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      Metagenome-assembled genomes of three Hepatoplasmataceae provide insights into isopod-mollicute symbiosis

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          Abstract

          The digestive organs of terrestrial isopods harbour bacteria of the recently proposed mollicute family Hepatoplasmataceae. The only complete genome available so far for Hepatoplasmataceae is that of ‘ Candidatus Hepatoplasma crinochetorum’. The scarcity of genome sequences has hampered our understanding of the symbiotic relationship between isopods and mollicutes. Here, we present four complete metagenome-assembled genomes (MAGs) of uncultured Hepatoplasmataceae members identified from shotgun sequencing data of isopods. We propose genomospecies names for three MAGs that show substantial sequence divergence from any previously known Hepatoplamsataceae members: ‘ Candidatus Tyloplasma litorale’ identified from the semiterrestrial isopod Tylos granuliferus, ‘ Candidatus Hepatoplasma vulgare’ identified from the common pill bug Armadillidium vulgare, and ‘ Candidatus Hepatoplasma scabrum’ identified from the common rough woodlouse Porcellio scaber. Phylogenomic analysis of 155 mollicutes confirmed that Hepatoplasmataceae is a sister clade of Metamycoplasmataceae in the order Mycoplasmoidales. The 16S ribosomal RNA gene sequences and phylogenomic analysis showed that ‘ Candidatus Tyloplasma litorale’ and other semiterrestrial isopod-associated mollicutes represent the placeholder genus ‘g_Bg2’ in the r214 release of the Genome Taxonomy Database, warranting their assignment to a novel genus. Our analysis also revealed that Hepatoplasmataceae lack major metabolic pathways but has a likely intact type IIA CRISPR-Cas9 machinery. Although the localization of the Hepatoplasmatacae members have not been verified microscopically in this study, these genomic characteristics are compatible with the idea that these mollicutes have an ectosymbiotic lifestyle with high nutritional dependence on their host, as has been demonstrated for other members of the family. We could not find evidence that Hepatoplasmataceae encode polysaccharide-degrading enzymes that aid host digestion. If they are to provide nutritional benefits, it may be through extra-copy nucleases, peptidases, and a patatin-like lipase. Exploration of potential host-symbiont interaction-associated genes revealed large, repetitive open reading frames harbouring beta-sandwich domains, possibly involved with host cell adhesion. Overall, genomic analyses suggest that isopod-mollicute symbiosis is not characterized by carbohydrate degradation, and we speculate on their potential role as defensive symbionts through spatial competition with pathogens to prevent infection.

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          The Sequence Alignment/Map format and SAMtools

          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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            Highly accurate protein structure prediction with AlphaFold

            Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort 1 – 4 , the structures of around 100,000 unique proteins have been determined 5 , but this represents a small fraction of the billions of known protein sequences 6 , 7 . Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’ 8 —has been an important open research problem for more than 50 years 9 . Despite recent progress 10 – 14 , existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14) 15 , demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.
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              fastp: an ultra-fast all-in-one FASTQ preprocessor

              Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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                Author and article information

                Journal
                Access Microbiol
                Access Microbiol
                acmi
                acmi
                Access Microbiology
                Microbiology Society
                2516-8290
                2024
                20 February 2024
                20 February 2024
                : 6
                : 2
                : 000592.v3
                Affiliations
                [ 1] departmentLaboratory of Genome Science , Tokyo University of Marine Science and Technology , Tokyo, Japan
                Author notes
                *Correspondence: Ikuo Hirono, hirono@ 123456kaiyodai.ac.jp
                Author information
                https://orcid.org/0000-0003-2401-5621
                https://orcid.org/0000-0001-5102-6831
                https://orcid.org/0000-0002-2355-3121
                Article
                000592.v3
                10.1099/acmi.0.000592.v3
                10928387
                38482369
                d2ad3b0e-ae11-4a85-ac4d-bfd64b45814c
                © 2024 The Authors

                This is an open-access article distributed under the terms of the Creative Commons Attribution License.

                History
                : 05 March 2023
                : 08 January 2024
                Funding
                Funded by: Japan Society for the Promotion of Science
                Award ID: 19J21518
                Award Recipient : SatoshiKawato
                Funded by: Japan Society for the Promotion of Science
                Award ID: JP19H00949
                Award Recipient : IkuoHirono
                Funded by: Japan Society for the Promotion of Science
                Award ID: JP15H02462
                Award Recipient : IkuoHirono
                Funded by: Japan Science and Technology Corporation
                Award ID: JPMJSA1806
                Award Recipient : IkuoHirono
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                isopods,mollicutes,mycoplasma,symbiosis,metagenome,hepatoplasma
                isopods, mollicutes, mycoplasma, symbiosis, metagenome, hepatoplasma

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