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Zhang Y, Lu HW, Ruan J. GAEP: a comprehensive genome assembly evaluating pipeline. J Genet Genomics 2023; 50:747-754. [PMID: 37245652 DOI: 10.1016/j.jgg.2023.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
With the rapid development of sequencing technologies, especially the maturity of third-generation sequencing technologies, there has been a significant increase in the number and quality of published genome assemblies. The emergence of these high-quality genomes has raised higher requirements for genome evaluation. Although numerous computational methods have been developed to evaluate assembly quality from various perspectives, the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality. To address this issue, we have developed the Genome Assembly Evaluating Pipeline (GAEP), which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives, including continuity, completeness, and correctness. Additionally, GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy, which performs well in our testing. GAEP is publicly available at https://github.com/zy-optimistic/GAEP under the GPL3.0 License. With GAEP, users can quickly obtain accurate and reliable evaluation results, facilitating the comparison and selection of high-quality genome assemblies.
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Affiliation(s)
- Yong Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hong-Wei Lu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang 311401, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
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Beres SB, Olsen RJ, Long SW, Eraso JM, Boukthir S, Faili A, Kayal S, Musser JM. Analysis of the Genomics and Mouse Virulence of an Emergent Clone of Streptococcus dysgalactiae Subspecies equisimilis. Microbiol Spectr 2023; 11:e0455022. [PMID: 36971562 PMCID: PMC10100674 DOI: 10.1128/spectrum.04550-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/04/2023] [Indexed: 03/29/2023] Open
Abstract
Streptococcus dysgalactiae subsp. equisimilis is a bacterial pathogen that is increasingly recognized as a cause of severe human infections. Much less is known about the genomics and infection pathogenesis of S. dysgalactiae subsp. equisimilis strains compared to the closely related bacterium Streptococcus pyogenes. To address these knowledge deficits, we sequenced to closure the genomes of seven S. dysgalactiae subsp. equisimilis human isolates, including six that were emm type stG62647. Recently, for unknown reasons, strains of this emm type have emerged and caused an increasing number of severe human infections in several countries. The genomes of these seven strains vary between 2.15 and 2.21 Mbp. The core chromosomes of these six S. dysgalactiae subsp. equisimilis stG62647 strains are closely related, differing on average by only 495 single-nucleotide polymorphisms, consistent with a recent descent from a common progenitor. The largest source of genetic diversity among these seven isolates is differences in putative mobile genetic elements, both chromosomal and extrachromosomal. Consistent with the epidemiological observations of increased frequency and severity of infections, both stG62647 strains studied were significantly more virulent than a strain of emm type stC74a in a mouse model of necrotizing myositis, as assessed by bacterial CFU burden, lesion size, and survival curves. Taken together, our genomic and pathogenesis data show the strains of emm type stG62647 we studied are closely genetically related and have enhanced virulence in a mouse model of severe invasive disease. Our findings underscore the need for expanded study of the genomics and molecular pathogenesis of S. dysgalactiae subsp. equisimilis strains causing human infections. IMPORTANCE Our studies addressed a critical knowledge gap in understanding the genomics and virulence of the bacterial pathogen Streptococcus dysgalactiae subsp. equisimilis. S. dysgalactiae subsp. equisimilis strains are responsible for a recent increase in severe human infections in some countries. We determined that certain S. dysgalactiae subsp. equisimilis strains are genetically descended from a common ancestor and that these strains can cause severe infections in a mouse model of necrotizing myositis. Our findings highlight the need for expanded studies on the genomics and pathogenic mechanisms of this understudied subspecies of the Streptococcus family.
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Affiliation(s)
- Stephen B. Beres
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - S. Wesley Long
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Jesus M. Eraso
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Sarrah Boukthir
- CHU de Rennes, Service de Bacteriologie-Hygiène Hospitalière, Rennes, France
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
| | - Ahmad Faili
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Pharmacie, Rennes, France
- Chemistry, Oncogenesis, Stress, and Signaling, INSERM 1242, Rennes, France
| | - Samer Kayal
- CHU de Rennes, Service de Bacteriologie-Hygiène Hospitalière, Rennes, France
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
- Chemistry, Oncogenesis, Stress, and Signaling, INSERM 1242, Rennes, France
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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Lai S, Pan S, Sun C, Coelho LP, Chen WH, Zhao XM. metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies. Genome Biol 2022; 23:242. [PMID: 36376928 PMCID: PMC9661791 DOI: 10.1186/s13059-022-02810-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and downstream analyses. Here, we present metaMIC ( https://github.com/ZhaoXM-Lab/metaMIC ), a machine learning-based tool for identifying and correcting misassemblies in metagenomic assemblies. Benchmarking results on both simulated and real datasets demonstrate that metaMIC outperforms existing tools when identifying misassembled contigs. Furthermore, metaMIC is able to localize the misassembly breakpoints, and the correction of misassemblies by splitting at misassembly breakpoints can improve downstream scaffolding and binning results.
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Affiliation(s)
- Senying Lai
- grid.8547.e0000 0001 0125 2443Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Shaojun Pan
- grid.8547.e0000 0001 0125 2443Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Chuqing Sun
- grid.33199.310000 0004 0368 7223Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Luis Pedro Coelho
- grid.8547.e0000 0001 0125 2443Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Wei-Hua Chen
- grid.33199.310000 0004 0368 7223Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China ,grid.462338.80000 0004 0605 6769College of Life Science, Henan Normal University, Xinxiang, Henan China
| | - Xing-Ming Zhao
- grid.8547.e0000 0001 0125 2443Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China ,International Human Phenome Institutes (Shanghai), Shanghai, China ,Zhangjiang Fudan International Innovation Center, Shanghai, China
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Achakkagari SR, Bozan I, Anglin NL, Ellis D, Tai HH, Strömvik MV. Complete mitogenome assemblies from a panel of 13 diverse potato taxa. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:894-897. [PMID: 33796671 PMCID: PMC7971228 DOI: 10.1080/23802359.2021.1886016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mitochondrial DNA is maternally inherited and is shown to affect nuclear–cytoplasmic interactions in potato. Analyzing the mitogenome helps understand the evolutionary relationships and improve breeding programs in potato. We report complete mitogenome sequences from a panel of 13 potato accessions of various taxa. Each mitogenome has three independent circular molecules, except one of the S. bukasovii sample BUK2, which has a single circular molecule. Each mitogenome code for 37 non-redundant protein-coding genes, three rRNAs, 20 tRNAs, and 19 hypothetical open reading frames. Phylogenetic analysis reveals congruency between plastome and mitogenome phylogeny.
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Affiliation(s)
| | - Ilayda Bozan
- Department of Plant Science, McGill University, Montreal, Canada
| | | | | | - Helen H Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
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