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Han S, Ji X, Huang L, Liu G, Ye J, Wang A. Effects of aftercrop tomato and maize on the soil microenvironment and microbial diversity in a long-term cotton continuous cropping field. Front Microbiol 2024; 15:1410219. [PMID: 39101036 PMCID: PMC11295657 DOI: 10.3389/fmicb.2024.1410219] [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: 03/31/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Long-term continuous cropping affects the soil microecological community and leads to nutrient imbalances, which reduces crop yields, and crop rotation can increase soil productivity. To study the effects of the cultivation of tomato (Solanum lycopersicum) and corn (Zea mays) on the microbial community, physical and chemical factors and the structure of aggregates in cotton (Gossypium hirsutum) long-term continuous cropping soils were examined. Four cropping patterns were established, including one continuous cropping pattern and three crop rotation patterns, and the diversity of the soil microecological community was measured using high-throughput sequencing. The physical and chemical properties of different models of soil were measured, and the soil aggregate structure was determined by dry and wet sieving. Planting of aftercrop tomato and corn altered the bacterial community of the cotton continuous soil to a lesser extent and the fungal community to a greater extent. In addition, continuous cropping reduced the diversity and richness of the soil fungal community. Different aftercrop planting patterns showed that there were very high contents of soil organic carbon and organic matter in the cotton-maize rotation model, while the soil aggregate structure was the most stable in the corn-cotton rotation model. Planting tomato in continuous cropping cotton fields has a greater effect on the soil microbial community than planting maize. Therefore, according to the characteristics of different succeeding crop planting patterns, the damage of continuous cropping of cotton to the soil microenvironment can be alleviated directionally, which will enable the sustainable development of cotton production.
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Affiliation(s)
- Shouyan Han
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Xiaohui Ji
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Liwen Huang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Gaijie Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Jingyi Ye
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Aiying Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
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2
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Yamauchi K, Sato M, Osawa L, Matsuda S, Komiyama Y, Nakakuki N, Takada H, Katoh R, Muraoka M, Suzuki Y, Tatsumi A, Miura M, Takano S, Amemiya F, Fukasawa M, Nakayama Y, Yamaguchi T, Inoue T, Maekawa S, Enomoto N. Analysis of direct-acting antiviral-resistant hepatitis C virus haplotype diversity by single-molecule and long-read sequencing. Hepatol Commun 2022; 6:1634-1651. [PMID: 35357088 PMCID: PMC9234623 DOI: 10.1002/hep4.1929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/08/2022] Open
Abstract
The method of analyzing individual resistant hepatitis C virus (HCV) by a combination of haplotyping and resistance-associated substitution (RAS) has not been fully elucidated because conventional sequencing has only yielded short and fragmented viral genomes. We performed haplotype analysis of HCV mutations in 12 asunaprevir/daclatasvir treatment-failure cases using the Oxford Nanopore sequencer. This enabled single-molecule long-read sequencing using rolling circle amplification (RCA) for correction of the sequencing error. RCA of the circularized reverse-transcription polymerase chain reaction products successfully produced DNA longer than 30 kilobase pairs (kb) containing multiple tandem repeats of a target 3 kb HCV genome. The long-read sequencing of these RCA products could determine the original sequence of the target single molecule as the consensus nucleotide sequence of the tandem repeats and revealed the presence of multiple viral haplotypes with the combination of various mutations in each host. In addition to already known signature RASs, such as NS3-D168 and NS5A-L31/Y93, there were various RASs specific to a different haplotype after treatment failure. The distribution of viral haplotype changed over time; some haplotypes disappeared without acquiring resistant mutations, and other haplotypes, which were not observed before treatment, appeared after treatment. Conclusion: The combination of various mutations other than the known signature RAS was suggested to influence the kinetics of individual HCV quasispecies in the direct-acting antiviral treatment. HCV haplotype dynamic analysis will provide novel information on the role of HCV diversity within the host, which will be useful for elucidating the pathological mechanism of HCV-related diseases.
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Affiliation(s)
- Kozue Yamauchi
- Department of Gastroenterology and HepatologyFaculty of MedicineUniversity of YamanashiYamanashiJapan
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3
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Mutational spectrum of hepatitis C virus in patients with chronic hepatitis C determined by single molecule real-time sequencing. Sci Rep 2022; 12:7083. [PMID: 35490163 PMCID: PMC9056513 DOI: 10.1038/s41598-022-11151-6] [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: 12/08/2021] [Accepted: 04/18/2022] [Indexed: 11/08/2022] Open
Abstract
The emergence of hepatitis C virus (HCV) with resistance-associated substitution (RAS), produced by mutations in the HCV genome, is a major problem in direct acting antivirals (DAA) treatment. This study aimed to clarify the mutational spectrum in HCV-RNA and the substitution pattern for the emergence of RASs in patients with chronic HCV infection. HCV-RNA from two HCV replicon cell lines and the serum HCV-RNA of four non-liver transplant and four post-liver transplant patients with unsuccessful DAA treatment were analyzed using high-accuracy single-molecule real-time long-read sequencing. Transition substitutions, especially A>G and U>C, occurred prominently under DAAs in both non-transplant and post-transplant patients, with a mutational bias identical to that occurring in HCV replicon cell lines during 10-year culturing. These mutational biases were reproduced in natural courses after DAA treatment. RASs emerged via both transition and transversion substitutions. NS3-D168 and NS5A-L31 RASs resulted from transversion mutations, while NS5A-Y93 RASs was caused by transition substitutions. The fidelity of the RNA-dependent RNA polymerase, HCV-NS5B, produces mutational bias in the HCV genome, characterized by dominant transition mutations, notably A>G and U>C substitutions. However, RASs are acquired by both transition and transversion substitutions, and the RASs-positive HCV clones are selected and proliferated under DAA treatment pressure.
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4
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Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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5
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Ertas YN, Mahmoodi M, Shahabipour F, Jahed V, Diltemiz SE, Tutar R, Ashammakhi N. Role of biomaterials in the diagnosis, prevention, treatment, and study of corona virus disease 2019 (COVID-19). EMERGENT MATERIALS 2021; 4:35-55. [PMID: 33748672 PMCID: PMC7962632 DOI: 10.1007/s42247-021-00165-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/12/2021] [Indexed: 05/02/2023]
Abstract
Recently emerged novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting corona virus disease 2019 (COVID-19) led to urgent search for methods to prevent and treat COVID-19. Among important disciplines that were mobilized is the biomaterials science and engineering. Biomaterials offer a range of possibilities to develop disease models, protective, diagnostic, therapeutic, monitoring measures, and vaccines. Among the most important contributions made so far from this field are tissue engineering, organoids, and organ-on-a-chip systems, which have been the important frontiers in developing tissue models for viral infection studies. Also, due to low bioavailability and limited circulation time of conventional antiviral drugs, controlled and targeted drug delivery could be applied alternatively. Fortunately, at the time of writing this paper, we have two successful vaccines and new at-home detection platforms. In this paper, we aim to review recent advances of biomaterial-based platforms for protection, diagnosis, vaccination, therapeutics, and monitoring of SARS-CoV-2 and discuss challenges and possible future research directions in this field.
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Affiliation(s)
- Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey
| | - Mahboobeh Mahmoodi
- Department of Bioengineering, Henry Samueli School of Engineering, University of California, Los Angeles, CA USA
- Department of Biomedical Engineering, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Fahimeh Shahabipour
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
- Skin Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Vahid Jahed
- Biomedical Engineering Division, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Rumeysa Tutar
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpasa, Avcilar, Istanbul, Turkey
| | - Nureddin Ashammakhi
- Department of Bioengineering, Henry Samueli School of Engineering, University of California, Los Angeles, CA USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI USA
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6
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Faizuloev E, Mintaev R, Petrusha O, Marova A, Smirnova D, Ammour Y, Meskina E, Sergeev O, Zhavoronok S, Karaulov A, Svitich O, Zverev V. New approach of genetic characterization of group A rotaviruses by the nanopore sequencing method. J Virol Methods 2021; 292:114114. [PMID: 33662411 DOI: 10.1016/j.jviromet.2021.114114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/17/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
Nanopore sequencing of virus genomes represented by segmented RNA (e.g. rotaviruses) requires the development of specific approaches. Due to the massive use of rotavirus vaccines, the relevance of monitoring the genetic diversity of circulating strains of group A rotaviruses (RVA) increased. The WHO recommended method of multiplex type-specific PCR does not allow genotyping of all clinically significant strains of RVA and identifying inter-strain differences within the genotype. We have described a new principle of amplification of RVA gene segments using six primers for reverse transcription and one universal primer for PCR for nanopore sequencing. The amplification of RVA genome was tested on clinical samples and three phylogenetically distant laboratory RVA strains, Wa (G1P[8]), DS-1 (G2P[4]) and 568 (G3P[3]). The developed protocol of sample preparation and nanopore sequencing allowed obtaining full-length sequences for gene segments of RVA, including the diagnostically significant segments 9 (VP7), 4 (VP4) and 6 (VP6) with high accuracy and coverage. The accuracy of sequencing of the rotavirus genome exceeded 99.5 %, and the genome coverage varied for different strains from 59.0 to 99.6 % (on average 86 %). The developed approach of nanopore sequencing of RVA genome could be a prospective tool for epidemiological studies and surveillance of rotavirus infection.
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Affiliation(s)
- Evgeny Faizuloev
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia.
| | - Ramil Mintaev
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia; FSBI «Center for Strategic Planning and Management of Medical and Biological Health Risks», Laboratory of Gene Therapy, Moscow, Russia
| | - Olga Petrusha
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia
| | - Anna Marova
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia
| | - Daria Smirnova
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia
| | - Yulia Ammour
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia
| | - Elena Meskina
- M. Vladimirsky Moscow Regional Research Clinical Institute (MONIKI), Department of Children's Infections, Moscow, Russia
| | - Oleg Sergeev
- Sechenov First Moscow State Medical University, Faculty of Preventive Medicine, Moscow, Russia
| | - Sergey Zhavoronok
- Belarusian State Medical University, Department of Infectious Diseases, Minsk, Belarus
| | - Alexander Karaulov
- Sechenov First Moscow State Medical University, Department of Clinical Immunology and Allergy, Moscow, Russia
| | - Oxana Svitich
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia; Sechenov First Moscow State Medical University, Faculty of Preventive Medicine, Moscow, Russia
| | - Vitaly Zverev
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia; Sechenov First Moscow State Medical University, Faculty of Preventive Medicine, Moscow, Russia
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7
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Yuan H, Zhang X, Zhao L, Chang H, Yang C, Qiu Z, Huang Y. Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus. Sci Rep 2020; 10:14228. [PMID: 32848169 PMCID: PMC7450073 DOI: 10.1038/s41598-020-71178-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Acrididae are diverse in size, body shape, behavior, ecology and life history; widely distributed; easy to collect; and important to agriculture. They represent promising model candidates for functional genomics, but their extremely large genomes have hindered this research; establishing a reference transcriptome for a species is the primary means of obtaining genetic information. Here, two Acrididae species, Gomphocerus licenti and Mongolotettix japonicus, were selected for full-length (FL) PacBio transcriptome sequencing. For G. licenti and M. japonicus, respectively, 590,112 and 566,165 circular consensus sequences (CCS) were generated, which identified 458,131 and 428,979 full-length nonchimeric (FLNC) reads. After isoform-level clustering, next-generation sequencing (NGS) short sequences were used for error correction, and remove redundant sequences with CD-HIT, 17,970 and 16,766 unigenes were generated for G. licenti and M. japonicus. In addition, we obtained 17,495 and 16,373 coding sequences, 1,082 and 813 transcription factors, 11,840 and 10,814 simple sequence repeats, and 905 and 706 long noncoding RNAs by analyzing the transcriptomes of G. licenti and M. japonicus, respectively, and 15,803 and 14,846 unigenes were annotated in eight functional databases. This is the first study to sequence FL transcriptomes of G. licenti and M. japonicus, providing valuable genetic resources for further functional genomics research.
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Affiliation(s)
- Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Xue Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Huihui Chang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Zhongying Qiu
- School of Basic Medical Sciences, Xi'an Medical University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
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8
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Batista FM, Stapleton T, Lowther JA, Fonseca VG, Shaw R, Pond C, Walker DI, van Aerle R, Martinez-Urtaza J. Whole Genome Sequencing of Hepatitis A Virus Using a PCR-Free Single-Molecule Nanopore Sequencing Approach. Front Microbiol 2020; 11:874. [PMID: 32523561 PMCID: PMC7261825 DOI: 10.3389/fmicb.2020.00874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatitis A virus (HAV) is one of the most common causes of acute viral hepatitis in humans. Although HAV has a relatively small genome, there are several factors limiting whole genome sequencing such as PCR amplification artefacts and ambiguities in de novo assembly. The recently developed Oxford Nanopore technologies (ONT) allows single-molecule sequencing of long-size fragments of DNA or RNA using PCR-free strategies. We have sequenced the whole genome of HAV using a PCR-free approach by direct reverse-transcribed sequencing. We were able to sequence HAV cDNA and obtain reads over 7 kilobases in length containing almost the whole genome of the virus. The comparison of these raw long nanopore reads with the HAV reference wild type revealed a nucleotide sequence identity between 81.1 and 96.6%. By de novo assembly of all HAV reads we obtained a consensus sequence of 7362 bases, with a nucleotide sequence identity of 99.0% with the genome of the HAV strain pHM175/18f. When the assembly was performed using as reference the HAV strain pHM175/18f a consensus with a sequence similarity of 99.8 % was obtained. We have also used an ONT amplicon-based assay to sequence two fragments of the VP3 and VP1 regions which showed a sequence similarity of 100% with matching regions of the consensus sequence obtained using the direct cDNA sequencing approach. This study showed the applicability of ONT sequencing technologies to obtain the whole genome of HAV by direct cDNA nanopore sequencing, highlighting the utility of this PCR-free approach for HAV characterization and potentially other viruses of the Picornaviridae family.
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Affiliation(s)
- Frederico M Batista
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Tina Stapleton
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - James A Lowther
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Vera G Fonseca
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Rebecca Shaw
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Christopher Pond
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - David I Walker
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Jaime Martinez-Urtaza
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom.,Department of Genetics and Microbiology, Facultat de Biociències - Edifici C, Campus Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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9
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Annis S, Fleischmann Z, Logan R, Mullin-Bernstein Z, Franco M, Saürich J, Tilly JL, Woods DC, Khrapko K. LUCS: a high-resolution nucleic acid sequencing tool for accurate long-read analysis of individual DNA molecules. Aging (Albany NY) 2020; 12:7603-7613. [PMID: 32345770 PMCID: PMC7202536 DOI: 10.18632/aging.103171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/21/2020] [Indexed: 12/26/2022]
Abstract
Nucleic acid sequence analyses are fundamental to all aspects of biological research, spanning aging, mitochondrial DNA (mtDNA) and cancer, as well as microbial and viral evolution. Over the past several years, significant improvements in DNA sequencing, including consensus sequence analysis, have proven invaluable for high-throughput studies. However, all current DNA sequencing platforms have limited utility for studies of complex mixtures or of individual long molecules, the latter of which is crucial to understanding evolution and consequences of single nucleotide variants and their combinations. Here we report a new technology termed LUCS (Long-molecule UMI-driven Consensus Sequencing), in which reads from third-generation sequencing are aggregated by unique molecular identifiers (UMIs) specific for each individual DNA molecule. This enables in-silico reconstruction of highly accurate consensus reads of each DNA molecule independent of other molecules in the sample. Additionally, use of two UMIs enables detection of artificial recombinants (chimeras). As proof of concept, we show that application of LUCS to assessment of mitochondrial genomes in complex mixtures from single cells was associated with an error rate of 1X10-4 errors/nucleotide. Thus, LUCS represents a major step forward in DNA sequencing that offers high-throughput capacity and high-accuracy reads in studies of long DNA templates and nucleotide variants in heterogenous samples.
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Affiliation(s)
- Sofia Annis
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
| | - Zoë Fleischmann
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
| | - Robert Logan
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
| | - Zachary Mullin-Bernstein
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
| | - Melissa Franco
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
| | - Josefin Saürich
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA.,On leave under a Student Exchange Program from the Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover D-30419, Germany
| | - Jonathan L Tilly
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
| | - Dori C Woods
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
| | - Konstantin Khrapko
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
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10
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Single-molecular real-time deep sequencing reveals the dynamics of multi-drug resistant haplotypes and structural variations in the hepatitis C virus genome. Sci Rep 2020; 10:2651. [PMID: 32060395 PMCID: PMC7021670 DOI: 10.1038/s41598-020-59397-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/24/2020] [Indexed: 12/25/2022] Open
Abstract
While direct-acting antivirals (DAAs) for hepatitis C virus (HCV) have dramatically progressed, patients still suffer from treatment failures. For the radical eradication of HCV, a deeper understanding of multiple resistance-associated substitutions (RASs) at the single-clone level is essential. To understand HCV quasispecies and their dynamics during DAA treatment, we applied single-molecule real-time (SMRT) deep sequencing on sera from 12 patients with genotype-1b HCV infections with DAA treatment failures, both pre- and post-treatment. We identified >3.2 kbp sequences between NS3 and NS5A genes of 187,539 clones in total, classifying into haplotype codes based on the linkage of seven RAS loci. The number of haplotype codes during the treatment, per sample, significantly decreased from 14.67 ± 9.12 to 6.58 ± 7.1, while the number of nonsynonymous codons on the seven RAS loci, per clone, significantly increased from 1.50 ± 0.92 to 3.64 ± 0.75. In five cases, the minority multi-drug resistant haplotypes at pre-treatment were identical to the major haplotypes at relapse. Moreover, various structural variations (SVs) were detected and their dynamics analysed. These results suggest that SMRT deep sequencing is useful for detecting minority haplotypes and SVs, and to evaluate the dynamics of viral genomes at the single-clone level.
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