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Liao T, Zhang L, Wang Y, Guo L, Cao J, Liu G. Full-length transcriptome characterization of Platycladus orientalis based on the PacBio platform. Front Genet 2024; 15:1345039. [PMID: 38304337 PMCID: PMC10830785 DOI: 10.3389/fgene.2024.1345039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
As a unique and native conifer in China, Platycladus orientalis is widely used in soil erosion control, garden landscapes, timber, and traditional Chinese medicine. However, due to the lack of reference genome and transcriptome, it is limited to the further molecular mechanism research and gene function mining. To develop a full-length reference transcriptome, tissues from five different parts of P. orientalis and four cone developmental stages were sequenced and analyzed by single-molecule real-time (SMRT) sequencing through the PacBio platform in this study. Overall, 37,111 isoforms were detected by PacBio with an N50 length of 2,317 nt, an average length of 1,999 bp, and the GC content of 41.81%. Meanwhile, 36,120 coding sequences, 5,645 simple sequence repeats (SSRs), 1,201 non-coding RNAs (lncRNAs), and 182 alternative splicing (AS) events with five types were identified using the results obtained from the PacBio transcript isoforms. Furthermore, 1,659 transcription factors (TFs) were detected and belonged to 51 TF families. A total of 35,689 transcripts (96.17%) were annotated through the NCBI nr, KOG, Swiss-Prot and KEGG databases, and 385 transcript isoforms related to 8 types of hormones were identified incorporated into plant hormone signal transduction pathways. The assembly and revelation of the full-length transcriptome of P. orientalis offer a pioneering insight for future investigations into gene function and genetic breeding within Platycladus species.
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Affiliation(s)
| | | | | | | | | | - Guobin Liu
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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2
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McDaniel MS, Sumpter NA, Lindgren NR, Billiot CE, Swords WE. Comparative genomics of clinical Stenotrophomonas maltophilia isolates reveals genetic diversity which correlates with colonization and persistence in vivo. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001408. [PMID: 37942787 PMCID: PMC10710838 DOI: 10.1099/mic.0.001408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
Stenotrophomonas maltophilia is a Gram-negative emerging opportunistic pathogen often present in people with respiratory diseases such as cystic fibrosis (CF). People with CF (pwCF) experience lifelong polymicrobial infections of the respiratory mucosa. Our prior work showed that Pseudomonas aeruginosa promotes persistence of S. maltophilia in mouse respiratory infections. As is typical for environmental opportunistic pathogens, S. maltophilia has a large genome and a high degree of genetic diversity. In this study, we evaluated the genomic content of S. maltophilia, combining short and long read sequencing to construct nearly complete genomes of 10 clinical isolates. The genomes of these isolates were then compared with all publicly available S. maltophilia genome assemblies, and each isolate was then evaluated for colonization/persistence in vivo, both alone and in coinfection with P. aeruginosa. We found that while the overall genome size and GC content were fairly consistent between strains, there was considerable variability in both genome structure and gene content. Similarly, there was significant variability in S. maltophilia colonization and persistence in experimental mouse respiratory infections in the presence or absence of P. aeruginosa. Ultimately, this study gives us a greater understanding of the genomic diversity of clinical S. maltophilia isolates, and how this genomic diversity relates to both interactions with other pulmonary pathogens and to host disease progression. Identifying the molecular determinants of infection with S. maltophilia can facilitate development of novel antimicrobial strategies for a highly drug-resistant pathogen.
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Affiliation(s)
- Melissa S. McDaniel
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Birmingham, AL, US
- Gregory Fleming James Center for Cystic Fibrosis Research, Birmingham, AL, US
| | - Nicholas A. Sumpter
- Department of Medicine, Division of Clinical Immunology and Rheumatology, Birmingham, AL, US
| | - Natalie R. Lindgren
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Birmingham, AL, US
- Gregory Fleming James Center for Cystic Fibrosis Research, Birmingham, AL, US
| | - Caitlin E. Billiot
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Birmingham, AL, US
- Gregory Fleming James Center for Cystic Fibrosis Research, Birmingham, AL, US
| | - W. Edward Swords
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Birmingham, AL, US
- Gregory Fleming James Center for Cystic Fibrosis Research, Birmingham, AL, US
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3
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Deng C, Ren J, Hong T, Liu Y, Li F, Zhang Y, Li C, Dong Z, Huang X, Zhang N. Full-length transcriptome of Oocystis borgei under stress condition. Front Genet 2023; 14:1255595. [PMID: 37915828 PMCID: PMC10616457 DOI: 10.3389/fgene.2023.1255595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023] Open
Affiliation(s)
- Chengcheng Deng
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jiajia Ren
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Ting Hong
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yang Liu
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Feng Li
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yulei Zhang
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Changling Li
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Xianghu Huang
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Ning Zhang
- Lab of Algae Resource Development and Aquaculture Environment Ecological Restoration, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
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4
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Exploration of Bioinformatics on Microbial Fuel Cell Technology: Trends, Challenges, and Future Prospects. J CHEM-NY 2023. [DOI: 10.1155/2023/6902054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Microbial fuel cells (MFCs) are a cost-effective and environmentally friendly alternative energy method. MFC technology has gained much interest in recent decades owing to its effectiveness in remediating wastewater and generating bioelectricity. The microbial fuel cell generates energy mainlybecause of oxidation-reduction reactions. In this reaction, electrons were transferred between two reactants. Bioinformatics is expanding across a wide range of microbial fuel cell technology. Electroactive species in the microbial community were evaluated using bioinformatics methodologies in whole genome sequencing, RNA sequencing, transcriptomics, metagenomics, and phylogenetics. Technology advancements in microbial fuel cells primarily produce power from organic and inorganic waste from various sources. Reduced chemical oxygen demand and waste degradation are two added advantages for microbial fuel cells. From plants, bacteria, and algae, microbial fuel cells were developed. Due to the rapid advancement of sequencing techniques, bioinformatics approaches are currently widely used in the technology of microbial fuel cells. In addition, they play an important role in determining the composition of electroactive species in microorganisms. The metabolic pathway is also possible to determine with bioinformatics resources. A computational technique that reveals the nature of the mediators and the substrate was also used to predict the electrochemical properties. Computational strategies were used to tackle significant challenges in experimental procedures, such as optimization and understanding microbiological systems. The main focus of this review is on utilizing bioinformatics techniques to improve microbial fuel cell technology.
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Yuan QS, Deng T, Gao Y, Jiang W, Ou X, Wang Y, Guo L, Zhou T. Genome Resource for Acinetobacter schindleri H4-3-C1: An Endophyte of Pseudostellaria heterophylla with Degradation Activity to Toxins Produced by Fungal Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1124-1126. [PMID: 36508486 DOI: 10.1094/mpmi-04-22-0088-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Acinetobacter schindleri is an endophyte of Pseudostellaria heterophylla, a traditional Chinese herbal plant. It has high degradation activity to toxins produced by fungal pathogen Fusarium graminearum. Here, we deployed PacBio single-molecule real-time long-read sequencing technology to generate a complete genome assembly for the Acinetobacter schindleri H4-3-C1 strain and obtained 1.59 Gb of clean reads. These reads were assembled to a single circular DNA chromosome with a length of 3,265,024 bp, and no plasmid was found in the genome. Totals of 3,193 coding sequences, 91 transfer RNA, 21 ribosomal RNA, and 75 small RNAs were identified in the genome. This high-quality genome assembly and gene annotation resource will facilitate the excavation of the zearalenone degradation gene and provide valuable resources for preventing and controlling toxigenic fungal diseases of P. heterophylla. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Qing-Song Yuan
- Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Tao Deng
- Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Yanping Gao
- Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Weike Jiang
- Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Xiaohong Ou
- Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Yanhong Wang
- Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Tao Zhou
- Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
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Draft Genome Sequence of Clostridium butyricum Strain 16-3, Isolated from Neonatal Feces. Microbiol Resour Announc 2022; 11:e0016322. [PMID: 35894620 PMCID: PMC9387228 DOI: 10.1128/mra.00163-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the genome sequence of Clostridium butyricum strain 16-3, which was isolated from infant feces. The genome contains circular contigs of 3,861,515 bp and 769,300 bp, with G+C contents of 28.8% and 28.3%, respectively.
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Giorgashvili E, Reichel K, Caswara C, Kerimov V, Borsch T, Gruenstaeudl M. Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow Endemic Calligonum bakuense. FRONTIERS IN PLANT SCIENCE 2022; 13:779830. [PMID: 35874012 PMCID: PMC9296850 DOI: 10.3389/fpls.2022.779830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice.
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Affiliation(s)
- Eka Giorgashvili
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Katja Reichel
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Calvinna Caswara
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Vuqar Kerimov
- Institute of Botany, Azerbaijan National Academy of Sciences (ANAS), Baku, Azerbaijan
| | - Thomas Borsch
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Michael Gruenstaeudl
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
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Yoshitake K, Ishikawa A, Yonezawa R, Kinoshita S, Kitano J, Asakawa S. Construction of a chromosome-level Japanese stickleback species genome using ultra-dense linkage analysis with single-cell sperm sequencing. NAR Genom Bioinform 2022; 4:lqac026. [PMID: 35372836 PMCID: PMC8969643 DOI: 10.1093/nargab/lqac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 11/30/2022] Open
Abstract
It is still difficult to construct the genomes of higher organisms as their genome sequences must be extended to the length of the chromosome by linkage analysis. In this study, we attempted to provide an innovative alternative to conventional linkage analysis by devising a method to genotype sperm using 10× Genomics single-cell genome sequencing libraries to generate a linkage map without interbreeding individuals. A genome was assembled using sperm from the Japanese stickleback Gasterosteus nipponicus, with single-cell genotyping yielding 1 864 430 very dense hetero-SNPs and an average coverage per sperm cell of 0.13×. In total, 1665 sperm were used, which is an order of magnitude higher than the number of recombinations used for conventional linkage analysis. We then improved the linkage analysis tool scaffold extender with low depth linkage analysis (SELDLA) to analyze the data according to the characteristics of the single-cell genotyping data. Finally, we were able to determine the chromosomal location (97.1%) and orientation (64.4%) of the contigs in the 456 Mb genome of G. nipponicus, sequenced using nanopores. This method promises to be a useful tool for determining the genomes of non-model organisms for which breeding systems have not yet been established by linkage analysis.
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Affiliation(s)
- Kazutoshi Yoshitake
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Ryo Yonezawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, Japan
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9
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Complete Genome Sequence of Lacticaseibacillus rhamnosus CAU 1365, Isolated from Kimchi. Microbiol Resour Announc 2021; 10:e0093221. [PMID: 34881978 PMCID: PMC8656391 DOI: 10.1128/mra.00932-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the whole-genome sequence of Lacticaseibacillus rhamnosus CAU 1365, which was isolated from kimchi. The genome was composed of 1 contig with a total length of 2,991,039 bp and had 2,658 coding sequences, including 62 tRNA genes and 15 rRNA genes.
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10
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Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease. Int J Mol Sci 2021; 22:ijms222011243. [PMID: 34681902 PMCID: PMC8540913 DOI: 10.3390/ijms222011243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal microbiota is a complex community that consists of an ecosystem with a dynamic interplay between bacteria, fungi, archaea, and viruses. Recent advances in model systems have revealed that the gut microbiome is critical for maintaining homeostasis through metabolic digestive function, immune regulation, and intestinal barrier integrity. Taxonomic shifts in the intestinal microbiota are strongly correlated with a multitude of human diseases, including inflammatory bowel disease (IBD). However, many of these studies have been descriptive, and thus the understanding of the cause and effect relationship often remains unclear. Using non-human experimental model systems such as gnotobiotic mice, probiotic mono-colonization, or prebiotic supplementation, researchers have defined numerous species-level functions of the intestinal microbiota that have produced therapeutic candidates for IBD. Despite these advances, the molecular mechanisms responsible for the function of much of the microbiota and the interplay with host cellular processes remain areas of tremendous research potential. In particular, future research will need to unlock the functional molecular units of the microbiota in order to utilize this untapped resource of bioactive molecules for therapy. This review will highlight the advances and remaining challenges of microbiota-based functional studies and therapeutic discovery, specifically in IBD. One of the limiting factors for reviewing this topic is the nascent development of this area with information on some drug candidates still under early commercial development. We will also highlight the current and evolving strategies, including in the biotech industry, used for the discovery of microbiota-derived bioactive molecules in health and disease.
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Ma T, Shen L, Wen Q, Lv R, Hou Q, Kwok LY, Sun Z, Zhang H. PacBio sequencing revealed variation in the microbiota diversity, species richness and composition between milk collected from healthy and mastitis cows. MICROBIOLOGY-SGM 2021; 167. [PMID: 34292863 DOI: 10.1099/mic.0.000968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mastitis is the economically most important disease of dairy cows. This study used PacBio single-molecule real-time sequencing technology to sequence the full-length 16S rRNAs from 27 milk samples (18 from mastitis and nine from healthy cows; the cows were at different stages of lactation). We observed that healthy or late stage milk microbiota had significantly higher microbial diversity and richness. The community composition of the microbiota of different groups also varied greatly. The healthy cow milk microbiota was predominantly comprised of Lactococcus lactis, Acinetobacter johnsonii, and Bacteroides dorei, while the milk from mastitis cows was predominantly comprised of Bacillus cereus. The prevalence of L. lactis and B. cereus in the milk samples was confirmed by digital droplets PCR. Differences in the milk microbiota diversity and composition could suggest an important role for some these microbes in protecting the host from mastitis while others associated with mastitis. The results of our research serve as useful references for designing strategies to prevent and treat mastitis.
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Affiliation(s)
- Teng Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Lingling Shen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Qiannan Wen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Ruirui Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Lai Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
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Cortese IJ, Castrillo ML, Onetto AL, Bich GÁ, Zapata PD, Laczeski ME. De novo genome assembly of Bacillus altitudinis 19RS3 and Bacillus altitudinis T5S-T4, two plant growth-promoting bacteria isolated from Ilex paraguariensis St. Hil. (yerba mate). PLoS One 2021; 16:e0248274. [PMID: 33705487 PMCID: PMC7954119 DOI: 10.1371/journal.pone.0248274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/23/2021] [Indexed: 11/18/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) are a heterogeneous group of bacteria that can exert beneficial effects on plant growth directly or indirectly by different mechanisms. PGPB-based inoculant formulation has been used to replace chemical fertilizers and pesticides. In our previous studies, two endophytic endospore-forming bacteria identified as Bacillus altitudinis were isolated from roots of Ilex paraguariensis St. Hil. seedlings and selected for their plant growth-promoting (PGP) properties shown in vitro and in vivo. The purposes of this work were to assemble the genomes of B. altitudinis 19RS3 and T5S-T4, using different assemblers available for Windows and Linux and to select the best assembly for each strain. Both genomes were also automatically annotated to detect PGP genes and compare sequences with other genomes reported. Library construction and draft genome sequencing were performed by Macrogen services. Raw reads were filtered using the Trimmomatic tool. Genomes were assembled using SPAdes, ABySS, Velvet, and SOAPdenovo2 assemblers for Linux, and Geneious and CLC Genomics Workbench assemblers for Windows. Assembly evaluation was done by the QUAST tool. The parameters evaluated were the number of contigs ≥ 500 bp and ≥ 1000 bp, the length of the longest contig, and the N50 value. For genome annotation PROKKA, RAST, and KAAS tools were used. The best assembly for both genomes was obtained using Velvet. The B. altitudinis 19RS3 genome was assembled into 15 contigs with an N50 value of 1,943,801 bp. The B. altitudinis T5S-T4 genome was assembled into 24 contigs with an N50 of 344,151 bp. Both genomes comprise several genes related to PGP mechanisms, such as those for nitrogen fixation, iron metabolism, phosphate metabolism, and auxin biosynthesis. The results obtained offer the basis for a better understanding of B. altitudinis 19RS3 and T5S-T4 and make them promissory for bioinoculant development.
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Affiliation(s)
- Iliana Julieta Cortese
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - María Lorena Castrillo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - Andrea Liliana Onetto
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - Gustavo Ángel Bich
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - Margarita Ester Laczeski
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
- Cátedra de Bacteriología, Dpto. de Microbiología, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
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13
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Paek J, Bai L, Shin Y, Kim H, Kook JK, Chang YH. Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33595431 DOI: 10.1099/ijsem.0.004707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains isolated from soil samples were designated as YH-JAE5T and YH-JAE2. The isolates were facultative anaerobic, Gram-stain-variable, motile, rod-shaped bacteria. Phylogenetic analysis indicated that the isolates belonged to the genus Paenibacillus, but the 16S rRNA gene sequence similarities were <98 % when compared with other species within the genus. Analysis of rpoB gene revealed the isolates formed a sub-cluster with P. chibensis. The only menaquinone identified was MK-7. The two isolates contained meso-diaminopimelic acid within their cell wall peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipid, aminophospholipids, and lipids. The major fatty acids were C15 : 0 anteiso and C15 : 0 iso. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between isolate YH-JAE5T and the most closely related reference strain (Paenibacillus chibensis KCTC 3758T) were 81.7, 84.8 and 23.4 %, respectively. The G+C content of the genomic DNA was 47.4 mol%. Thus, the polyphasic data revealed that YH-JAE2 (=KCTC 43239=JCM 34435) and YH-JAE5T (=KCTC 43059=JCM 33533) represent a new species. The name Paenibacillus dokdonensis sp. nov. is proposed.
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Affiliation(s)
- Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Lu Bai
- Industrial bio-Materials Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Biotechnology, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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14
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Reiter T, Brooks† PT, Irber† L, Joslin† SEK, Reid† CM, Scott† C, Brown CT, Pierce-Ward NT. Streamlining data-intensive biology with workflow systems. Gigascience 2021; 10:giaa140. [PMID: 33438730 PMCID: PMC8631065 DOI: 10.1093/gigascience/giaa140] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/14/2022] Open
Abstract
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter modifications. These workflows can produce hundreds to thousands of intermediate files and results that must be integrated for biological insight. Data-centric workflow systems that internally manage computational resources, software, and conditional execution of analysis steps are reshaping the landscape of biological data analysis and empowering researchers to conduct reproducible analyses at scale. Adoption of these tools can facilitate and expedite robust data analysis, but knowledge of these techniques is still lacking. Here, we provide a series of strategies for leveraging workflow systems with structured project, data, and resource management to streamline large-scale biological analysis. We present these practices in the context of high-throughput sequencing data analysis, but the principles are broadly applicable to biologists working beyond this field.
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Affiliation(s)
- Taylor Reiter
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Phillip T Brooks†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Luiz Irber†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Shannon E K Joslin†
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Charles M Reid†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Camille Scott†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - N Tessa Pierce-Ward
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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15
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Ou Y, Sheng Y, Hu X, Leng D, Huang J, Hu Z, Bai L, Deng Z, Kang Q, Wu Y. Nonomuraea nitratireducens sp. nov., a new actinobacterium isolated from Suaeda australis Moq. rhizosphere. Int J Syst Evol Microbiol 2020; 70:5026-5031. [DOI: 10.1099/ijsem.0.004377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated WYY166T, was isolated from the rhizosphere of Suaeda australis Moq. collected in Dongfang, PR China. The taxonomic position of this strain was investigated using a polyphasic approach. Phylogenetic analysis based on its 16S rRNA gene referred strain WYY166T to the genus
Nonomuraea
, and it was most closely related to the type strains
Nonomuraea candida
HMC10T,
Nonomuraea turkmeniaca
DSM 43926T,
Nonomuraea maritima
NBRC 106687T and
Nonomuraea polychroma
DSM 43925T (98.35, 97.60, 97.36 and 97.30% sequence similarity, respectively). Genome sequencing revealed a genome size of 11.27 Mbp and a G+C content of 71.10 mol%. The genome average nucleotide identity (ANI) values and the digital DNA - DNA hybridization (dDDH) values between strain WYY166T and the other species of the genus were found to be low (ANI 81.63~85.23 %, dDDH 23.6~31.6 %), suggesting that it represented a new species. The physiological evaluation showed that it had remarkable nitrate reduction activity. The whole-cell hydrolysates contained meso-diaminopimelic acid and madurose. The N-acyl type of muramic acid was acetyl. The major menaquinones were MK-9 (H4) (86.9 %) and MK-9 (H2) (13.1 %). The predominant fatty acids were iso-C16 : 0 (53.2 %), 10-methyl C17 : 0 (10.7 %), C17 : 1
ω6c (8.3 %) and iso-C16 : 1 h (7.3 %). These physiological, biochemical and chemotaxonomic data suggested that strain WYY166T should be classified as representing a novel species of the genus
Nonomuraea
, for which the name Nonomuraea nitratireducens sp. nov. is proposed. The type strain is WYY166T (=MCCC 1K03779T=KCTC 49343T).
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Affiliation(s)
- Yixin Ou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yong Sheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xiaojing Hu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Dongjin Leng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jiafu Huang
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, Fujian 363000, PR China
| | - Zhiyu Hu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, PR China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yingying Wu
- National Engineering Research Center of Edible Fungi; Key Laboratory of Applied Mycological Resources and Utilization (South), Ministry of Agriculture and Rural Affairs; Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
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16
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Complete Genome Sequence of Weissella cibaria Strain BM2, Isolated from Korean Kimchi. Microbiol Resour Announc 2020; 9:9/34/e00534-20. [PMID: 32816971 PMCID: PMC7441229 DOI: 10.1128/mra.00534-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Weissella cibaria appears to have broad-spectrum health benefits. Here, we report the genome sequence of Weissella cibaria strain BM2, which was isolated from homemade kimchi; it consists of one circular chromosome of 2,462,443 bp and one plasmid of 11,067 bp. A total of 2,337 coding sequences were predicted, including 2,117 protein-coding sequences and a G+C content of 45.06%. Weissella cibaria appears to have broad-spectrum health benefits. Here, we report the genome sequence of Weissella cibaria strain BM2, which was isolated from homemade kimchi; it consists of one circular chromosome of 2,462,443 bp and one plasmid of 11,067 bp. A total of 2,337 coding sequences were predicted, including 2,117 protein-coding sequences and a G+C content of 45.06%.
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17
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Complete Genome Sequence of Bacillus velezensis Strain DKU_NT_04, Isolated from a Traditional Korean Food Made from Soybeans (Cheonggukjang). Microbiol Resour Announc 2020; 9:9/24/e00477-20. [PMID: 32527778 PMCID: PMC7291103 DOI: 10.1128/mra.00477-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In the present work, we report the complete genome sequence of Bacillus velezensis DKU_NT_04, isolated from cheonggukjang, which is a traditional Korean fermented soybean paste. The final genome assembly consists of a 4.328-Mbp chromosome with 4,134 coding sequences and a G+C content of 45.21%.
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18
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Jayakumar V, Sakakibara Y. Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data. Brief Bioinform 2020; 20:866-876. [PMID: 29112696 PMCID: PMC6585154 DOI: 10.1093/bib/bbx147] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/22/2017] [Indexed: 12/20/2022] Open
Abstract
Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms.
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19
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Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets. Methods Mol Biol 2020; 2075:323-339. [PMID: 31584173 DOI: 10.1007/978-1-4939-9877-7_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mobile Genetic Elements (MGE) play essential roles in adaptive bacterial evolution, facilitating genetic exchange for extrachromosomal DNA, especially antibiotic resistance genes and virulence factors. For this reason, high-throughput next-generation sequencing of bacteria is of great relevance, especially for clinical pathogenic bacteria. Accurate identification of MGE from whole-genome sequencing (WGS) datasets is one of the major challenges, still hindered by methodological limitations and high sequencing costs.This chapter encompasses the protocol used for plasmid reconstruction by applying the PLACNETw methodology, from raw reads to assembled plasmids and chromosome. PLACNETw is a graphical user-friendly interface to visualize and reconstruct MGE from short-read WGS datasets. No bioinformatic background or sophisticated computational resources are required and high precision and sensitivity are achieved.
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20
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Multiplexed Non-barcoded Long-Read Sequencing and Assembling Genomes of Bacillus Strains in Error-Free Simulations. Curr Microbiol 2019; 77:79-84. [PMID: 31722044 DOI: 10.1007/s00284-019-01808-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/02/2019] [Indexed: 10/25/2022]
Abstract
The generation of genomic data from microorganisms has revolutionized our abilities to understand their biology, but it is still challenging to obtain complete genome sequences of microbes in an automated high-throughput and cost-effective manner. While the advent of second-generation sequencing technologies provided significantly higher throughput, their shorter lengths and more pronounced sequence-context bias led to a shift towards resequencing applications. Recently, single molecule real-time (SMRT) DNA sequencing has been used to generate sequencing reads that are much longer than other sequencing platforms, facilitating de novo genome assembly and genome finishing. Here we introduced a novel multiplex strategy to make full use of the capacity and characteristics of SMRT sequencing in microbe genome assembly. We used error-free simulations to evaluate the practicability of assembling SMRT genomic sequencing data from multiple microbes into finished genomes once at a time. Then we compared the influence of two key factors, including sequencing coverage and read length, on multiplex assembling. Our results showed that long-read genomic sequencing inherently provided the ability to assemble genomic sequencing data from multiple microbes into finished genomes due to its long length. This approach might be helpful for the various groups of microbial genome projects or metagenomics research.
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21
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Mustapha MM, Li B, Pacey MP, Mettus RT, McElheny CL, Marshall CW, Ernst RK, Cooper VS, Doi Y. Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii. J Antimicrob Chemother 2019; 73:2952-2959. [PMID: 30124845 DOI: 10.1093/jac/dky290] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/25/2018] [Indexed: 12/26/2022] Open
Abstract
Background Acinetobacter baumannii is a healthcare-associated pathogen with high rates of carbapenem resistance. Colistin is now routinely used for treatment of infections by this pathogen. However, colistin use has been associated with development of resistance to this agent. Objectives To elucidate the phylogenomics of colistin-susceptible and -resistant A. baumannii strain pairs from a cohort of hospitalized patients at a tertiary medical centre in the USA. Methods WGS data from 21 pairs of colistin-susceptible and -resistant, XDR clinical strains were obtained and compared using phylogeny of aligned genome sequences, assessment of pairwise SNP differences and gene content. Results Fourteen patients had colistin-resistant strains that were highly genetically related to their own original susceptible strain with a median pairwise SNP distance of 5.5 (range 1-40 SNPs), while seven other strain pairs were divergent with ≥84 SNP differences. In addition, several strains from different patients formed distinct clusters on the phylogeny in keeping with closely linked transmission chains. The majority of colistin-resistant strains contained non-synonymous mutations within the pmrAB locus suggesting a central role for pmrAB mutations in colistin resistance. Excellent genotype-phenotype correlation was also observed for carbapenems, aminoglycosides and tetracyclines. Conclusions The findings suggest that colistin resistance in the clinical setting arises through both in vivo evolution from colistin-susceptible strains and reinfection by unrelated colistin-resistant strains, the latter of which may involve patient-to-patient transmission.
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Affiliation(s)
- Mustapha M Mustapha
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bin Li
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Marissa P Pacey
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Roberta T Mettus
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christi L McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christopher W Marshall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Vaughn S Cooper
- Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Microbiology, Fujita Health University, Aichi, Japan
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22
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Liao YC, Cheng HW, Wu HC, Kuo SC, Lauderdale TLY, Chen FJ. Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding. Front Microbiol 2019; 10:2068. [PMID: 31551994 PMCID: PMC6737777 DOI: 10.3389/fmicb.2019.02068] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/22/2019] [Indexed: 11/13/2022] Open
Abstract
The Oxford Nanopore MinION is an affordable and portable DNA sequencer that can produce very long reads (tens of kilobase pairs), which enable de novo bacterial genome assembly. Although many algorithms and tools have been developed for base calling, read mapping, de novo assembly, and polishing, an automated pipeline is not available for one-stop analysis for circular bacterial genome reconstruction. In this paper, we present the pipeline CCBGpipe for completing circular bacterial genomes. Raw current signals are demultiplexed and base called to generate sequencing data. Sequencing reads are de novo assembled several times by using a sampling strategy to produce circular contigs that have a sequence in common between their start and end. The circular contigs are polished by using raw signals and sequencing reads; then, duplicated sequences are removed to form a linear representation of circular sequences. The circularized contigs are finally rearranged to start at the start position of dnaA/repA or a replication origin based on the GC skew. CCBGpipe implemented in Python is available at https://github.com/jade-nhri/CCBGpipe. Using sequencing data produced from a single MinION run, we obtained 48 circular sequences, comprising 12 chromosomes and 36 plasmids of 12 bacteria, including Acinetobacter nosocomialis, Acinetobacter pittii, and Staphylococcus aureus. With adequate quantities of sequencing reads (80×), CCBGpipe can provide a complete and automated assembly of circular bacterial genomes.
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Affiliation(s)
- Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Hung-Wei Cheng
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Tsai-Ling Yang Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
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23
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Sukhum KV, Diorio-Toth L, Dantas G. Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance. Clin Pharmacol Ther 2019; 106:512-524. [PMID: 31172511 PMCID: PMC6692204 DOI: 10.1002/cpt.1535] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
Antibiotic-resistant organisms (AROs) are a major concern to public health worldwide. While antibiotics have been naturally produced by environmental bacteria for millions of years, modern widespread use of antibiotics has enriched resistance mechanisms in human-impacted bacterial environments. Antibiotic resistance genes (ARGs) continue to emerge and spread rapidly. To combat the global threat of antibiotic resistance, researchers must develop methods to rapidly characterize AROs and ARGs, monitor their spread across space and time, and identify novel ARGs and resistance pathways. We review how high-throughput sequencing-based methods can be combined with classic culture-based assays to characterize, monitor, and track AROs and ARGs. Then, we evaluate genomic and metagenomic methods for identifying ARGs and biosynthetic pathways for novel antibiotics from genomic data sets. Together, these genomic analyses can improve surveillance and prediction of emerging resistance threats and accelerate the development of new antibiotic therapies to combat resistance.
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Affiliation(s)
- Kimberley V. Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Luke Diorio-Toth
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- To whom correspondence should be addressed during review: LD-T ()
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA
- Corresponding author: GD ()
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24
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Boolchandani M, D'Souza AW, Dantas G. Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet 2019; 20:356-370. [PMID: 30886350 PMCID: PMC6525649 DOI: 10.1038/s41576-019-0108-4] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial resistance are imperative for clinical practice to treat resistant infections and for public health efforts to limit the spread of resistance. Technologies such as next-generation sequencing are expanding our abilities to detect and study antimicrobial resistance. This Review provides a detailed overview of antimicrobial resistance identification and characterization methods, from traditional antimicrobial susceptibility testing to recent deep-learning methods. We focus on sequencing-based resistance discovery and discuss tools and databases used in antimicrobial resistance studies.
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Affiliation(s)
- Manish Boolchandani
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Alaric W D'Souza
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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25
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TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data. G3-GENES GENOMES GENETICS 2019; 9:1371-1376. [PMID: 30850377 PMCID: PMC6505135 DOI: 10.1534/g3.118.200900] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PacBio sequencing is a powerful approach to study DNA or RNA sequences in a longer scope. It is especially useful in exploring the complex structural variants generated by random integration or multiple rearrangement of endogenous or exogenous sequences. Here, we present a tool, TSD, for complex structural variant discovery using PacBio targeted sequencing data. It allows researchers to identify and visualize the genomic structures of targeted sequences by unlimited splitting, alignment and assembly of long PacBio reads. Application to the sequencing data derived from an HBV integrated human cell line(PLC/PRF/5) indicated that TSD could recover the full profile of HBV integration events, especially for the regions with the complex human-HBV genome integrations and multiple HBV rearrangements. Compared to other long read analysis tools, TSD showed a better performance for detecting complex genomic structural variants. TSD is publicly available at: https://github.com/menggf/tsd.
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26
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Sohn JI, Nam JW. The present and future of de novo whole-genome assembly. Brief Bioinform 2018; 19:23-40. [PMID: 27742661 DOI: 10.1093/bib/bbw096] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 12/15/2022] Open
Abstract
As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity. Then, we discuss how the limitations of the short reads can be overcome by using a single-molecule sequencing platform that generates long reads of up to several kilobases. In fact, the long read assembly has caused a paradigm shift in whole-genome assembly in terms of algorithms and supporting steps. We also summarize (i) hybrid assemblies using both short and long reads and (ii) overlap-based assemblies for long reads and discuss their challenges and future prospects. This review provides guidelines to determine the optimal approach for a given input data type, computational budget or genome.
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27
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Liao X, Zhao Y, Kong X, Khan A, Zhou B, Liu D, Kashif MH, Chen P, Wang H, Zhou R. Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants. Sci Rep 2018; 8:12714. [PMID: 30143661 PMCID: PMC6109132 DOI: 10.1038/s41598-018-30297-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 07/27/2018] [Indexed: 01/01/2023] Open
Abstract
Plant mitochondrial (mt) genomes are species specific due to the vast of foreign DNA migration and frequent recombination of repeated sequences. Sequencing of the mt genome of kenaf (Hibiscus cannabinus) is essential for elucidating its evolutionary characteristics. In the present study, single-molecule real-time sequencing technology (SMRT) was used to sequence the complete mt genome of kenaf. Results showed that the complete kenaf mt genome was 569,915 bp long and consisted of 62 genes, including 36 protein-coding, 3 rRNA and 23 tRNA genes. Twenty-five introns were found among nine of the 36 protein-coding genes, and five introns were trans-spliced. A comparative analysis with other plant mt genomes showed that four syntenic gene clusters were conserved in all plant mtDNAs. Fifteen chloroplast-derived fragments were strongly associated with mt genes, including the intact sequences of the chloroplast genes psaA, ndhB and rps7. According to the plant mt genome evolution analysis, some ribosomal protein genes and succinate dehydrogenase genes were frequently lost during the evolution of angiosperms. Our data suggest that the kenaf mt genome retained evolutionarily conserved characteristics. Overall, the complete sequencing of the kenaf mt genome provides additional information and enhances our better understanding of mt genomic evolution across angiosperms.
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Affiliation(s)
- Xiaofang Liao
- College of Life Sciences and Technology, Guangxi University, Nanning, 530005, China
- Key Laboratory of Plant Genetic and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
- Cash Crop Institute of Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yanhong Zhao
- Cash Crop Institute of Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xiangjun Kong
- Key Laboratory of Plant Genetic and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Aziz Khan
- Key Laboratory of Plant Genetic and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Bujin Zhou
- Key Laboratory of Plant Genetic and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Dongmei Liu
- Key Laboratory of Plant-Microbe Interactions, Department of Life Science and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Muhammad Haneef Kashif
- Key Laboratory of Plant Genetic and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Peng Chen
- Key Laboratory of Plant Genetic and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Hong Wang
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, S7N5E5, Canada
| | - Ruiyang Zhou
- Key Laboratory of Plant Genetic and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China.
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Complete Genome Sequence of Bacillus subtilis Strain DKU_NT_02, Isolated from Traditional Korean Food Using Soybean (Chung-gook-jang) for High-Quality Poly-γ-Glutamic Acid Activity. GENOME ANNOUNCEMENTS 2018; 6:6/25/e00525-18. [PMID: 29930043 PMCID: PMC6013634 DOI: 10.1128/genomea.00525-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genome sequence of Bacillus subtilis strain DKU_NT_02, isolated from traditional Korean food using soybeans (chung-gook-jang), is presented here. This strain was chosen to help identify genetic factors with high-quality poly-γ-glutamic acid (γPGA) activity. The complete genome sequence of Bacillus subtilis strain DKU_NT_02, isolated from traditional Korean food using soybeans (chung-gook-jang), is presented here. This strain was chosen to help identify genetic factors with high-quality poly-γ-glutamic acid (γPGA) activity.
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29
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Complete Genome Sequence of Bacillus subtilis Strain DKU_NT_03, Isolated from a Traditional Korean Food Using Soybean (Chung-gook-jang) for High-Quality Nattokinase Activity. GENOME ANNOUNCEMENTS 2018; 6:6/25/e00526-18. [PMID: 29930044 PMCID: PMC6013627 DOI: 10.1128/genomea.00526-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present here the complete genome sequence of Bacillus subtilis strain DKU_NT_03 isolated from the traditional Korean food chung-gook-jang, which is made from soybeans. This strain was chosen to identify genetic factors with high-quality nattokinase activity.
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30
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Chen JW, Lau YY, Krishnan T, Chan KG, Chang CY. Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques. Front Microbiol 2018; 9:1104. [PMID: 29892277 PMCID: PMC5985333 DOI: 10.3389/fmicb.2018.01104] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.
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Affiliation(s)
- Jian-Woon Chen
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yin Yin Lau
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Thiba Krishnan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Chien-Yi Chang
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
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31
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Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461-466. [PMID: 29292687 DOI: 10.1099/ijsem.0.002516] [Citation(s) in RCA: 2038] [Impact Index Per Article: 339.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.
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Affiliation(s)
- Jongsik Chun
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Henrik Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Ruiz Arahal
- Departamento de Microbiología y Ecología, and Colección Española de Cultivos Tipo (CECT), Universitat de València, València, Spain
| | - Milton S da Costa
- Center for Neurosciences and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Alejandro P Rooney
- U.S. Department of Agriculture, Agricultural Research Service, Crop Bioprotection Research Unit, Peoria, IL 61604, USA
| | - Hana Yi
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Xue-Wei Xu
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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32
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Genome characterization of two bile-isolated Vibrio fluvialis strains: an insight into pathogenicity and bile salt adaption. Sci Rep 2017; 7:11827. [PMID: 28928424 PMCID: PMC5605694 DOI: 10.1038/s41598-017-12304-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/06/2017] [Indexed: 12/26/2022] Open
Abstract
Vibrio fluvialis is recognized as an emerging pathogen. However, not much is known about the mechanism of its pathogenesis, and its adaptation to a special niche such as the gall bladder. Here we describe two V. fluvialis strains that cause acute cholecystitis. It is noteworthy that both strains were susceptible to all antibiotics tested, which is in contrast to previous studies, suggesting substantial genetic diversity among V. fluvialis isolates. In agreement with their survival and growth in the gall bladder, the genomes of strains 12605 and 3663 contain a considerable number of genes that confer resistance to bile, including toxR, ompU, tolC, cmeABC, rlpB, yrbK, rpoS, damX and gltK. Furthermore, integrative and conjugative elements (ICEs), virulence factors and prophage regions were also detected in strains 12605 and 3663, reflecting their flexibility in recombination during the evolution of pathogenicity. Comparative analysis of nine available genomes of V. fluvialis revealed a core genome consisting of 3,147 genes. Our results highlight the association of V. fluvialis with a rare disease profile and shed light on the evolution of pathogenesis and niche adaptation of V. fluvialis.
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33
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Teng JLL, Yeung ML, Chan E, Jia L, Lin CH, Huang Y, Tse H, Wong SSY, Sham PC, Lau SKP, Woo PCY. PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome. Front Microbiol 2017; 8:1448. [PMID: 28824579 PMCID: PMC5539568 DOI: 10.3389/fmicb.2017.01448] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/17/2017] [Indexed: 12/19/2022] Open
Abstract
Although PacBio third-generation sequencers have improved the read lengths of genome sequencing which facilitates the assembly of complete genomes, no study has reported success in using PacBio data alone to completely sequence a two-chromosome bacterial genome from a single library in a single run. Previous studies using earlier versions of sequencing chemistries have at most been able to finish bacterial genomes containing only one chromosome with de novo assembly. In this study, we compared the robustness of PacBio RS II, using one SMRT cell and the latest P6-C4 chemistry, with Illumina HiSeq 1500 in sequencing the genome of Burkholderia pseudomallei, a bacterium which contains two large circular chromosomes, very high G+C content of 68–69%, highly repetitive regions and substantial genomic diversity, and represents one of the largest and most complex bacterial genomes sequenced, using a reference genome generated by hybrid assembly using PacBio and Illumina datasets with subsequent manual validation. Results showed that PacBio data with de novo assembly, but not Illumina, was able to completely sequence the B. pseudomallei genome without any gaps or mis-assemblies. The two large contigs of the PacBio assembly aligned unambiguously to the reference genome, sharing >99.9% nucleotide identities. Conversely, Illumina data assembled using three different assemblers resulted in fragmented assemblies (201–366 contigs), sharing only 92.2–100% and 92.0–100% nucleotide identities to chromosomes I and II reference sequences, respectively, with no indication that the B. pseudomallei genome consisted of two chromosomes with four copies of ribosomal operons. Among all assemblies, the PacBio assembly recovered the highest number of core and virulence proteins, and housekeeping genes based on whole-genome multilocus sequence typing (wgMLST). Most notably, assembly solely based on PacBio outperformed even hybrid assembly using both PacBio and Illumina datasets. Hybrid approach generated only 74 contigs, while the PacBio data alone with de novo assembly achieved complete closure of the two-chromosome B. pseudomallei genome without additional costly bench work and further sequencing. PacBio RS II using P6-C4 chemistry is highly robust and cost-effective and should be the platform of choice in sequencing bacterial genomes, particularly for those that are well-known to be difficult-to-sequence.
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Affiliation(s)
- Jade L L Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Elaine Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Lilong Jia
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Chi Ho Lin
- Centre for Genomic Sciences, The University of Hong KongHong Kong, Hong Kong
| | - Yi Huang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Herman Tse
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Samson S Y Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Pak Chung Sham
- Centre for Genomic Sciences, The University of Hong KongHong Kong, Hong Kong.,Department of Psychiatry, The University of Hong KongHong Kong, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, Hong Kong
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, Hong Kong
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34
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Thomas P, Semmler T, Eichhorn I, Lübke-Becker A, Werckenthin C, Abdel-Glil MY, Wieler LH, Neubauer H, Seyboldt C. First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis. INFECTION GENETICS AND EVOLUTION 2017; 54:287-298. [PMID: 28720440 DOI: 10.1016/j.meegid.2017.07.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/28/2022]
Abstract
Clostridium (C.) chauvoei is a Gram-positive, spore forming, anaerobic bacterium. It causes black leg in ruminants, a typically fatal histotoxic myonecrosis. High quality circular genome sequences were generated for the C. chauvoei type strain DSM 7528T (ATCC 10092T) and a field strain 12S0467 isolated in Germany. The origin of replication (oriC) was comparable to that of Bacillus subtilis in structure with two regions containing DnaA boxes. Similar prophages were identified in the genomes of both C. chauvoei strains which also harbored hemolysin and bacterial spore formation genes. A CRISPR type I-B system with limited variations in the repeat number was identified. Sporulation and germination process related genes were homologous to that of the Clostridia cluster I group but novel variations for regulatory genes were identified indicative for strain specific control of regulatory events. Phylogenomics showed a higher relatedness to C. septicum than to other so far sequenced genomes of species belonging to the genus Clostridium. Comparative genome analysis of three C. chauvoei circular genome sequences revealed the presence of few inversions and translocations in locally collinear blocks (LCBs). The species genome also shows a large number of genes involved in proteolysis, genes for glycosyl hydrolases and metal iron transportation genes which are presumably involved in virulence and survival in the host. Three conserved flagellar genes (fliC) were identified in each of the circular genomes. In conclusion this is the first comparative analysis of circular genomes for the species C. chauvoei, enabling insights into genome composition and virulence factor variation.
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Affiliation(s)
- Prasad Thomas
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743 Jena, Germany.
| | | | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität, Robert-von-Ostertag-Str. 7-13, Building 35, 14163, Berlin, Germany.
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität, Robert-von-Ostertag-Str. 7-13, Building 35, 14163, Berlin, Germany.
| | - Christiane Werckenthin
- LAVES, Lebensmittel- und Veterinärinstitut Oldenburg, Martin-Niemöller-Straße 2, 26133 Oldenburg, Germany.
| | - Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743 Jena, Germany.
| | | | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743 Jena, Germany.
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743 Jena, Germany.
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35
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Kayansamruaj P, Dong HT, Hirono I, Kondo H, Senapin S, Rodkhum C. Comparative genome analysis of fish pathogen Flavobacterium columnare reveals extensive sequence diversity within the species. INFECTION GENETICS AND EVOLUTION 2017. [PMID: 28624550 DOI: 10.1016/j.meegid.2017.06.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Flavobacterium columnare is one of the deadliest fish pathogens causing devastating mortality in various freshwater fish species globally. To gain an insight into bacterial genomic contents and structures, comparative genome analyses were performed using the reference and newly sequenced genomes of F. columnare including genomovar I, II and I/II strains isolated from Thailand, Europe and the USA. Bacterial genomes varied in size from 3.09 to 3.39Mb (2714 to 3101 CDSs). The pan-genome analysis revealed open pan-genome nature of F. columnare strains, which possessed at least 4953 genes and tended to increase progressively with the addition of a new genome. Genomic islands (GIs) present in bacterial genomes were diverse, in which 65% (39 out of 60) of possible GIs were strain-specific. A CRISPR/cas investigation indicated at least two different CRISPR systems with varied spacer profiles. On the other hand, putative virulence genes, including those related to gliding motility, type IX secretion system (T9SS), outer membrane proteins (Omp), were equally distributed among F. columnare strains. The MLSA scheme categorized bacterial strains into nine different sequence types (ST 9-17). Phylogenetic analyses based on either 16S rRNA, MLSA and concatenated SNPs of core genome revealed the diversity of F. columnare strains. DNA homology analysis indicated that the estimated digital DNA-DNA hybridization (dDDH) between strains of genomovar I and II can be as low as 42.6%, while the three uniquely tilapia-originated strains from Thailand (1214, NK01 and 1215) were clearly dissimilar to other F. columnare strains as the dDDH values were only 27.7-30.4%. Collectively, this extensive diversity among bacterial strains suggested that species designation of F. columnare would potentially require re-emendation.
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Affiliation(s)
- Pattanapon Kayansamruaj
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand; Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand.
| | - Ha Thanh Dong
- Department Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Saengchan Senapin
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Channarong Rodkhum
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
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36
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Peeters C, Cooper VS, Hatcher PJ, Verheyde B, Carlier A, Vandamme P. Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure. PLoS One 2017; 12:e0176191. [PMID: 28430818 PMCID: PMC5400248 DOI: 10.1371/journal.pone.0176191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/06/2017] [Indexed: 12/23/2022] Open
Abstract
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence.
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Affiliation(s)
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Philip J. Hatcher
- Department of Computer Science, University of New Hampshire, Durham, NH, United States of America
| | - Bart Verheyde
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | | | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
- * E-mail:
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37
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Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci 2016; 1388:59-77. [PMID: 28009051 DOI: 10.1111/nyas.13273] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission.
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Affiliation(s)
- Jennifer L Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.,Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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38
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Shen X, Ngoh SY, Thevasagayam NM, Prakki SRS, Bhandare P, Tan AWK, Tan GQ, Singh S, Phua NCH, Vij S, Orbán L. BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome. Sci Rep 2016; 6:36647. [PMID: 27821852 PMCID: PMC5099610 DOI: 10.1038/srep36647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 10/19/2016] [Indexed: 12/31/2022] Open
Abstract
The Asian seabass is an important marine food fish that has been cultured for several decades in Asia Pacific. However, the lack of a high quality reference genome has hampered efforts to improve its selective breeding. A 3D BAC pool set generated in this study was screened using 22 SSR markers located on linkage group 2 which contains a growth-related QTL region. Seventy-two clones corresponding to 22 FPC contigs were sequenced by Illumina MiSeq technology. We co-assembled the MiSeq-derived scaffolds from each FPC contig with error-corrected PacBio reads, resulting in 187 sequences covering 9.7 Mb. Eleven genes annotated within this region were found to be potentially associated with growth and their tissue-specific expression was investigated. Correlation analysis demonstrated that SNPs in ctsb, skp1 and ppp2ca can be potentially used as markers for selecting fast-growing fingerlings. Conserved syntenies between seabass LG2 and five other teleosts were identified. This study i) provided a 10 Mb targeted genome assembly; ii) demonstrated NGS of BAC pools as a potential approach for mining candidates underlying QTLs of this species; iii) detected eleven genes potentially responsible for growth in the QTL region; and iv) identified useful SNP markers for selective breeding programs of Asian seabass.
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Affiliation(s)
- Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | - Si Yan Ngoh
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.,Nanyang Technological University, 639798 Singapore
| | | | | | - Pranjali Bhandare
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | - Andy Wee Kiat Tan
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | - Gui Quan Tan
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | | | | | - Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.,Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, 8360 Keszthely, Hungary.,Centre for Comparative Genomics, Murdoch University, Murdoch 6150, Australia
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Ronholm J, Nasheri N, Petronella N, Pagotto F. Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev 2016; 29:837-57. [PMID: 27559074 PMCID: PMC5010751 DOI: 10.1128/cmr.00056-16] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generate in silico results for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.
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Affiliation(s)
- J Ronholm
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Neda Nasheri
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Nicholas Petronella
- Biostatistics and Modelling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada Listeriosis Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
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40
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Lu H, Giordano F, Ning Z. Oxford Nanopore MinION Sequencing and Genome Assembly. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:265-279. [PMID: 27646134 PMCID: PMC5093776 DOI: 10.1016/j.gpb.2016.05.004] [Citation(s) in RCA: 425] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/07/2016] [Accepted: 05/31/2016] [Indexed: 11/28/2022]
Abstract
The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT). MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.
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Affiliation(s)
- Hengyun Lu
- National Centre of Gene Research, Chinese Academy of Sciences, Shanghai 200233, China
| | - Francesca Giordano
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Zemin Ning
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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41
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Lavezzo E, Barzon L, Toppo S, Palù G. Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis. Expert Rev Mol Diagn 2016; 16:1011-23. [PMID: 27453996 DOI: 10.1080/14737159.2016.1217158] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION The diagnosis of infectious diseases is among the most successful areas of application of new generation sequencing technologies. The field has seen the development of numerous experimental and analytical approaches for the detection and the fine description of pathogenic and non-pathogenic microorganisms. AREAS COVERED Without claiming to be exhaustive with respect to all applications and methods developed over the years, this review focuses on the advantages and the issues brought by the new technologies, with an eye in particular to third generation sequencing methods. Both experimental procedures and algorithmic strategies are presented, following the most relevant publications which have led to progress in our ability of detecting infectious agents. Expert commentary: The technical advance brought by third generation sequencing platforms has the potential to significantly expand the range of diagnostic tools that will be available to clinicians. Nonetheless, the implementation of these technologies in clinical practice is still far from being actionable and will temporally follow the path undertaken by second generation methods, which still require the setup of standardized pipelines in both wet and dry laboratory procedures.
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Affiliation(s)
- Enrico Lavezzo
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Luisa Barzon
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Stefano Toppo
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Giorgio Palù
- a Department of Molecular Medicine , University of Padova , Padova , Italy
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42
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Guo J, Jing X, Peng WL, Nie Q, Zhai Y, Shao Z, Zheng L, Cai M, Li G, Zuo H, Zhang Z, Wang RR, Huang D, Cheng W, Yu Z, Chen LL, Zhang J. Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316. Sci Rep 2016; 6:29211. [PMID: 27384076 PMCID: PMC4935845 DOI: 10.1038/srep29211] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 02/07/2023] Open
Abstract
We isolated Pseudomonas putida (P. putida) strain 1A00316 from Antarctica. This bacterium has a high efficiency against Meloidogyne incognita (M. incognita) in vitro and under greenhouse conditions. The complete genome of P. putida 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 Pseudomonas strains revealed that although P. putida 1A00316 belonged to P. putida, it was phenotypically more similar to nematicidal Pseudomonas fluorescens (P. fluorescens) strains. We characterized the diversity and specificity of nematicidal factors in P. putida 1A00316 with comparative genomics and functional analysis, and found that P. putida 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(l-isoleucyl-l-proline). We show for the first time that cyclo-(l-isoleucyl-l-proline) exhibit nematicidal activity in P. putida. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in P. putida 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in P. putida strain 1A00316.
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Affiliation(s)
- Jing Guo
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xueping Jing
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Wen-Lei Peng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qiyu Nie
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yile Zhai
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, China
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Guangyu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, China
| | - Huaiyu Zuo
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zhitao Zhang
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Rui-Ru Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Dian Huang
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Wanli Cheng
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Ling-Ling Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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43
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Sović I, Križanović K, Skala K, Šikić M. Evaluation of hybrid and non-hybrid methods forde novoassembly of nanopore reads. Bioinformatics 2016; 32:2582-9. [DOI: 10.1093/bioinformatics/btw237] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/25/2016] [Indexed: 11/13/2022] Open
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44
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Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis. PLoS One 2016; 11:e0148676. [PMID: 26849565 PMCID: PMC4744016 DOI: 10.1371/journal.pone.0148676] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
The advent and widespread application of next-generation sequencing (NGS) technologies to the study of microbial genomes has led to a substantial increase in the number of studies in which whole genome sequencing (WGS) is applied to the analysis of microbial genomic epidemiology. However, microorganisms such as Mycobacterium tuberculosis (MTB) present unique problems for sequencing and downstream analysis based on their unique physiology and the composition of their genomes. In this study, we compare the quality of sequence data generated using the Nextera and TruSeq isolate preparation kits for library construction prior to Illumina sequencing-by-synthesis. Our results confirm that MTB NGS data quality is highly dependent on the purity of the DNA sample submitted for sequencing and its guanine-cytosine content (or GC-content). Our data additionally demonstrate that the choice of library preparation method plays an important role in mitigating downstream sequencing quality issues. Importantly for MTB, the Illumina TruSeq library preparation kit produces more uniform data quality than the Nextera XT method, regardless of the quality of the input DNA. Furthermore, specific genomic sequence motifs are commonly missed by the Nextera XT method, as are regions of especially high GC-content relative to the rest of the MTB genome. As coverage bias is highly undesirable, this study illustrates the importance of appropriate protocol selection when performing NGS studies in order to ensure that sound inferences can be made regarding mycobacterial genomes.
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45
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Lin HH, Liao YC. Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches. PLoS One 2015; 10:e0144305. [PMID: 26641475 PMCID: PMC4671558 DOI: 10.1371/journal.pone.0144305] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/16/2015] [Indexed: 11/23/2022] Open
Abstract
Despite the ever-increasing output of next-generation sequencing data along with developing assemblers, dozens to hundreds of gaps still exist in de novo microbial assemblies due to uneven coverage and large genomic repeats. Third-generation single-molecule, real-time (SMRT) sequencing technology avoids amplification artifacts and generates kilobase-long reads with the potential to complete microbial genome assembly. However, due to the low accuracy (~85%) of third-generation sequences, a considerable amount of long reads (>50X) are required for self-correction and for subsequent de novo assembly. Recently-developed hybrid approaches, using next-generation sequencing data and as few as 5X long reads, have been proposed to improve the completeness of microbial assembly. In this study we have evaluated the contemporary hybrid approaches and demonstrated that assembling corrected long reads (by runCA) produced the best assembly compared to long-read scaffolding (e.g., AHA, Cerulean and SSPACE-LongRead) and gap-filling (SPAdes). For generating corrected long reads, we further examined long-read correction tools, such as ECTools, LSC, LoRDEC, PBcR pipeline and proovread. We have demonstrated that three microbial genomes including Escherichia coli K12 MG1655, Meiothermus ruber DSM1279 and Pdeobacter heparinus DSM2366 were successfully hybrid assembled by runCA into near-perfect assemblies using ECTools-corrected long reads. In addition, we developed a tool, Patch, which implements corrected long reads and pre-assembled contigs as inputs, to enhance microbial genome assemblies. With the additional 20X long reads, short reads of S. cerevisiae W303 were hybrid assembled into 115 contigs using the verified strategy, ECTools + runCA. Patch was subsequently applied to upgrade the assembly to a 35-contig draft genome. Our evaluation of the hybrid approaches shows that assembling the ECTools-corrected long reads via runCA generates near complete microbial genomes, suggesting that genome assembly could benefit from re-analyzing the available hybrid datasets that were not assembled in an optimal fashion.
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Affiliation(s)
- Hsin-Hung Lin
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
- * E-mail:
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46
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Antipov D, Korobeynikov A, McLean JS, Pevzner PA. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics 2015; 32:1009-15. [PMID: 26589280 DOI: 10.1093/bioinformatics/btv688] [Citation(s) in RCA: 338] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/13/2015] [Indexed: 12/27/2022] Open
Abstract
MOTIVATION Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost. RESULTS We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads. AVAILABILITY AND IMPLEMENTATION hybridSPAdes is implemented in C++ as a part of SPAdes genome assembler and is publicly available at http://bioinf.spbau.ru/en/spades CONTACT d.antipov@spbu.ru SUPPLEMENTARY INFORMATION supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dmitry Antipov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Pavel A Pevzner
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, Department of Computer Science and Engineering, University of California, San Diego, USA and
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47
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Rhoads A, Au KF. PacBio Sequencing and Its Applications. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:278-89. [PMID: 26542840 PMCID: PMC4678779 DOI: 10.1016/j.gpb.2015.08.002] [Citation(s) in RCA: 1140] [Impact Index Per Article: 126.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/06/2015] [Accepted: 08/11/2015] [Indexed: 12/15/2022]
Abstract
Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with diseases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Additionally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone.
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Affiliation(s)
- Anthony Rhoads
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Kin Fai Au
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.
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48
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Mind the gap; seven reasons to close fragmented genome assemblies. Fungal Genet Biol 2015; 90:24-30. [PMID: 26342853 DOI: 10.1016/j.fgb.2015.08.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions.
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49
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Belcher T, Preston A. Bordetella pertussis evolution in the (functional) genomics era. Pathog Dis 2015; 73:ftv064. [PMID: 26297914 DOI: 10.1093/femspd/ftv064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2015] [Indexed: 11/12/2022] Open
Abstract
The incidence of whooping cough caused by Bordetella pertussis in many developed countries has risen dramatically in recent years. This has been linked to the use of an acellular pertussis vaccine. In addition, it is thought that B. pertussis is adapting under acellular vaccine mediated immune selection pressure, towards vaccine escape. Genomics-based approaches have revolutionized the ability to resolve the fine structure of the global B. pertussis population and its evolution during the era of vaccination. Here, we discuss the current picture of B. pertussis evolution and diversity in the light of the current resurgence, highlight import questions raised by recent studies in this area and discuss the role that functional genomics can play in addressing current knowledge gaps.
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Affiliation(s)
- Thomas Belcher
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Andrew Preston
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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50
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Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome. mBio 2015; 6:mBio.00936-15. [PMID: 26286689 PMCID: PMC4542186 DOI: 10.1128/mbio.00936-15] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio-generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. Studying whole-genome sequences has become an important aspect of biological research. The advent of next-generation sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBio-generated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome analyses to facilitate functional studies into an organism’s biology.
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