Wenyan Nong

Chinese University of Hong Kong

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Jerome H. L. Hui

Chinese University of Hong Kong

120

Ho Yin Yip

Hong Kong Science and Technology Parks Corporation

Thomas Swale

Dovetail Genomics (United States)

Wai Lok So

Chinese University of Hong Kong

Ting‐Fung Chan

Chinese University of Hong Kong

Alexander Hayward

University of Exeter

Tobias Baril

University of Exeter

Sean T.S. Law

Chinese University of Hong Kong

Hoi Shan Kwan

Chinese University of Hong Kong

Yichun Xie

Chinese University of Hong Kong

Cooperative Institutions

Chinese University of Hong Kong

165

University of Hong Kong

Hong Kong University of Science and Technology

Prince of Wales Hospital

Chinese Academy of Sciences

Hong Kong Baptist University

Sun Yat-sen University

City University of Hong Kong

Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)

Sichuan University

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Genome of tropical bed bug Cimex hemipterus (Cimicidae, Hemiptera) reveals tetraspanin expanded in bed bug ancestor

Insect Science (2024)

Sean T.S. Law Wenyan Nong Chade Li Tze Kiu Chong Ho Yin Yip

Abstract Cimex species are ectoparasites that exclusively feed on warm‐blooded animals such as birds and mammals. Three cimicid species are known to be persistent pests for humans, including the tropical bed bug Cimex hemipterus , common bed bug Cimex lectularius , and Eastern bat bug Leptocimex boueti . To date, genomic information is restricted to the common bed bug C. lectularius , which limits understanding their biology and to provide controls of bed bug infestations. Here, a chromosomal‐level genome assembly of C. hemipterus (495 Mb [megabase pairs]) contained on 16 pseudochromosomes (scaffold N50 = 34 Mb), together with 9 messenger RNA and small RNA transcriptomes were obtained. In comparison between hemipteran genomes, we found that the tetraspanin superfamily was expanded in the Cimex ancestor. This study provides the first genome assembly for the tropical bed bug C. hemipterus , and offers an unprecedented opportunity to address questions relating to bed bug infestations, as well as genomic evolution to hemipterans more widely.

Cimex lectularius

Bed bug

Phylogenomics

10.1111/1744-7917.13388

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Genome of the ramshorn snail Biomphalaria straminea an important intermediate vector of schistosomiasis

Figshare (2022)

Wenyan Nong

BackgroundSchistosomiasis or bilharzia is a parasitic disease caused by trematode flatworms of the genus Schistosoma. Infection of S. mansoni in humans results when cercariae emerge into the water from freshwater snails in the genus Biomphalaria, and seek out and penetrate human skin. The snail B. straminea is now present at several locations in southern China, and represents a potential reservoir for spreading schistosomiasis. To date, genomic information for the species is only available for the species B. glabrata, which mainly inhabits Central and South America. This hinders understanding of the biology and management of other important schistosomiasis vectors, such as B. straminea.FindingsUsing a combination of Illumina short‐read, 10X Genomics linked‐read, and Hi‐C sequencing data, our 1.005 Gbp B. straminea genome assembly is of high physical contiguity, with a scaffold N50 of 25.3 Mbp, and high completeness with 87.0% BUSCO score. Developmental homeobox genes, hormonal genes, and stress-response genes were also identified. Comparisons with other mollusc genomes revealed syntenic conservation, dynamic expansion of heat shock protein genes, and the presence of sesquiterpenoid and cholesterol in certain lineages among mollusc diversity.ConclusionThis study provides the first genome assembly for snail Biomphalaria straminea and provides an unprecedented opportunity to address a variety of evolutionary, genomic, and disease questions relating to molluscs more widely.

Biomphalaria

Biomphalaria glabrata

10.6084/m9.figshare.14578362

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A Proposal of Genomic Analytical Workflow in a Bacterial Pathogen Outbreak Investigation

Nature Precedings (2011)

Wenyan Nong Man Chun Wong Hoi Shan Kwan Chun Hang Au Eric C. K. Cheng

Abstract The German Escherichia coli O104:H4 outbreak causing Hemolytic Uremic Syndrome (HUS) started in early May 2011. Conventional typing methods including serotyping, multi-locus sequence typing (MLST) and pulse-field gel electrophoresis (PFGE) seemed to yield only limited information about the causative agent. The advantages of the Genome sequencing approach are apparent compared to conventional methods. Genome sequencing and analyses with an appropriate workflow would be the new paradigm in bacterial outbreak investigation.

Multilocus sequence typing

10.1038/npre.2011.6663.1

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Genome and sex-biased transcriptomic response to temperature change of common yellow butterfly Eurema hecabe (Family Pieridae)

Figshare (2023)

Wenyan Nong

The Lepidoptera, including butterflies and moths, is one of the most widespread insect orders in the world. They play important roles in the environment as pollinators and agricultural pests. The common yellow butterfly Eurema hecabe (Family Pieridae) is a dominant species found in Hong Kong and Asia, and a high-quality genome is established in this study. The genome assembly size is 296.5 Mb with high sequence continuity (scaffold N50 = 9.3Mb) and BUSCO completeness (93.0%). Messenger RNA and small RNA transcriptomes were obtained from eight developmental stages (egg, 1st to 5th instars, pupa, adult), which allowed us to annotate a total of 20,164 protein-coding genes in the genome. Comparison to other pierid butterfly genomes revealed the reorganisation of Hox and NK homeobox genes in their last common ancestor. Adult butterflies of different sexes were cultured at three temperatures, and mRNA and microRNA transcriptomes obtained separately from head and body revealed sex-specific/biased expression, including neuropeptide and sesquiterpenoid biosynthetic pathway genes. This study established a new model to understand different environmental stresses for lepidopterans in Asia, and demonstrated the differential response of sexes under climate change.

Pieridae

10.6084/m9.figshare.19634646.v3

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Supplementary information from The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes

Figshare (2023)

Sean T.S. Law Yifei Yu Wenyan Nong Wai Lok So Yiqian Li

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 to 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.

Mega-

Sea anemone

Homeobox A1

10.6084/m9.figshare.24288688

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Population genomic analyses of protected incense trees Aquilaria sinensis reveal the existence of genetically distinct subpopulations

Figshare (2023)

Sean T.S. Law Wenyan Nong Ho Yin Yip Eric Liu Terence P. T. Ng

The incense tree Aquilaria sinensis (Thymelaeaceae) can produce agarwood with commercial values and is now under threat from illegal exploitation in Hong Kong, impairing the local population and biodiversity. Together with other species of Aquilaria, it is listed in the CITES Appendix II, which strictly regulates its international trade. To understand the population structure of A. sinensis and to make relevant conservation measures, we have sequenced 346 individuals collected in Hong Kong and southern mainland China. Population genomic analyses including principal component analysis, neighbor-joining tree construction, ADMIXTURE, and hierarchical pairwise-F_ST analyses suggested that genetically distinct populations are contained in certain areas. Genomic scan analyses further detected single-nucleotide polymorphism (SNP) outliers related to plant defense, including the CYP71BE gene cluster. In addition to the population analyses, we have developed a modified hexadecyltrimethyl-ammonium bromide (CTAB) DNA extraction protocol for obtaining DNA from agarwood samples in this study, and resequencing of DNA extracted from two agarwood samples using this method allows us to successfully map to the sample corresponding localities in the phylogenetic tree. To sum up, this study suggested that there is a genetically distinct subpopulation of incense tree in Hong Kong that would require special conservation measures and established a foundation for future conservation measures.

Incense

10.6084/m9.figshare.24098433

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Genomes of two indigenous clams Anomalocardia flexuosa (Linnaeus, 1767) and Meretrix petechialis (Lamarck, 1818)

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Sean T.S. Law Wenyan Nong Ming Fung Franco Au Leni Hiu Tong Cheung Cheryl Wood Yee Shum

Abstract Clam digging has a long history in Hong Kong, but unregulated clam digging activities depletes clam populations and threatens the ecosystem. Population genomics is useful to unravel the connectivity of clams at different geographical locations and to provide necessary conservation measures; and yet, only limited number of clams in Hong Kong have genomic resources. Here, we present chromosomal-level genome assemblies for two clams commonly found in Hong Kong, Anomalocardia flexuosa and Meretrix petechialis , using a combination of PacBio HiFi and Omni-C reads. We assembled each genome (∼1.04-1.09 Gb) into 19 pseudochromosomes with high sequence continuity (scaffold N50 = 58.5 Mb and 53.5 Mb) and high completeness (BUSCO scores 94.4% and 95.7%). A total of 20,881 and 20,084 gene models were also predicted for A. flexuosa and M. petechialis respectively using transcriptomes generated in this study. The two new genomic resources established in this study will be useful for further study of the biology, ecology, and evolution of clams, as well as setting up a foundation for evidence-informed decision making in conservation measures and implementation.

10.1101/2024.05.03.592324

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Supplementary material from "MicroRNAs regulate the sesquiterpenoid hormonal pathway in Drosophila and other arthropods"

Zhe Qu William G. Bendena Wenyan Nong K. Siggens Fernando G. Noriega

10.6084/m9.figshare.c.3940264.v1

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Chromosome-level genome assembly of the common chiton,Liolophura japonica(Lischke, 1873)

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Jerome H. L. Hui Ting‐Fung Chan Leo L. Chan Siu Gin Cheung Chi Chiu Cheang

Abstract Chitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. Nevertheless, there remains only two chiton genomes sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of ∼609 Mb with a scaffold N50 length of 37.34 Mb (96.1% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding genes. The repeat content (27.89%) was similar to the other Chitonidae species and approximately three times lower than in the genome of the Hanleyidae chiton. The genomic resources provided in this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.

Polyplacophora

Sequence assembly

10.1101/2024.01.15.575488

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Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea

Figshare (2018)

Amy Yuet-Ting Lau Xuanjin Cheng Eric C. K. Cheng Wenyan Nong Man Kit Cheung

#miRCc Version 1.0 (June 2018)#This program develops algorithms for predicting microRNA-like RNAs in the model mushroom Coprinopsis cinerea
Please read carefully the README.txt file before running the programs.
The algorithms are implemented in Perl. Please make sure that Perl (https://www.perl.org/) is properly installed on your computer.
All source codes are included in this fileset. You can modify some of the codes to suit the purpose of your study.

10.6084/m9.figshare.6652283

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