes are under the precise control of distinct hormonal regulators, including the sesquiterpenoids juvenile hormone (JH) and methyl farnesoate. The control of the synthesis and mode of action of these hormones played important roles in the evolution of arthropods and their adaptation to diverse habitats. However, the precise roles of non-coding RNAs, such as microRNAs (miRNAs), controlling arthropod hormonal pathways are unknown. Here, we investigated the miRNA regulation of the expression of the juvenile hormone acid methyltransferase gene (JHAMT), which encodes a rate-determining sesquiterpenoid biosynthetic enzyme. Loss of function of the miRNA bantam in the fly Drosophila melanogaster increased JHAMT expression, while overexpression of the bantam repressed JHAMT expression and resulted in pupal lethality. The male genital organs of the pupae were malformed, and exogenous sesquiterpenoid application partially rescued the genital deformities. The role of the bantam in the regulation of sesquiterpenoid biosynthesis was validated by transcriptomic, qPCR and hormone titre (JHB3 and JH III) analyses. In addition, we found a conserved set of miRNAs that interacted with JHAMT, and the sesquiterpenoid receptor methoprene-tolerant (Met) in different arthropod lineages, including insects (fly, mosquito and beetle), crustaceans (water flea and shrimp), myriapod (centipede) and chelicerate (horseshoe crab). This suggests that these miRNAs might have conserved roles in the post-transcriptional regulation of genes in sesquiterpenoid pathways across the Panarthropoda. Some of the identified lineage-specific miRNAs are potential targets for the development of new strategies in aquaculture and agricultural pest control.
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Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | | | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | | | - Fernando G Noriega
- Department of Biological Sciences and Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Zhen-Peng Kai
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, People's Republic of China
| | - Yang-Yang Zang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, People's Republic of China
| | - Alex C Koon
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Ho Yin Edwin Chan
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Ting Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Hon Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Michael Akam
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada M5S 3G5
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
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31
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Zeng X, Yiu WC, Cheung KH, Yip HY, Nong W, He P, Yuan D, Rollinson D, Qiu JW, Fung MC, Wu Z, Hui JHL. Distribution and current infection status of Biomphalaria straminea in Hong Kong. Parasit Vectors 2017; 10:351. [PMID: 28743308 PMCID: PMC5526268 DOI: 10.1186/s13071-017-2285-3] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/12/2017] [Indexed: 03/11/2023] Open
Abstract
Background Schistosomiasis, also generally known as snail fever, is a parasitic disease caused by trematode flatworms of the genus Schistosoma. In Hong Kong and mainland China, the freshwater snail Biomphalaria straminea has been introduced and has the potential to transmit intestinal schistosomiasis caused by S. mansoni, a parasite of man which has a wide distribution in Africa and parts of the New World, especially Brazil. The first identification of B. straminea in Hong Kong dates back to the 1970s, and its geographical distribution, phylogenetic relationships, and infection status have not been updated for more than 30 years. Thus, this study aims to reveal the distribution and current infection status of B. straminea in contemporary Hong Kong. Methods Snails were collected from different parts of Hong Kong from July 2016 to January 2017. Both anatomical and molecular methods were applied to identify B. straminea. Cytochrome c oxidase subunit 1 (cox1), internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), and 16S ribosomal DNA (rDNA) were sequenced from individual snails and analyzed. To detect the presence of S. mansoni, both biopsy and PCR analyses were carried out. Results Using both anatomical and molecular analyses, this study demonstrated the existence of black- and red-coloured shell B. straminea in different districts in the New Territories in Hong Kong, including places close to the mainland China border. None of the B. straminea (n = 87) investigated were found to be infected with S. mansoni when tested by biopsy and PCR. The Hong Kong B. straminea are genetically indistinguishable, based on the chosen molecular markers (cox1, ITS1-5.8S-ITS2, and 16S rDNA), and are similar to those obtained in mainland China and South America. Conclusion Biomphalaria straminea is now well established in freshwater habitats in Hong Kong. No evidence of infection with S. mansoni has been found. Surveillance should be continued to monitor and better understand this schistosomiasis intermediate host in mainland China and Hong Kong. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2285-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Zeng
- School of Life Science, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.,Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, People's Republic of China.,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, Guangdong Province, People's Republic of China
| | - Wing Chung Yiu
- School of Life Science, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Kwan Ho Cheung
- School of Life Science, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Ho Yin Yip
- School of Life Science, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Wenyan Nong
- School of Life Science, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Ping He
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, People's Republic of China.,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, Guangdong Province, People's Republic of China
| | - Dongjuan Yuan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, People's Republic of China.,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, Guangdong Province, People's Republic of China
| | - David Rollinson
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, Special Administrative Region, People's Republic of China
| | - Ming Chiu Fung
- School of Life Science, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, Guangdong Province, People's Republic of China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, People's Republic of China. .,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, Guangdong Province, People's Republic of China.
| | - Jerome Ho Lam Hui
- School of Life Science, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.
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32
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Sun J, Zhang Y, Xu T, Zhang Y, Mu H, Zhang Y, Lan Y, Fields CJ, Hui JHL, Zhang W, Li R, Nong W, Cheung FKM, Qiu JW, Qian PY. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nat Ecol Evol 2017; 1:121. [PMID: 28812709 DOI: 10.1038/s41559-017-0121] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/16/2017] [Indexed: 01/08/2023]
Abstract
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro-benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The innate immune system of B. platifrons is considerably more complex than that of other lophotrochozoan species, including M. philippinarum, with substantial expansion and high expression levels of gene families that are related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons shows methanotrophy, assimilatory sulfate reduction and ammonia metabolic pathways in the symbionts, providing energy and nutrients, which allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.
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Affiliation(s)
- Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.,Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yu Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Science, Shenzhen University, Shenzhen, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yi Lan
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Christopher J Fields
- High Performance Computing in Biology, Roy J. Carver Biotechnology Centre, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jerome Ho Lam Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Wenyan Nong
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Fiona Ka Man Cheung
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.,HKUST-CAS Joint Laboratory, Sanya Institute of Deep Sea Science and Engineering, Sanya 572000, China
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33
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Li C, Gong W, Zhang L, Yang Z, Nong W, Bian Y, Kwan HS, Cheung MK, Xiao Y. Association Mapping Reveals Genetic Loci Associated with Important Agronomic Traits in Lentinula edodes, Shiitake Mushroom. Front Microbiol 2017; 8:237. [PMID: 28261189 PMCID: PMC5314409 DOI: 10.3389/fmicb.2017.00237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 08/26/2016] [Accepted: 02/03/2017] [Indexed: 12/28/2022] Open
Abstract
Association mapping is a robust approach for the detection of quantitative trait loci (QTLs). Here, by genotyping 297 genome-wide molecular markers of 89 Lentinula edodes cultivars in China, the genetic diversity, population structure and genetic loci associated with 11 agronomic traits were examined. A total of 873 alleles were detected in the tested strains with a mean of 2.939 alleles per locus, and the Shannon's information index was 0.734. Population structure analysis revealed two robustly differentiated groups among the Chinese L. edodes cultivars (FST = 0.247). Using the mixed linear model, a total of 43 markers were detected to be significantly associated with four traits. The number of markers associated with traits ranged from 9 to 26, and the phenotypic variations explained by each marker varied from 12.07% to 31.32%. Apart from five previously reported markers, the remaining 38 markers were newly reported here. Twenty-one markers were identified as simultaneously linked to two to four traits, and five markers were associated with the same traits in cultivation tests performed in two consecutive years. The 43 traits-associated markers were related to 97 genes, and 24 of them were related to 10 traits-associated markers detected in both years or identified previously, 13 of which had a >2-fold expression change between the mycelium and primordium stages. Our study has provided candidate markers for marker-assisted selection (MAS) and useful clues for understanding the genetic architecture of agronomic traits in the shiitake mushroom.
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Affiliation(s)
- Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Wenbing Gong
- Institute of Applied Mycology, Huazhong Agricultural UniversityHubei, China; Institute of Bast Fiber Crops, Chinese Academy of Agricultural SciencesChangsha, China
| | - Lin Zhang
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Zhiquan Yang
- College of Informatics, Huazhong Agricultural University Hubei, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Hoi-Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Man-Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
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34
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Xiao Y, Cheng X, Liu J, Li C, Nong W, Bian Y, Cheung MK, Kwan HS. Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China. Sci Rep 2016; 6:36789. [PMID: 27830835 PMCID: PMC5103288 DOI: 10.1038/srep36789] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 06/08/2016] [Accepted: 09/26/2016] [Indexed: 01/06/2023] Open
Abstract
The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China.
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Affiliation(s)
- Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China.,School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Xuanjin Cheng
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Jun Liu
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
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35
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36
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Kenny NJ, Chan KW, Nong W, Qu Z, Maeso I, Yip HY, Chan TF, Kwan HS, Holland PWH, Chu KH, Hui JHL. Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs. Heredity (Edinb) 2016; 116:190-9. [PMID: 26419336 PMCID: PMC4806888 DOI: 10.1038/hdy.2015.89] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 01/03/2023] Open
Abstract
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
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Affiliation(s)
- N J Kenny
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - K W Chan
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - W Nong
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - Z Qu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - I Maeso
- Centro Andaluz de Biología del
Desarrollo (CABD), Consejo Superior de Investigaciones
Científicas/Universidad Pablo de Olavide, Sevilla,
Spain
| | - H Y Yip
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - T F Chan
- School of Life Sciences, Center of
Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - H S Kwan
- School of Life Sciences, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - P W H Holland
- Department of Zoology, University of
Oxford, Oxford, UK
| | - K H Chu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, The Chinese University of Hong Kong,
Shatin, Hong Kong
| | - J H L Hui
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
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37
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Cheung MK, Yip HY, Nong W, Law PTW, Chu KH, Kwan HS, Hui JHL. Rapid Change of Microbiota Diversity in the Gut but Not the Hepatopancreas During Gonadal Development of the New Shrimp Model Neocaridina denticulata. Mar Biotechnol (NY) 2015; 17:811-819. [PMID: 26319409 DOI: 10.1007/s10126-015-9662-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
During evolution of animals, their co-evolution with bacteria has generally been ignored. Recent studies have provided evidences that the symbiotic bacteria in the animal gut can either be essential or contributing to the plasticity of the host. The Crustacea includes crab, crayfish, lobster, and shrimp and represents the second largest subphylum on the planet. Although there are already studies investigating the intestinal bacterial communities in crustaceans, none of them has examined the microbiota in different parts of the digestive system during the gonad development of the host. Here, we utilized a new shrimp model Neocaridina denticulata and sequenced the 16S rRNA using the Ion Torrent platform to survey the bacterial populations colonizing the hepatopancreas, foregut, and intestine, including midgut and hindgut, of the early, mid, and late ovarian maturation stages of the shrimp. The predominant bacteria phylum was found to be Proteobacteria, with more than 80 % reads from the gut flora at the early gonad development belonged to a Coxiella-type bacterium. Distinct bacterial communities can be detected between the hepatopancreas and gut, although no significant difference could be revealed between the different regions of the gut investigated. Surprisingly, during the gonad development, bacterial diversity changed rapidly in the gut but not the hepatopancreas. This study provides the first evidence that microbiota modified differentially in specific regions of the digestive tract during gonadal development of crustaceans.
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Affiliation(s)
- Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Ho Yin Yip
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Wenyan Nong
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Patrick Tik Wan Law
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
- The Nethersole School of Nursing, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Jerome Ho Lam Hui
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR.
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Nong W, Xie TS, Li LY, Lu AG, Mo J, Gou YF, Lan G, Jiang H, Len J, Li MM, Jiang QY, Huang B. Qualitative Analyses of Protein Phosphorylation in Bovine Pluripotent Stem Cells Generated from Embryonic Fibroblasts. Reprod Domest Anim 2015; 50:989-98. [DOI: 10.1111/rda.12619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 09/07/2015] [Indexed: 12/19/2022]
Affiliation(s)
- W Nong
- College of Animal Science and Technology; Guangxi University; Nanning China
- Guangxi University of Chinese Medicine; Nanning China
| | - TS Xie
- College of Animal Science and Technology; Guangxi University; Nanning China
- Nanning Languang Biotechnology Inc.; Nanning China
| | - LY Li
- College of Animal Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources; Guangxi University; Nanning China
| | - AG Lu
- College of Animal Science and Technology; Guangxi University; Nanning China
- Guangxi Analysis and Testing Center; Nanning China
| | - J Mo
- Guangxi Analysis and Testing Center; Nanning China
| | - YF Gou
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - G Lan
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - H Jiang
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - J Len
- Guangxi University of Chinese Medicine; Nanning China
| | - MM Li
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - QY Jiang
- College of Animal Science and Technology; Guangxi University; Nanning China
| | - B Huang
- College of Animal Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources; Guangxi University; Nanning China
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Cheng CK, Cheung MK, Nong W, Law PTW, Qin J, Ling JML, Kam KM, Cheung WMW, Kwan HS. Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong. BMC Genomics 2015; 16:688. [PMID: 26370680 PMCID: PMC4570558 DOI: 10.1186/s12864-015-1900-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 10/23/2014] [Accepted: 09/08/2015] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Salmonella Typhimurium is frequently isolated from foodborne infection cases in Hong Kong, but the lack of genome sequences has hindered in-depth epidemiological and phylogenetic studies. In this study, we sought to reconstruct the phylogenetic relationship and investigate the distribution and mutation patterns of virulence determinants among local S. Typhimurium clinical isolates using their genome sequences. RESULTS We obtained genome sequences of 20 S. Typhimurium clinical isolates from a local hospital cluster using a 454 GS FLX Titanium sequencing platform. Phylogenetic analysis was performed based on single nucleotide polymorphism positions of the core genome against the reference strain LT2. Antimicrobial susceptibility was determined using minimal inhibitory concentration for five antimicrobial agents and analyses of virulence determinants were performed through referencing to various databases. Through phylogenetic analysis, we revealed two distinct clades of S. Typhimurium isolates and three outliers in Hong Kong, which differ remarkably in antimicrobial susceptibility and presentation and mutations of virulence determinants. The local isolates were not closely related to many of the previously sequenced S. Typhimurium isolates, except LT2. As the isolates in the two clades spanned over 10 years of isolation, they probably represent endemic strains. The outliers are possibly introduced from outside of Hong Kong. The close relatedness of members in one of the clades to LT2 and the Japanese stool isolate T000240 suggests the potential reemergence of LT2 progeny in regions nearby. CONCLUSIONS Our study demonstrated the utility of next-generation sequencing coupled to traditional microbiological testing method in a retrospective epidemiological study involving multiple clinical isolates. The evolution of multidrug- and ciprofloxacin-resistant strains among the more virulent clade is also an increasing concern.
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Affiliation(s)
- Chi Keung Cheng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Patrick Tik Wan Law
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jing Qin
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Julia Mei-Lun Ling
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China.
| | - Kai Man Kam
- Centre for Health Protection, Department of Health, Hong Kong SAR, China. .,Current address: Stanley Ho Centre for Emerging Infectious Diseases, JC School of Public Health, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | | | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Li L, Wong HC, Nong W, Cheung MK, Law PTW, Kam KM, Kwan HS. Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus. BMC Genomics 2014; 15:1135. [PMID: 25518728 PMCID: PMC4320434 DOI: 10.1186/1471-2164-15-1135] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 09/05/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinical isolates of V. parahaemolyticus are currently available, but the genome dynamics across the species and virulence potential of environmental strains on a genome-scale have not been described before. RESULTS Here we present genome sequences of four V. parahaemolyticus clinical strains from stool samples of patients and five environmental strains in Hong Kong. Phylogenomics analysis based on single nucleotide polymorphisms revealed a clear distinction between the clinical and environmental isolates. A new gene cluster belonging to the biofilm associated proteins of V. parahaemolyticus was found in clincial strains. In addition, a novel small genomic island frequently found among clinical isolates was reported. A few environmental strains were found harboring virulence genes and prophage elements, indicating their virulence potential. A unique biphenyl degradation pathway was also reported. A database for V. parahaemolyticus (http://kwanlab.bio.cuhk.edu.hk/vp) was constructed here as a platform to access and analyze genome sequences and annotations of the bacterium. CONCLUSIONS We have performed a comparative genomics analysis of clinical and environmental strains of V. parahaemolyticus. Our analyses could facilitate understanding of the phylogenetic diversity and niche adaptation of this bacterium.
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Affiliation(s)
| | | | | | | | | | | | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China.
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Huang Q, Chang J, Cheung MK, Nong W, Li L, Lee MT, Kwan HS. Human proteins with target sites of multiple post-translational modification types are more prone to be involved in disease. J Proteome Res 2014; 13:2735-48. [PMID: 24754740 DOI: 10.1021/pr401019d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many proteins can be modified by multiple types of post-translational modifications (Mtp-proteins). Although some post-translational modifications (PTMs) have recently been found to be associated with life-threatening diseases like cancers and neurodegenerative disorders, the underlying mechanisms remain enigmatic to date. In this study, we examined the relationship of human Mtp-proteins and disease and systematically characterized features of these proteins. Our results indicated that Mtp-proteins are significantly more inclined to participate in disease than proteins carrying no known PTM sites. Mtp-proteins were found significantly enriched in protein complexes, having more protein partners and preferred to act as hubs/superhubs in protein-protein interaction (PPI) networks. They possess a distinct functional focus, such as chromatin assembly or disassembly, and reside in biased, multiple subcellular localizations. Moreover, most Mtp-proteins harbor more intrinsically disordered regions than the others. Mtp-proteins carrying PTM types biased toward locating in the ordered regions were mainly related to protein-DNA complex assembly. Examination of the energetic effects of PTMs on the stability of PPI revealed that only a small fraction of single PTM events influence the binding energy of >2 kcal/mol, whereas the binding energy can change dramatically by combinations of multiple PTM types. Our work not only expands the understanding of Mtp-proteins but also discloses the potential ability of Mtp-proteins to act as key elements in disease development.
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Affiliation(s)
- Qianli Huang
- School of Life Sciences, The Chinese University of Hong Kong , Shatin, Hong Kong SAR 852000, China
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Cheung MK, Lam WY, Fung WYW, Law PTW, Au CH, Nong W, Kam KM, Kwan HS, Tsui SKW. Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing. PLoS One 2013; 8:e54574. [PMID: 23365674 PMCID: PMC3554703 DOI: 10.1371/journal.pone.0054574] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/12/2012] [Indexed: 01/31/2023] Open
Abstract
Background Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease. Methodology/Principal Findings Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples. Conclusions/Significance The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.
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Affiliation(s)
- Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wai Yip Lam
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wendy Yin Wan Fung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Patrick Tik Wan Law
- Core Facilities Genome Sequencing Laboratory, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Hang Au
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kai Man Kam
- Tuberculosis Reference Laboratory, Department of Health, Hong Kong SAR, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- * E-mail: (HSK); (SKWT)
| | - Stephen Kwok Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
- * E-mail: (HSK); (SKWT)
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Abstract
In bacteria, small regulatory non-coding RNAs (sRNAs) are the most abundant class of post-transcriptional regulators. They are involved in diverse processes including quorum sensing, stress response, virulence and carbon metabolism. Recent developments in high-throughput techniques, such as genomic tiling arrays and RNA-Seq, have allowed efficient detection and characterization of bacterial sRNAs. However, a comprehensive repository to host sRNAs and their annotations is not available. Existing databases suffer from a limited number of bacterial species or sRNAs included. In addition, these databases do not have tools to integrate or analyse high-throughput sequencing data. Here, we have developed BSRD (http://kwanlab.bio.cuhk.edu.hk/BSRD), a comprehensive bacterial sRNAs database, as a repository for published bacterial sRNA sequences with annotations and expression profiles. BSRD contains over nine times more experimentally validated sRNAs than any other available databases. BSRD also provides combinatorial regulatory networks of transcription factors and sRNAs with their common targets. We have built and implemented in BSRD a novel RNA-Seq analysis platform, sRNADeep, to characterize sRNAs in large-scale transcriptome sequencing projects. We will update BSRD regularly.
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Affiliation(s)
- Lei Li
- Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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Cheung MK, Li L, Nong W, Kwan HS. 2011 German Escherichia coli O104:H4 outbreak: whole-genome phylogeny without alignment. BMC Res Notes 2011; 4:533. [PMID: 22166159 DOI: 10.1186/1756-0500-4-533] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/13/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A large-scale Escherichia coli O104:H4 outbreak occurred in Germany from May to July 2011, causing numerous cases of hemolytic-uremic syndrome (HUS) and deaths. Genomes of ten outbreak isolates and a historical O104:H4 strain isolated in 2001 were sequenced using different new generation sequencing platforms. Phylogenetic analyses were performed using various approaches which either are not genome-wide or may be subject to errors due to poor sequence alignment. Also, detailed pathogenicity analyses on the 2001 strain were not available. FINDINGS We reconstructed the phylogeny of E. coli using the genome-wide and alignment-free feature frequency profile method and revealed the 2001 strain to be the closest relative to the 2011 outbreak strain among all available E. coli strains at present and confirmed findings from previous alignment-based phylogenetic studies that the HUS-causing O104:H4 strains are more closely related to typical enteroaggregative E. coli (EAEC) than to enterohemorrhagic E. coli. Detailed re-examination of pathogenicity-related virulence factors and secreted proteins showed that the 2001 strain possesses virulence factors shared between typical EAEC and the 2011 outbreak strain. CONCLUSIONS Our study represents the first attempt to elucidate the whole-genome phylogeny of the 2011 German outbreak using an alignment-free method, and suggested a direct line of ancestry leading from a putative EAEC-like ancestor through the 2001 strain to the 2011 outbreak strain.
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Affiliation(s)
- Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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