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11. Construction and comparison of three reference‐quality genome assemblies for soybean

Author

Valliyodan, Babu, Cannon, Steven B, Bayer, Philipp E, Shu, Shengqiang, Brown, Anne V, Ren, Longhui, Jenkins, Jerry, Chung, Claire Y‐L, Chan, Ting‐Fung, Daum, Christopher G, Plott, Christopher, Hastie, Alex, Baruch, Kobi, Barry, Kerrie W, Huang, Wei, Patil, Gunvant, Varshney, Rajeev K, Hu, Haifei, Batley, Jacqueline, Yuan, Yuxuan, Song, Qijian, Stupar, Robert M, Goodstein, David M, Stacey, Gary, Lam, Hon‐Ming, Jackson, Scott A, Schmutz, Jeremy, Grimwood, Jane, Edwards, David, and Nguyen, Henry T

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Alleles, Centromere, Disease Resistance, Fabaceae, Genetic Variation, Genetics, Population, Genome, Plant, Genotype, Haplotypes, Hardness, Multigene Family, Phylogeny, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Repetitive Sequences, Nucleic Acid, Seed Bank, Sequence Inversion, Telomere, Glycine max, Glycine soja, soybean, genome assembly, domestication, comparative genomics, Biochemistry and Cell Biology, Plant Biology, Plant Biology & Botany, Biochemistry and cell biology, Plant biology
Abstract

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

Published
2019

12. OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps.

Author

Leung, Alden King-Yung, Liu, Melissa Chun-Jiao, Li, Le, Lai, Yvonne Yuk-Yin, Chu, Catherine, Kwok, Pui-Yan, Ho, Pak-Leung, Yip, Kevin Y, and Chan, Ting-Fung

Subjects
Humans, Sequence Analysis, DNA, Genomics, Phylogeny, Polymorphism, Genetic, Genome, Human, Software, Population, Optical Restriction Mapping, comparative genomics, copy number variation, haplotypes, optical mapping, single-molecule analysis, structural variation, Human Genome, Genetics
Abstract

BackgroundOptical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1 Mb) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples.FindingsWe present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g., multiple haplotypes, copy number variations, and subtelomeric structures when applied to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains.ConclusionsWith the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools.

Published
2019

13. Genome maps across 26 human populations reveal population-specific patterns of structural variation.

Author

Levy-Sakin, Michal, Pastor, Steven, Mostovoy, Yulia, Li, Le, Leung, Alden KY, McCaffrey, Jennifer, Young, Eleanor, Lam, Ernest T, Hastie, Alex R, Wong, Karen HY, Chung, Claire YL, Ma, Walfred, Sibert, Justin, Rajagopalan, Ramakrishnan, Jin, Nana, Chow, Eugene YC, Chu, Catherine, Poon, Annie, Lin, Chin, Naguib, Ahmed, Wang, Wei-Ping, Cao, Han, Chan, Ting-Fung, Yip, Kevin Y, Xiao, Ming, and Kwok, Pui-Yan

Subjects
Chromosomes, Human, Y, Humans, Chromosome Mapping, Sequence Analysis, DNA, Computational Biology, Genomics, Phylogeny, Base Sequence, Gene Dosage, Mutation, Genome, Human, Algorithms, Female, Male, Genomic Structural Variation, Segmental Duplications, Genomic, Genetic Linkage, Chromosomes, Human, Y, Sequence Analysis, DNA, Genome, Segmental Duplications, Genomic
Abstract

Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome.

Published
2019

17. Nonalbuminuric Diabetic Kidney Disease and Risk of All-Cause Mortality and Cardiovascular and Kidney Outcomes in Type 2 Diabetes: Findings From the Hong Kong Diabetes Biobank

Author

Ma, Ronald C.W., Chan, Juliana C.N., Ozaki, Risa, Luk, Andrea O., So, Wing Yee, Poo Lim, Cadmon King, Lee, Ka Fai, Siu, Shing Chung, Hui, Grace, Tsang, Chiu Chi, Lau, Kam Piu, Leung, Jenny Y.Y., Tsang, Man Wo, Kam, Grace, Cheung, Elaine, Lau, Ip Tim, Li, June Kam-yin, Yeung, Vincent T.F., Fung, Samuel K.S., Lo, Stanley, Lau, Emmy, Cheng, Yuk Lun, Tsui, Stephen Kwok-wing, Huang, Yu, Lan, Hui-yao, Yu, Weichuan, Tomlinson, Brian, Lok, Si, Chan, Ting Fung, Yip, Kevin Yuk-lap, Szeto, Cheuk Chun, Fan, Xiaodan, Tang, Nelson L.S., Tian, Xiaoyu, Tam, Claudia H.T., Jiang, Guozhi, Mai, Shi, Fan, Baoqi, Lau, Eric S., Xie, Fei, Zhang, Sen, Yu, Pu, Wang, Meng, Lee, Heung Man, Xie, Fangying, Ng, Alex C.W., Cheung, Grace, Kong, Alice P.S., Chow, Elaine Y.K., Yeung, Ming Wai, Chow, Chun Chung, Cheung, Kitty K.T., Wong, Rebecca Y.M., Cheong, So Hon, Chan, Katie K.H., Law, Chin-san, Yuen Lock, Anthea Ka, Ying Tsang, Ingrid Kwok, Pun Chan, Susanna Chi, Chan, Yin Wah, Chiu, Cherry, Hung, Chi Sang, Ho, Cheuk Wah, Yee Ng, Ivy Hoi, Chun Fok, Juliana Mun, Lee, Kai Man, Candy Leung, Hoi Sze, Lee, Ka Wah, Chan, Hui Ming, Wat, Winnie, Lau, Tracy, Law, Rebecca, Chan, Ryan, Lau, Candice, Tsang, Pearl, Chan, Vince, Ho, Lap Ying, Wong, Eva, Chan, Josephine, Lam, Sau Fung, Pang, Jessy, Lee, Yee Mui, Jin, Qiao, Lau, Eric S.H., Lim, Cadmon K.P., Wu, Hongjiang, Ng, Jack K., Leung, Jenny Y., Tsang, Man-wo, Li, June K., Yeung, Vincent T., and Fung, Samuel

Published
2022
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26. Mutant huntingtin induces neuronal apoptosis via derepressing the non-canonical poly(A) polymerase PAPD5

Author

Chan, Ho Yin Edwin, primary, Peng, Shaohong Isaac, additional, Chen, Zhefan Stephen, additional, Leong, Lok I, additional, Lin, Xiao, additional, Wei, Yuming, additional, Koon, Alex Chun, additional, Huang, Junzhe, additional, SUN, Jacquelyne, additional, Kwan, Kin-Ming, additional, Chow, Kim, additional, Ko, Ho, additional, and Chan, Ting-Fung, additional

Published
2024
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29. OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

Author

Li, Le, Leung, Alden King-Yung, Kwok, Tsz-Piu, Lai, Yvonne YY, Pang, Iris K, Chung, Grace Tin-Yun, Mak, Angel CY, Poon, Annie, Chu, Catherine, Li, Menglu, Wu, Jacob JK, Lam, Ernest T, Cao, Han, Lin, Chin, Sibert, Justin, Yiu, Siu-Ming, Xiao, Ming, Lo, Kwok-Wai, Kwok, Pui-Yan, Chan, Ting-Fung, and Yip, Kevin Y

Subjects
Computational Biology, Computer Simulation, Genome, Human, Genomic Structural Variation, Genomics, Humans, Software, Optical mapping, Nanochannel, Single-molecule analysis, Structural variation, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with or without creating or destroying restriction sites. We show that OMSV has high sensitivity and specificity, with clear performance gains over the latest method. Applying OMSV to a human cell line, we identified hundreds of SVs >2 kbp, with 68 % of them missed by sequencing-based callers. Independent experimental validation confirmed the high accuracy of these SVs. The OMSV software is available at http://yiplab.cse.cuhk.edu.hk/omsv/ .

Published
2017

32. OMBlast: alignment tool for optical mapping using a seed-and-extend approach

Author

Leung, Alden King-Yung, Kwok, Tsz-Piu, Wan, Raymond, Xiao, Ming, Kwok, Pui-Yan, Yip, Kevin Y, and Chan, Ting-Fung

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Bioengineering, Generic health relevance, Animals, Caenorhabditis elegans, Escherichia coli, Genome, Genomics, Humans, Optical Restriction Mapping, Saccharomyces cerevisiae, Sequence Alignment, Sequence Analysis, DNA, Software, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences
Abstract

BackgroundOptical mapping is a technique for capturing fluorescent signal patterns of long DNA molecules (in the range of 0.1–1 Mbp). Recently, it has been complementing the widely used short-read sequencing technology by assisting with scaffolding and detecting large and complex structural variations (SVs). Here, we introduce a fast, robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations on the molecules generated from optical mapping. Our method is based on the seed-and-extend approach from sequence alignment, with modifications specific to optical mapping.ResultsExperiments with both synthetic and our real data demonstrate that OMBlast has higher accuracy and faster mapping speed than existing alignment methods. Our tool also shows significant improvement when aligning data with SVs.Availability and implementationOMBlast is implemented for Java 1.7 and is released under a GPL license. OMBlast can be downloaded from https://github.com/aldenleung/OMBlast and run directly on machines equipped with a Java virtual machine.Contactkevinyip@cse.cuhk.edu.hk and tf.chan@cuhk.edu.hkSupplementary informationSupplementary data are available at Bioinformatics online.

Published
2017

35. Quantification of breast milk trans fatty acids and trans fat intake by Hong Kong lactating women

Author

Yip, Pui Sze Peggy, Chan, Ting Fung Judith, He, Zouyan, Leung, Lai Kwok, Leung, Suk Fong Sophie, and Chen, Zhen-Yu

Subjects
World Health Organization, Analysis, International economic relations, Trans fatty acids -- Analysis, Chromatography -- Analysis, Women -- Analysis, Saturated fatty acids -- Analysis, Essential fatty acids -- Analysis
Abstract

Author(s): Pui Sze Peggy Yip [sup.1], Ting Fung Judith Chan [sup.1], Zouyan He [sup.1], Lai Kwok Leung [sup.1], Suk Fong Sophie Leung [sup.2], Zhen-Yu Chen [sup.1] Author Affiliations: (1) Food [...], Background/objectives Diet westernization in Hong Kong may increase trans fat intake, whereas it may decrease intake of polyunsaturated fatty acids. The present study was to determine the current breast milk fatty acid composition and trans fat intake by Hong Kong lactating mothers. Methods Sixty lactating women were recruited for the study. Each participant donated 15 ml of milk at week 4 and 6 after delivery. Dietary data were collected using a 3-day food record method, covering 2 weekdays and 1 weekend day. Milk fatty acids were analyzed using a gas chromatography method. Trans fat consumption was assessed using the Nutrition Data System for Research or calculating the intake based on percentage of trans fatty acids in the breast milk. Results Linoleic acid, [alpha]-linolenic acid, arachidonic acid, and docosahexaenoic acid in breast milk were 16.23%, 1.52%, 0.59%, and 0.66% total milk lipids, respectively. Mean daily intakes of total fat, saturated fatty acids, monounsaturated fatty acids, were 79, 24, 29, and 18 g, respectively. Total trans fat intake was estimated to be 1.15-1.20 g daily and accounted for 0.50-0.52% total energy. Conclusions Breast milk of Hong Kong Chinese lactating women contained relatively higher contents of arachidonic and docosahexaenoic acids compared with those of Western countries. Compared with the previous study conducted in 1995, breast milk total trans fatty acids in 2018 still remained low. Total trans fat intake by Hong Kong lactating women in 2018 was a half of WHO's recommendation that total trans fat intake should be

Published
2020
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36. Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

Author

Mak, Angel CY, Lai, Yvonne YY, Lam, Ernest T, Kwok, Tsz-Piu, Leung, Alden KY, Poon, Annie, Mostovoy, Yulia, Hastie, Alex R, Stedman, William, Anantharaman, Thomas, Andrews, Warren, Zhou, Xiang, Pang, Andy WC, Dai, Heng, Chu, Catherine, Lin, Chin, Wu, Jacob JK, Li, Catherine ML, Li, Jing-Woei, Yim, Aldrin KY, Chan, Saki, Sibert, Justin, Džakula, Željko, Cao, Han, Yiu, Siu-Ming, Chan, Ting-Fung, Yip, Kevin Y, Xiao, Ming, and Kwok, Pui-Yan

Subjects
Cell Line, Humans, Microarray Analysis, Chromosome Mapping, Genome, Human, Genomic Structural Variation, biotechnology, genome mapping, structural variation detection, Genome, Human, Developmental Biology, Genetics
Abstract

Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation.

Published
2016

37. Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)

Author

Hui, Jerome H.L., Chan, Ting Fung, Chan, Leo Lai, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James Kar-Hei, Gaitan-Espitia, Juan Diego, Lau, Chun Kwan Stanley, HeiSung, Yik, Wong, Chris Kong Chu, Yip, Kevin Yuk-Lap, Wei, Yingying, Chong, Tze Kiu, Law, Sean Tsz Sum, Nong, Wenyan, Yip, Ho Yin, Hui, Jerome H.L., Chan, Ting Fung, Chan, Leo Lai, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James Kar-Hei, Gaitan-Espitia, Juan Diego, Lau, Chun Kwan Stanley, HeiSung, Yik, Wong, Chris Kong Chu, Yip, Kevin Yuk-Lap, Wei, Yingying, Chong, Tze Kiu, Law, Sean Tsz Sum, Nong, Wenyan, and Yip, Ho Yin

Abstract

The edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has found application in food additives, given its ability to synthesize long-chain glycolipids, among other uses. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size is 29.2 Mb. It has high sequence contiguity and completeness, with a scaffold N50 of 1.925 Mb and a 92.0% BUSCO score. A total of 11,510 protein-coding genes and 474.7 kb repeats (accounting for 1.62% of the genome) were predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology, such as their wood-decaying capability, their evolutionary relationships with other fungi, and their unique biology and applications in the food industry. © 2024 GigaScience Press. All rights reserved.

Published
2024

38. Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

Author

Hui, Jerome H.L., Chan, Ting Fung, Chan, Leo Lai, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James Kar-Hei, Gaitan-Espitia, Juan Diego, Lau, Chun Kwan Stanley, Sung, Yik Hei, Wong, Chris Kong Chu, Yip, Kevin Yuk-Lap, Wei, Yingying, So, Wai Lok, Nong, Wenyan, Pun, Hydrogen Sui Fai, Yau, Wing Kwong, Chiu, Colleen Yuk Lin, Chan, Sammi Shan Shan, Man, Kacy Ka Ling, Yip, Ho Yin, Hui, Jerome H.L., Chan, Ting Fung, Chan, Leo Lai, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James Kar-Hei, Gaitan-Espitia, Juan Diego, Lau, Chun Kwan Stanley, Sung, Yik Hei, Wong, Chris Kong Chu, Yip, Kevin Yuk-Lap, Wei, Yingying, So, Wai Lok, Nong, Wenyan, Pun, Hydrogen Sui Fai, Yau, Wing Kwong, Chiu, Colleen Yuk Lin, Chan, Sammi Shan Shan, Man, Kacy Ka Ling, and Yip, Ho Yin

Abstract

The golden birdwing Troides aeacus (Lepidoptera, Papilionidae), a significant species in Asia, faces habitat loss due to urbanization and human activities, necessitating its protection. However, the lack of genomic resources hinders our understanding of their biology and diversity, and impedes our conservation efforts based on genetic information or markers. Here, we present the first chromosomal-level genome assembly of T. aeacus using PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (351 Mb) contains 98.94% of the sequences anchored to 30 pseudo-molecules. The genome assembly has high sequence continuity with contig length N50 = 11.67 Mb and L50 = 14, and scaffold length N50 = 12.2 Mb and L50 = 13. A total of 24,946 protein-coding genes were predicted, with high BUSCO score completeness (98.8% and 94.7% of genome and proteome BUSCO, respectively. This genome offers a significant resource for understanding the swallowtail butterfly biology and carrying out its conservation. © 2024 GigaScience Press. All rights reserved.

Published
2024

39. Genome assembly of the rare and endangered Grantham’s camellia, Camellia granthamiana

Author

Hong Kong Biodiversity Genomics Consortium, Hui, Jerome H.L., Chan, Ting Fung, Chan, Leo Lai, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James Kar-Hei, Gaitan-espitia, Juan Diego, Lau, Chun Kwan Stanley, Sung, Yik Hei, Wong, Chris Kong Chu, Yip, Kevin Yuk-Lap, Wei, Yingying, Law, Sean Tsz Sum, So, Wai Lok, Nong, Wenyan, Lau, David Tai Wai, Yip, Ho Yin, Hong Kong Biodiversity Genomics Consortium, Hui, Jerome H.L., Chan, Ting Fung, Chan, Leo Lai, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James Kar-Hei, Gaitan-espitia, Juan Diego, Lau, Chun Kwan Stanley, Sung, Yik Hei, Wong, Chris Kong Chu, Yip, Kevin Yuk-Lap, Wei, Yingying, Law, Sean Tsz Sum, So, Wai Lok, Nong, Wenyan, Lau, David Tai Wai, and Yip, Ho Yin

Abstract

Grantham’s camellia (Camellia granthamiana Sealy) is a rare and endangered tea species discovered in Hong Kong in 1955 and endemic to southern China. Despite its high conservation value, the genomic resources of C. granthamiana are limited. Here, we present a chromosome-scale draft genome of the tetraploid C. granthamiana (2n = 4x = 60), combining PacBio long-read sequencing and Omni-C data. The assembled genome size is ∼2.4 Gb, with most sequences anchored to 15 pseudochromosomes resembling a monoploid genome. The genome has high contiguity, with a scaffold N50 of 139.7 Mb, and high completeness (97.8% BUSCO score). Our gene model prediction resulted in 68,032 protein-coding genes (BUSCO score of 90.9%). We annotated 1.65 Gb of repeat content (68.48% of the genome). Our Grantham’s camellia genome assembly is a valuable resource for investigating Grantham’s camellia’s biology, ecology, and phylogenomic relationships with other Camellia species, and provides a foundation for further conservation measures. © 2024 GigaScience Press. All rights reserved.

Published
2024

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

Author

Hui, Jerome, Chan, Ting Fung, Chan, Leo, Cheung, Siu Gin, Cheang, Chi Chiu, Gaitan-espitia, Juan Diego, Fang, James, Lau, Stanley Chun Kwan, Sung, Yik Hei, Wong, Chris, Yip, Kelvin, Wei, Yingying, Au, Franco, So, Wai Lok, Nong, Wenyan, Hui, Tin Yan, Leung, Brian, Williams, Gray, Hui, Jerome, Chan, Ting Fung, Chan, Leo, Cheung, Siu Gin, Cheang, Chi Chiu, Gaitan-espitia, Juan Diego, Fang, James, Lau, Stanley Chun Kwan, Sung, Yik Hei, Wong, Chris, Yip, Kelvin, Wei, Yingying, Au, Franco, So, Wai Lok, Nong, Wenyan, Hui, Tin Yan, Leung, Brian, and Williams, Gray

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. However, only two chiton genomes have been 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 ones. The repeat content (27.89%) was similar to that of other Chitonidae species and approximately three times lower than that of the Hanleyidae chiton genome. The genomic resources provided by this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.

Published
2024

41. Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

Author

Hui, Jerome, Chan, Ting Fung, Chan, Leo, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James, Gaitan-espitia, Juan Diego, Lau, Stanley Chun Kwan, Sung, Yik Hei, Wong, Chris, Yip, Kevin, Wei, Yingying, So, Wai Lok, Nong, Wenyan, Chui, Apple, Fong, Thomas, Yip, Hon Yin, Hui, Jerome, Chan, Ting Fung, Chan, Leo, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James, Gaitan-espitia, Juan Diego, Lau, Stanley Chun Kwan, Sung, Yik Hei, Wong, Chris, Yip, Kevin, Wei, Yingying, So, Wai Lok, Nong, Wenyan, Chui, Apple, Fong, Thomas, and Yip, Hon Yin

Abstract

The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific that can cause severe bioerosion on the reef community. However, the lack of genomic information has hindered the study of its ecology and evolution. Here, we report the chromosomal-level genome (885.8 Mb) of the long-spined sea urchin D. setosum using a combination of PacBio long-read sequencing and Omni-C scaffolding technology. The assembled genome contains a scaffold N50 length of 38.3 Mb, 98.1% of complete BUSCO (Geno, metazoa_odb10) genes (the single copy score is 97.8% and the duplication score is 0.3%), and 98.6% of the sequences are anchored to 22 pseudo-molecules/chromosomes. A total of 27,478 gene models have were annotated, reaching a total of 28,414 transcripts, including 5,384 tRNA and 23,030 protein-coding genes. The high-quality genome of D. setosum presented here is a valuable resource for the ecological and evolutionary studies of this coral reef-associated sea urchin.

Published
2024

42. Genome assembly of the milky mangrove Excoecaria agallocha

Author

Hiu, Jerome, Chan, Ting Fung, Chan, Leo, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James, Gaitan-espitia, JD, Lau, Stanley Chun Kwan, Sung, Yik Hei, Wong, Chirs, Yip, Kevin, Wei, Yingying, Law, Sean, So, Wai Lok, Nong, Wenyan, Lau, David, Lee, Shing Yip, Yip, Hon Yin, Hiu, Jerome, Chan, Ting Fung, Chan, Leo, Cheung, Siu Gin, Cheang, Chi Chiu, Fang, James, Gaitan-espitia, JD, Lau, Stanley Chun Kwan, Sung, Yik Hei, Wong, Chirs, Yip, Kevin, Wei, Yingying, Law, Sean, So, Wai Lok, Nong, Wenyan, Lau, David, Lee, Shing Yip, and Yip, Hon Yin

Abstract

The milky mangrove Excoecaria agallocha is a latex-secreting mangrove that are distributed in tropical and subtropical regions. While its poisonous latex is regarded as a potential source of phytochemicals for biomedical applications, the genomic resources of E. agallocha remains limited. Here, we present a chromosomal level genome of E. agallocha, assembled from the combination of PacBio long-read sequencing and Omni-C data. The resulting assembly size is 1,332.45 Mb and has high contiguity and completeness with a scaffold N50 of 58.9 Mb and a BUSCO score of 98.4%, with 86.08% of sequences anchored to 18 pseudomolecules. 73,740 protein-coding genes were also predicted. The milky mangrove genome provides a useful resource for further understanding the biosynthesis of phytochemical compounds in E. agallocha.

Published
2024

43. Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

Author

Nong, Wenyan, Qu, Zhe, Li, Yiqian, Barton-Owen, Tom, Wong, Annette Y. P., Yip, Ho Yin, Lee, Hoi Ting, Narayana, Satya, Baril, Tobias, Swale, Thomas, Cao, Jianquan, Chan, Ting Fung, Kwan, Hoi Shan, Ngai, Sai Ming, Panagiotou, Gianni, Qian, Pei-Yuan, Qiu, Jian-Wen, Yip, Kevin Y., Ismail, Noraznawati, Pati, Siddhartha, John, Akbar, Tobe, Stephen S., Bendena, William G., Cheung, Siu Gin, Hayward, Alexander, and Hui, Jerome H. L.

Published
2021
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46. Progression of diabetic kidney disease and trajectory of kidney function decline in Chinese patients with Type 2 diabetes

Author

Ma, Ronald C.W., Chan, Juliana C.N., Huang, Yu, Lan, Hui-yao, Lok, Si, Tomlinson, Brian, Tsui, Stephen K.W., Yu, Weichuan, Yip, Kevin Y.L., Chan, Ting Fung, Fan, Xiaodan, So, Wing Yee, Szeto, Cheuk Chun, Tang, Nelson L.S., Luk, Andrea O., Tian, Xiaoyu, Jiang, Guozhi, Tam, Claudia H.T., Lee, Heung Man, Lim, Cadmon K.P., Chan, Katie K.H., Xie, Fangying, Ng, Alex C.W., Cheung, Grace P.Y., Yeung, Ming-wai, Mai, Shi, Xie, Fei, Zhang, Sen, Yu, Pu, Weng, Meng, Luk, Andrea On Yan, Tam, Claudia Ha Ting, Carstensen, Bendix, Lau, Eric Siu Him, Lim, Cadmon King Poo, Ng, Alex Chi Wai, Ng, Maggie Chor Yin, Ozaki, Risa, Kong, Alice Pik Shan, Chow, Chun Chung, Yang, Xilin, Tsui, Stephen Kwok Wing, Chan, Juliana Chung Ngor, and Ma, Ronald Ching Wan

Published
2019
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