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      • Record: found
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      Genome assembly of the milky mangrove Excoecaria agallocha

      research-article
      Author(s): Hong Kong Biodiversity Genomics Consortium
      Jerome H. L. Hui:
      ORCID: https://orcid.org/0000-0003-1355-8495
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Ting Fung Chan:
      ORCID: https://orcid.org/0000-0002-0489-3884
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Leo Lai Chan:
      ORCID: https://orcid.org/0000-0002-2755-3268
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Siu Gin Cheung:
      ORCID: https://orcid.org/0000-0001-8091-7385
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Chi Chiu Cheang:
      ORCID: https://orcid.org/0000-0003-3554-6647
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      James Kar-Hei Fang:
      ORCID: https://orcid.org/0000-0002-2969-7978
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Juan Diego Gaitan-Espitia:
      ORCID: https://orcid.org/0000-0001-8781-5736
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Stanley Chun Kwan Lau:
      ORCID: https://orcid.org/0000-0002-9978-2422
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Yik Hei Sung:
      ORCID: https://orcid.org/0000-0003-0026-8624
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Chris Kong Chu Wong:
      ORCID: https://orcid.org/0000-0001-5449-5836
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Kevin Yuk-Lap Yip:
      ORCID: https://orcid.org/0000-0001-5516-9944
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Yingying Wei:
      ORCID: https://orcid.org/0000-0003-3826-336X
      Role: Funding acquisitionRole: Project administrationRole: Writing - original draftRole: Writing - review editing
      Sean Tsz Sum Law:
      ORCID: https://orcid.org/0000-0003-2613-1108
      Role: Data curationRole: MethodologyRole: Writing - original draftRole: Writing - review editing
      Wai Lok So:
      ORCID: https://orcid.org/0000-0001-5048-5454
      Role: Data curationRole: MethodologyRole: Writing - original draftRole: Writing - review editing
      Wenyan Nong:
      ORCID: https://orcid.org/0000-0002-3277-716X
      Role: MethodologyRole: Writing - original draftRole: Writing - review editing
      David Tai Wai Lau:
      ORCID: https://orcid.org/0000-0002-3443-1808
      Role: ResourcesRole: Writing - review editing
      Shing Yip Lee:
      ORCID: https://orcid.org/0000-0001-9336-2323
      Role: ResourcesRole: Writing - review editing
      Ho Yin Yip:
      ORCID: https://orcid.org/0000-0002-0022-5045
      Role: ResourcesRole: Writing - original draftRole: Writing - review editing
      * ,
      Publication date (Electronic):
      Journal: GigaByte
      Publisher: GigaScience Press

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          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.

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          BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

          Mosè Manni, Matthew Berkeley, Mathieu Seppey … (2021)
          Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate BUSCO data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.
          Article 0 comments Cited 2021 times – based on 0 reviews     Review now
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            Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

            Haoyu Cheng, Gregory Concepcion, Xiaowen Feng … (2021)
            Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.
            Article 0 comments Cited 1919 times – based on 0 reviews     Review now
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              • Record: found
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              Identifying and removing haplotypic duplication in primary genome assemblies

              Dengfeng Guan, Shane A. McCarthy, Jonathan Wood … (2020)
              Abstract Motivation Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors. Results Here we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with current tools, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can easily be integrated into assembly pipelines. Availability and implementation The source code is written in C and is available at https://github.com/dfguan/purge_dups. Supplementary information Supplementary data are available at Bioinformatics online.
              Article 0 comments Cited 1219 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): GigaByte
                Journal ID (iso-abbrev): GigaByte
                Journal ID (publisher-id): Gigabyte
                Title: GigaByte
                Publisher: GigaScience Press (Sha Tin, New Territories, Hong Kong SAR )
                ISSN (Electronic): 2709-4715
                Publication date (Electronic): 25 April 2024
                Publication date Collection: 2024
                Volume: 2024
                Electronic Location Identifier: gigabyte119
                Affiliations
                [ 1 ] 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
                [ 2 ] School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong , Hong Kong SAR, China
                [ 3 ] State Key Laboratory of Marine Pollution and Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
                [ 4 ] State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong , Hong Kong SAR, China
                [ 5 ] Department of Science and Environmental Studies, The Education University of Hong Kong , Hong Kong SAR, China
                [ 6 ] EcoEdu PEI , Charlottetown, PE, C1A 4B7, Canada
                [ 7 ] Department of Food Science and Nutrition, Research Institute for Future Food, and State Key Laboratory of Marine Pollution, The Hong Kong Polytechnic University , Hong Kong SAR, China
                [ 8 ] The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong , Hong Kong SAR, China
                [ 9 ] Department of Ocean Science, The Hong Kong University of Science and Technology , Hong Kong SAR, China
                [ 10 ] Science Unit, Lingnan University , Hong Kong SAR, China
                [ 11 ] School of Allied Health Sciences, University of Suffolk , Ipswich, IP4 1QJ, UK
                [ 12 ] Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University , Hong Kong SAR, China
                [ 13 ] Department of Computer Science and Engineering, The Chinese University of Hong Kong , Hong Kong SAR, China
                [ 14 ] Sanford Burnham Prebys Medical Discovery Institute , La Jolla, CA, USA
                [ 15 ] Department of Statistics, The Chinese University of Hong Kong , Hong Kong SAR, China
                [ 16 ] Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong , Hong Kong SAR, China
                [ 17 ] Simon F.S. Li Marine Science Laboratory, The Chinese University of Hong Kong , Hong Kong SAR, China
                Author notes
                [ * ] Correspondence on behalf of the consortium. E-mail: jeromehui@ 123456cuhk.edu.hk
                [ † ]

                Collaborative Authors: Entomological experts who validated the dataset and their affiliations appears at the end of the document

                Article
                Publisher-manuscript ID: DRR-202401-03 Publisher ID: 119
                DOI: 10.46471/gigabyte.119
                PMC ID: 11066562
                PubMed ID: 38707633
                SO-VID: 3a514e11-5603-4652-add4-e275caaebfd7
                Copyright © © The Author(s) 2024.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 11 January 2024
                Date accepted : 13 April 2024
                Funding
                Funded by: Hong Kong Research Grant Council Collaborative Research Fund;
                Award ID: C4015-20EF
                Funded by: CUHK Strategic Seed Funding for Collaborative Research Scheme;
                Award ID: 3133356
                Funded by: CUHK Group Research Scheme;
                Award ID: 3110154
                This work was funded and supported by the Hong Kong Research Grant Council Collaborative Research Fund (C4015-20EF), CUHK Strategic Seed Funding for Collaborative Research Scheme (3133356) and CUHK Group Research Scheme (3110154).
                Categories
                Subject: Data Release
                Subject: Genetics and Genomics
                Subject: Plant Genetics
                Subject: Botany

                Data availability:

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