Chromosome-level genome assembly of the cave leech <i>Sinospelaeobdella cavatuses</i> (Hirudinea: Haemadipsidae)

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Abstract

Leeches are famous for their high medical value and wide environmental adaptability. Among them, cave leeches are a very fascinating and rare group, which is an important component in the study of adaptive evolution of leeches. However, no study has yet reported a reference genome for this group. In this study, we assembled a high-quality chromosome-level genome of the cave terrestrial leech Sinospelaeobdella cavatuses, through Illumina and PacBio sequencing, alongside chromosome conformation capture techniques. The resulting genome spans 153.67 Mb across 9 pseudochromosomes(range: 11.33 to 23.53 Mb), with a mounting rate of up to 95.37% and features an N50 length of 17.15 Mb. This genome is composed of 35.16% repetitive elements and contains 21180 predicted protein-coding genes. Decoding the S. cavatuses genome not only promotes future studies on study of its phylogeny, evolution, and behavior, but also provides valuable resources for in-depth investigation on adaptive evolution of leech.

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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim, Joseph M Paggi, Chanhee Park … (2021)

Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT2, for representing and searching an expanded model of the human reference genome, in which a large catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate two initial applications of HISAT2: HLA typing, a critical need in human organ transplantation, and DNA fingerprinting, widely used in forensics. These applications are part of HISAT-genotype, with performance not only surpassing earlier computational methods, but matching or exceeding the accuracy of laboratory-based assays.

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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.

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Author and article information

Contributors

Delong Guan: 2023660006@hcnu.edu.cn

Sheng-Quan Xu:

ORCID: http://orcid.org/0000-0001-7630-632X

xushengquan@snnu.edu.cn

Journal

Journal ID (nlm-ta): Sci Data

Journal ID (iso-abbrev): Sci Data

Title: Scientific Data

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2052-4463

Publication date (Electronic): 13 November 2024

Publication date PMC-release: 13 November 2024

Publication date Collection: 2024

Volume: 11

Electronic Location Identifier: 1223

Affiliations

[1 ]College of Life Sciences, Shaanxi Normal University, ( https://ror.org/0170z8493) Xi’an, China

[2 ]Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, Hechi University, ( https://ror.org/05pjkyk24) Hechi, China

[3 ]Guangxi Collaborative Innovation Center of Modern Sericulture and Silk, Hechi University, ( https://ror.org/05pjkyk24) Hechi, China

Author information

Binbin Yao http://orcid.org/0000-0003-1496-4380

Sheng-Quan Xu http://orcid.org/0000-0001-7630-632X

Article

Publisher ID: 4007

DOI: 10.1038/s41597-024-04007-3

PMC ID: 11561068

PubMed ID: 39537640

SO-VID: af465e84-e59c-4769-8d4c-8f06d62de5ca

License:

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

History

Date received : 13 May 2024

Date accepted : 15 October 2024

Custom metadata

Keywords: molecular evolution,genome informatics

Data availability:

Keywords: molecular evolution, genome informatics

Chromosome-level genome assembly of the cave leech Sinospelaeobdella cavatuses (Hirudinea: Haemadipsidae)

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