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Huang R, Liu Y, Xu J, Lin D, Mao A, Yang L, Zhong G, Wang H, Xu R, Chen Y, Zhou Q. Back-to-Back Comparison of Third-Generation Sequencing and Next-Generation Sequencing in Carrier Screening of Thalassemia. Arch Pathol Lab Med 2024; 148:797-804. [PMID: 36630651 DOI: 10.5858/arpa.2022-0168-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 01/13/2023]
Abstract
CONTEXT.— Recently, new technologies, such as next-generation sequencing and third-generation sequencing, have been used in carrier screening of thalassemia. However, there is no direct comparison between the 2 methods in carrier screening of thalassemia. OBJECTIVE.— To compare the clinical performance of third-generation sequencing with next-generation sequencing in carrier screening of thalassemia. DESIGN.— Next-generation sequencing and third-generation sequencing were simultaneously conducted for 1122 individuals in Hainan Province. RESULTS.— Among 1122 genetic results, 1105 (98.48%) were concordant and 17 (1.52%) were discordant between the 2 methods. Among the 17 discordant results, 4 were common thalassemia variants, 9 were rare thalassemia variants, and 4 were variations with unknown pathogenicity. Sanger sequencing and polymerase chain reaction for discordant samples confirmed all the results of third-generation sequencing. Among the 685 individuals with common and rare thalassemia variants detected by third-generation sequencing, 512 (74.74%) were carriers of α-thalassemia, 110 (16.06%) were carriers of β-thalassemia, and 63 (9.20%) had coinheritance of α-thalassemia and β-thalassemia. Three thalassemia variants were reported for the first time in Hainan Province, including -THAI, -α2.4, and ααααanti3.7. Eleven variants with potential pathogenicity were identified in 36 patients with positive hemoglobin test results. Among 52 individuals with negative hemoglobin test results, 17 were identified with thalassemia variants. In total, third-generation sequencing and next-generation sequencing correctly detected 763 and 746 individuals with variants, respectively. Third-generation sequencing yielded a 2.28% (17 of 746) increment compared with next-generation sequencing. CONCLUSIONS.— Third-generation sequencing was demonstrated to be a more accurate and reliable approach in carrier screening of thalassemia compared with next-generation sequencing.
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Affiliation(s)
- Renliang Huang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Jing Xu
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Dan Lin
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Liuqing Yang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Gaobu Zhong
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Huoniao Wang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Ruofan Xu
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Yiwei Chen
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Qiaomiao Zhou
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
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Thingujam D, Pajerowska-Mukhtar KM, Mukhtar MS. Duckweed: Beyond an Efficient Plant Model System. Biomolecules 2024; 14:628. [PMID: 38927032 PMCID: PMC11201744 DOI: 10.3390/biom14060628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Duckweed (Lemnaceae) rises as a crucial model system due to its unique characteristics and wide-ranging utility. The significance of physiological research and phytoremediation highlights the intricate potential of duckweed in the current era of plant biology. Special attention to duckweed has been brought due to its distinctive features of nutrient uptake, ion transport dynamics, detoxification, intricate signaling, and stress tolerance. In addition, duckweed can alleviate environmental pollutants and enhance sustainability by participating in bioremediation processes and wastewater treatment. Furthermore, insights into the genomic complexity of Lemnaceae species and the flourishing field of transgenic development highlight the opportunities for genetic manipulation and biotechnological innovations. Novel methods for the germplasm conservation of duckweed can be adopted to preserve genetic diversity for future research endeavors and breeding programs. This review centers around prospects in duckweed research promoting interdisciplinary collaborations and technological advancements to drive its full potential as a model organism.
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Affiliation(s)
- Doni Thingujam
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA;
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA
| | - Karolina M. Pajerowska-Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA;
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA
| | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA;
- Department of Genetics & Biochemistry, Clemson University, 105 Collings St. Biosystems Research Complex, Clemson, SC 29634, USA
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Dayi M. Diversity and evolution of transposable elements in the plant-parasitic nematodes. BMC Genomics 2024; 25:511. [PMID: 38783171 PMCID: PMC11118728 DOI: 10.1186/s12864-024-10435-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/21/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Transposable elements (TEs) are mobile DNA sequences that propagate within genomes, occupying a significant portion of eukaryotic genomes and serving as a source of genetic variation and innovation. TEs can impact genome dynamics through their repetitive nature and mobility. Nematodes are incredibly versatile organisms, capable of thriving in a wide range of environments. The plant-parasitic nematodes are able to infect nearly all vascular plants, leading to significant crop losses and management expenses worldwide. It is worth noting that plant parasitism has evolved independently at least three times within this nematode group. Furthermore, the genome size of plant-parasitic nematodes can vary substantially, spanning from 41.5 Mbp to 235 Mbp. To investigate genome size variation and evolution in plant-parasitic nematodes, TE composition, diversity, and evolution were analysed in 26 plant-parasitic nematodes from 9 distinct genera in Clade IV. RESULTS Interestingly, despite certain species lacking specific types of DNA transposons or retrotransposon superfamilies, they still exhibit a diverse range of TE content. Identification of species-specific TE repertoire in nematode genomes provides a deeper understanding of genome evolution in plant-parasitic nematodes. An intriguing observation is that plant-parasitic nematodes possess extensive DNA transposons and retrotransposon insertions, including recent sightings of LTR/Gypsy and LTR/Pao superfamilies. Among them, the Gypsy superfamilies were found to encode Aspartic proteases in the plant-parasitic nematodes. CONCLUSIONS The study of the transposable element (TE) composition in plant-parasitic nematodes has yielded insightful discoveries. The findings revealed that certain species exhibit lineage-specific variations in their TE makeup. Discovering the species-specific TE repertoire in nematode genomes is a crucial element in understanding the evolution of genomes in plant-parasitic nematodes. It allows us to gain a deeper insight into the intricate workings of these organisms and their genetic makeup. With this knowledge, we are gaining a fundamental piece in the puzzle of understanding the evolution of these parasites. Moreover, recent transpositions have led to the acquisition of new TE superfamilies, especially Gypsy and Pao retrotransposons, further expanding the diversity of TEs in these nematodes. Significantly, the widely distributed Gypsy superfamily possesses proteases that are exclusively associated with parasitism during nematode-host interactions. These discoveries provide a deeper understanding of the TE landscape within plant-parasitic nematodes.
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Affiliation(s)
- Mehmet Dayi
- Forestry Vocational School, Düzce University, Konuralp Campus, 81620, Düzce, Türkiye.
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan.
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Chen Y, Huang JH, Sun Y, Zhang Y, Li Y, Xu X. Haplotype-resolved assembly of diploid and polyploid genomes using quantum computing. CELL REPORTS METHODS 2024; 4:100754. [PMID: 38614089 PMCID: PMC11133727 DOI: 10.1016/j.crmeth.2024.100754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/03/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]
Abstract
Precision medicine's emphasis on individual genetic variants highlights the importance of haplotype-resolved assembly, a computational challenge in bioinformatics given its combinatorial nature. While classical algorithms have made strides in addressing this issue, the potential of quantum computing remains largely untapped. Here, we present the vehicle routing problem (VRP) assembler: an approach that transforms this task into a vehicle routing problem, an optimization formulation solvable on a quantum computer. We demonstrate its potential and feasibility through a proof of concept on short synthetic diploid and triploid genomes using a D-Wave quantum annealer. To tackle larger-scale assembly problems, we integrate the VRP assembler with Google's OR-Tools, achieving a haplotype-resolved local assembly across the human major histocompatibility complex (MHC) region. Our results show encouraging performance compared to Hifiasm with phasing accuracy approaching the theoretical limit, underscoring the promising future of quantum computing in bioinformatics.
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Affiliation(s)
- Yibo Chen
- BGI Research, Shenzhen 518083, China
| | | | - Yuhui Sun
- BGI Research, Shenzhen 518083, China
| | - Yong Zhang
- BGI Research, Wuhan 430047, China; Guangdong Bigdata Engineering Technology Research Center for Life Sciences, BGI Research, Shenzhen 518083, China.
| | - Yuxiang Li
- BGI Research, Wuhan 430047, China; Guangdong Bigdata Engineering Technology Research Center for Life Sciences, BGI Research, Shenzhen 518083, China.
| | - Xun Xu
- BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430047, China.
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5
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024; 25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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6
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Hiralal A, Geelhoed JS, Hidalgo-Martinez S, Smets B, van Dijk JR, Meysman FJR. Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads. Microb Genom 2024; 10:001197. [PMID: 38376381 PMCID: PMC10926707 DOI: 10.1099/mgen.0.001197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.
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Affiliation(s)
- Anwar Hiralal
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | | | - Bent Smets
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | - Filip J. R. Meysman
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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Fernandez LA, Martin-Mayor V, Yllanes D. Phase transition in the computational complexity of the shortest common superstring and genome assembly. Phys Rev E 2024; 109:014133. [PMID: 38366408 DOI: 10.1103/physreve.109.014133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 12/11/2023] [Indexed: 02/18/2024]
Abstract
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle formulation. That is, the computing time is believed to grow exponentially with the problem size in the worst case. Despite this fact, high-throughput technologies and modern algorithms currently allow bioinformaticians to handle datasets of billions of reads. Using methods from statistical mechanics, we address this conundrum by demonstrating the existence of a phase transition in the computational complexity of the problem and showing that practical instances always fall in the "easy" phase (solvable by polynomial-time algorithms). In addition, we propose a Markov-chain Monte Carlo method that outperforms common deterministic algorithms in the hard regime.
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Affiliation(s)
- L A Fernandez
- Departamento de Física Teórica, Universidad Complutense, 28040 Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), 50018 Zaragoza, Spain
| | - V Martin-Mayor
- Departamento de Física Teórica, Universidad Complutense, 28040 Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), 50018 Zaragoza, Spain
| | - D Yllanes
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), 50018 Zaragoza, Spain
- Chan Zuckerberg Biohub - SF, 499 Illinois Street, San Francisco, California 94158, USA
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Yu C, Zhao Y, Zhao C, Jin J, Mao K, Wang G. MiniDBG: A Novel and Minimal De Bruijn Graph for Read Mapping. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:129-142. [PMID: 38060353 DOI: 10.1109/tcbb.2023.3340251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The De Bruijn graph (DBG) has been widely used in the algorithms for indexing or organizing read and reference sequences in bioinformatics. However, a DBG model that can locate each node, edge and path on sequence has not been proposed so far. Recently, DBG has been used for representing reference sequences in read mapping tasks. In this process, it is not a one-to-one correspondence between the paths of DBG and the substrings of reference sequence. This results in the false path on DBG, which means no substrings of reference producing the path. Moreover, if a candidate path of a read is true, we need to locate it and verify the candidate on sequence. To solve these problems, we proposed a DBG model, called MiniDBG, which stores the position lists of a minimal set of edges. With the position lists, MiniDBG can locate any node, edge and path efficiently. We also proposed algorithms for generating MiniDBG based on an original DBG and algorithms for locating edges or paths on sequence. We designed and ran experiments on real datasets for comparing them with BWT-based and position list-based methods. The experimental results show that MiniDBG can locate the edges and paths efficiently with lower memory costs.
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Rattanapan Y, Charong N, Narkpetch S, Chareonsirisuthigul T. Genotyping of the rare Para-Bombay blood group in southern Thailand. Hematol Transfus Cell Ther 2023; 45:449-455. [PMID: 36241527 PMCID: PMC10627842 DOI: 10.1016/j.htct.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/15/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023] Open
Abstract
INTRODUCTION The para-Bombay phenotype, or H-deficient secretor, results from different mutations of the FUT1, with or without the FUT2 mutation. Consequently, there is an absent or weak expression of the H antigen on red blood cells (RBCs). Routine ABO blood grouping for two siblings with blood group O showed discrepant results with their parental blood group AB. Fragments encompassing the entire coding region of the FUT1 and FUT2 genes were investigated. METHODS Blood and saliva specimens were collected to verify the correct ABO grouping by cell grouping, serum grouping and the hemagglutination inhibition (HI) test, respectively. The FUT1 and FUT2 genomes were identified using the whole-exome sequencing (WES) in two children's DNA blood specimens and may have caused, or been relative to, their blood group. Genetic variations of the FUT1 and FUT2 genes have been investigated in the other family members using the Sanger sequencing. RESULTS The serologic reaction results of the proband revealed that A, B and H antigens were absent on RBCs, and that the serum contained anti-H. However, ABH and AH antigens were present in the saliva PB1 and PB2, respectively. The probands PB1 and PB2 were assigned as AB and A blood groups, respectively. Blood genotyping confirmed that heterozygous mutations of the FUT1 gene, c.551_552delAG, were identified. Three family members, PB3, PB, and PB8, also showed normal ABO blood groups, but their genotypes were also the FUT1 mutation c.551_552delAG. CONCLUSIONS The FUT1 mutation c.551_552delAG may result in the reduced or absent H antigen production on RBCs, which characterizes the para-Bombay phenotypes. Blood genotyping is essential if these individuals need a blood transfusion or are planning to donate blood.
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Affiliation(s)
- Yanisa Rattanapan
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand; Hematology and Transfusion Science Research Center, Walailak University, Nakhon Si Thammarat, Thailand
| | - Nurdina Charong
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand; Hematology and Transfusion Science Research Center, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sodsai Narkpetch
- Blood Bank, Maharaj Nakhon Si Thammarat Hospital, Nakhon Si Thammarat, Thailand
| | - Takol Chareonsirisuthigul
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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Yang Y, Guo X, Zhang M, Wang H, Mu S, Peng H, Yao Y. A study of application effects of next-generation sequencing based preimplantation genetic testing for aneuploidies in advanced maternal age women. Taiwan J Obstet Gynecol 2023; 62:729-734. [PMID: 37679003 DOI: 10.1016/j.tjog.2023.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 09/09/2023] Open
Abstract
OBJECTIVE To investigate if next-generation sequencing-based preimplantation genetic testing for aneuploidies could improve pregnancy outcomes in women of advanced maternal age. MATERIALS AND METHODS A retrospective analysis. The clinical data of 1099 couples treated in the First Medical Center of the Chinese PLA General Hospital from January 2019 to December 2021 were analyzed. They were divided into two groups based on whether they underwent a Next-generation sequencing-based preimplantation genetic test for aneuploidies. We analyzed and compared the biochemical pregnancy rate, clinical pregnancy rate, abortion rate, and live birth rate between the two groups. RESULTS The Preimplantation genetic testing for aneuploidies (PGT-A) group was associated with higher rate of biochemical pregnancy and clinical pregnancy than the non-PGT-A group, which were 63.9% vs. 56.4% (P = 0.009) and 54.4% vs. 45.6% (P < 0.001), respectively. The abortion rate was significantly lower in the PGT-A group compared to the non-PGT-A group (2.3% vs. 14.7%, P < 0.001). In addition, the live birth rate was significantly higher in the PGT-A group compared to the non-PGT-A group (52.1% and 30.9%, respectively, P < 0.001). CONCLUSION Next-generation sequencing-based preimplantation genetic testing for aneuploidies significantly improved the pregnancy outcomes in women of advanced maternal age.
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Affiliation(s)
- Yizhuo Yang
- Department of Obstetrics and Gynecology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Xinmeng Guo
- College of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Ming Zhang
- Department of Obstetrics and Gynecology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Hui Wang
- Department of Obstetrics and Gynecology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Sha Mu
- Department of Obstetrics and Gynecology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Hongmei Peng
- Department of Obstetrics and Gynecology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
| | - Yuanqing Yao
- Department of Obstetrics and Gynecology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China; College of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China; The University of Hong Kong - Shenzhen Hospital, 1 Haiyuan Road, Shenzhen, Guangdong, 518053, China.
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Ribeiro M, Maciel C, Cruz P, Darmancier H, Nogueira T, Costa M, Laranjeira J, Morais RMSC, Teixeira P. Exploiting Potential Probiotic Lactic Acid Bacteria Isolated from Chlorella vulgaris Photobioreactors as Promising Vitamin B12 Producers. Foods 2023; 12:3277. [PMID: 37685210 PMCID: PMC10486965 DOI: 10.3390/foods12173277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Lactic acid bacteria (LAB) have been documented as potential vitamin B12 producers and may constitute an exogenous source of cobalamin for the microalga Chlorella vulgaris, which has been described as being able to perform vitamin uptake. Hence, there is an interest in discovering novel B12-producing probiotic LAB. Therefore, the purpose of the current work was to perform a phenotype-genotype analysis of the vitamin B12 biosynthesis capacity of LAB isolated from C. vulgaris bioreactors, and investigate their probiotic potential. Among the selected strains, Lactococcus lactis E32, Levilactobacillus brevis G31, and Pediococcus pentosaceus L51 demonstrated vitamin B12 biosynthesis capacity, with the latter producing the highest (28.19 ± 2.27 pg mL-1). The genomic analysis confirmed the presence of pivotal genes involved in different steps of the biosynthetic pathway (hemL, cbiT, cobC, and cobD). Notably, P. pentosaceus L51 was the only strain harboring cobA, pduU, and pduV genes, which may provide evidence for the presence of the cobalamin operon. All strains demonstrated the capability to withstand harsh gastrointestinal conditions, although P. pentosaceus L51 was more resilient. The potential for de novo cobalamin biosynthesis and remarkable probiotic features highlighted that P. pentosaceus L51 may be considered the most promising candidate strain for developing high-content vitamin B12 formulations.
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Affiliation(s)
- Mónica Ribeiro
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal (R.M.S.C.M.)
| | - Cláudia Maciel
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal (R.M.S.C.M.)
| | - Pedro Cruz
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal (R.M.S.C.M.)
| | - Helena Darmancier
- INIAV—Instituto Nacional de Investigação Agrária e Veterinária, I.P., 2780-159 Oeiras, Portugal
| | - Teresa Nogueira
- INIAV—Instituto Nacional de Investigação Agrária e Veterinária, I.P., 2780-159 Oeiras, Portugal
- cE3c—Center for Ecology, Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute, 1749-016 Lisbon, Portugal
| | - Margarida Costa
- ALLMICROALGAE Natural Products S.A., R&D Department, Rua 25 de Abril s/n, 2445-413 Pataias, Portugal
| | - Joana Laranjeira
- ALLMICROALGAE Natural Products S.A., R&D Department, Rua 25 de Abril s/n, 2445-413 Pataias, Portugal
| | - Rui M. S. C. Morais
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal (R.M.S.C.M.)
| | - Paula Teixeira
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal (R.M.S.C.M.)
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12
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de Souza LM, de Oliveira ID, Sales FCS, da Costa AC, Campos KR, Abbud A, Guerra JM, Dos Santos Cirqueira Borges C, Takahashi CPFJ, de Araújo LJT. Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples. J Genet Eng Biotechnol 2023; 21:88. [PMID: 37642827 PMCID: PMC10465416 DOI: 10.1186/s43141-023-00536-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/27/2023] [Indexed: 08/31/2023]
Abstract
New-generation sequencing (NGS) techniques have brought the opportunity for genomic monitoring of several microorganisms potentially relevant to public health. The establishment of different methods with different mechanisms provides a wide choice, taking into account several aspects. With that in mind, the present aim of the study was to compare basic genomic sequencing metrics that could potentially impact genotyping by nanopores from Oxford Nanopore Technologies and by synthesis from Illumina in clinical samples positive for Chikungunya (CHIKV). Among the metrics studied, running time, read production, and Q score were better represented in Illumina sequencing, while the MinIOn platform showed better response time and greater diversity of generated files. That said, it was possible to establish differences between the studied metrics in addition to verifying that the distinctions in the methods did not impact the identification of the CHIKV virus genotype.
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Affiliation(s)
- Leandro Menezes de Souza
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil
| | - Isabelle Dias de Oliveira
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil
| | - Flávia Cristina Silva Sales
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | | | - Adriano Abbud
- Centro de Respostas Rápidas, Instituto Adolfo Lutz, Sao Paulo, Brazil
| | | | | | | | - Leonardo José Tadeu de Araújo
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil.
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil.
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil.
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13
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Liu P, Ewald J, Pang Z, Legrand E, Jeon YS, Sangiovanni J, Hacariz O, Zhou G, Head JA, Basu N, Xia J. ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species. Nat Commun 2023; 14:2995. [PMID: 37225696 DOI: 10.1038/s41467-023-38785-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/16/2023] [Indexed: 05/26/2023] Open
Abstract
The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst ( www.expressanalyst.ca ), a web-based platform for processing, analyzing, and interpreting RNA-sequencing data from any eukaryotic species. ExpressAnalyst contains a series of modules that cover from processing and annotation of FASTQ files to statistical and functional analysis of count tables or gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst allows researchers to obtain global expression profiles and gene-level insights from raw RNA-sequencing reads within 24 h. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-sequencing data from multiple non-model salamander species, including two that do not have a reference transcriptome.
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Affiliation(s)
- Peng Liu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Zhiqiang Pang
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Elena Legrand
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Yeon Seon Jeon
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Jonathan Sangiovanni
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Orcun Hacariz
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Guangyan Zhou
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Jessica A Head
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada.
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14
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Wang Y, Cai X, Hu S, Qin S, Wang Z, Cao Y, Hou C, Yang J, Zhou W. Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2. Gene 2023; 855:147118. [PMID: 36521669 DOI: 10.1016/j.gene.2022.147118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/21/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium.
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Affiliation(s)
- Yongqiang Wang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Xunhui Cai
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shengnan Hu
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Sidong Qin
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Ziqi Wang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Yixiang Cao
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Chaoliang Hou
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Jiangshan Yang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Wei Zhou
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
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15
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Zhou QM, Jiang F, Xu J, Lin D, Huang RL, Zhou JY, Qu YX, Li DZ. High accuracy of single-molecule real-time sequencing in detecting a rare α-globin fusion gene in carrier screening population. Ann Hum Genet 2023; 87:9-17. [PMID: 36317495 DOI: 10.1111/ahg.12486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
INTRODUCTION The α-globin fusion gene between the HBA2 and HBAP1 genes becomes clinically important in thalassemia screening because this fusion gene can cause severe hemoglobin (Hb) H disease when combining with α0 -thalassemia (α0 -thal). Due to its uncommon rearrangement in the α gene cluster without dosage changes, this fusion gene is undetectable by common molecular testing approaches used for α-thal diagnosis. METHODS In this study, we used the single-molecule real-time (SMRT) sequencing technique to detect this fusion gene in 23 carriers identified by next-generation sequencing (NGS) among 16,504 screened individuals. Five primers for α and β thalassemia were utilized. RESULTS According to the NGS results, the 23 carriers include 14 pure heterozygotes, eight compound heterozygotes with common α-thal alleles, and one homozygote. By using SMRT, the fusion mutant was successfully detected in all 23 carriers. Furthermore, SMRT corrected the diagnosis in two "pure" heterozygotes: one was compound heterozygote with anti-3.7 triplication, and the other was homozygote. CONCLUSION Our results indicate that SMRT is a superior method compared to NGS in detecting the α fusion gene, attributing to its efficient, accurate, and one-step properties.
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Affiliation(s)
- Qiao-Miao Zhou
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
| | - Jing Xu
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Dan Lin
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Ren-Liang Huang
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Xia Qu
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
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16
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Anwar N, Jiang Y, Ma W, Yao Y, Li J, Ababaikeli G, Li G, Ma T. Culturable bacteria diversity in stem liquid and resina from Populus euphratica and screening of plant growth-promoting bacteria. BMC Microbiol 2022; 22:322. [PMID: 36581840 PMCID: PMC9798617 DOI: 10.1186/s12866-022-02731-7] [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: 05/09/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Populus euphratica Olivier is a kind of tree capable of growing in extremely arid desert and semi-desert environments. In this study, a culture-dependent method was used to analyze the bacterial diversity of stem liquid of P. euphratica and resina of P. euphratica, and to further evaluate plant growth promoting (PGP) activity. RESULTS A total of 434 bacteria were isolated from stem fluid and resina of P. euphratica in Ebinur Lake Wetland Nature Reserve and Mulei Primitive forest. The results of taxonomic composition analysis shows that Gammaproteobacteria, Firmicutes, and Actinobacteria_c are the three dominant groups in all the communities, and the representative genera are Bacillus, Nesterenkonia and Halomonas. The diversity analysis shows that the culturable bacterial community diversity of P. euphratica in Ebinur Lake Wetland Nature Reserve is higher than that in Mulei Primitive forest, and the bacterial community diversity of P. euphratica stem fluid is higher than that of resina. According to PGP activity evaluation, 158 functional bacteria with plant growth promoting potential were screened. Among them, 61 strains havephosphorus solubilizing abilities, 80 strains have potassium solubilizing abilities, 32 strains have nitrogen fixation abilities, and 151 strains have iron ammonia salt utilization abilities. The germination rate, plant height, and dry weight of the maize seedlings treated with strains BB33-1, TC10 and RC6 are significantly higher than those of the control group. CONCLUSION In this study, a large number of culturable bacteria were isolated from P. euphratica, which provides new functional bacteria sources for promoting plant growth.
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Affiliation(s)
- Nusratgul Anwar
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Yuhang Jiang
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Wenbo Ma
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Yuhao Yao
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Jue Li
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Gulibahaer Ababaikeli
- grid.464477.20000 0004 1761 2847College of Life Sciences, Xinjiang Normal University, Urumqi, 830054 China
| | - Guoqiang Li
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Ting Ma
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
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17
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Tounsi WA, Lenis VP, Tammi SM, Sainio S, Haimila K, Avent ND, Madgett TE. Rh Blood Group D Antigen Genotyping Using a Portable Nanopore-based Sequencing Device: Proof of Principle. Clin Chem 2022; 68:1196-1201. [PMID: 35652461 DOI: 10.1093/clinchem/hvac075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Nanopore sequencing is direct sequencing of a single-stranded DNA molecule using biological pores. A portable nanopore-based sequencing device from Oxford Nanopore Technologies (MinION) depends on driving a DNA molecule through nanopores embedded in a membrane using a voltage. Changes in current are then measured by a sensor, thousands of times per second and translated to nucleobases. METHODS Genomic DNA (gDNA) samples (n = 13) were tested for Rh blood group D antigen (RHD) gene zygosity using droplet digital PCR. The RHD gene was amplified in 6 overlapping amplicons using long-range PCR. Amplicons were purified, and the sequencing library was prepared following the 1D Native barcoding gDNA protocol. Sequencing was carried out with 1D flow cells R9 version. Data analysis included basecalling, aligning to the RHD reference sequence, and calling variants. Variants detected were compared to the results acquired previously by the Ion Personal Genome Machine (Ion PGM). RESULTS Up to 500× sequence coverage across the RHD gene allowed accurate variant calling. Exonic changes in the RHD gene allowed RHD allele determination for all samples sequenced except 1 RHD homozygous sample, where 2 heterozygous RHD variant alleles are suspected. There were 3 known variant RHD alleles (RHD*01W.02, RHD*11, and RHD*15) and 6 novel RHD variant alleles, as previously seen in Ion PGM sequencing data for these samples. CONCLUSIONS MinION was effective in blood group genotyping, provided enough sequencing data to achieve high coverage of the RHD gene, and enabled confident calling of variants and RHD allele determination.
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Affiliation(s)
- Wajnat A Tounsi
- Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Vasileios P Lenis
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
- School of Health and Life Sciences, Teesside University, Middlesbrough, Tees Valley, UK
| | - Silja M Tammi
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Susanna Sainio
- Blood Group Unit, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Katri Haimila
- Blood Group Unit, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Neil D Avent
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Tracey E Madgett
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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Yu C, Mao K, Zhao Y, Chang C, Wang G. StLiter: A Novel Algorithm to Iteratively Build the Compacted de Bruijn Graph From Many Complete Genomes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2471-2483. [PMID: 33630738 DOI: 10.1109/tcbb.2021.3062068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, the compacted de Bruijn graph (cDBG) of complete genome sequences was successfully used in read mapping due to its ability to deal with the repetitions in genomes. However, current approaches are not flexible enough to fit frequently building the graphs with different k-mer lengths. Instead of building the graph directly, how can we build the compacted de Bruijin graph of longer k-mer based on the one of short k-mer? In this article, we present StLiter, a novel algorithm to build the compacted de Bruijn graph either directly from genome sequences or indirectly based on the graph of a short k-mer. For 100 simulated human genomes, StLiter can construct the graph of k-mer length 15-18 in 2.5-3.2 hours with maximal ∼70GB memory in the case of without considering the reverese complements of the reference genomes. And it costs 4.5-5.9 hours when considering the reverse complements. In experiments, we compared StLiter with TwoPaCo, the state-of-art method for building the graph, on 4 datasets. For k-mer length 15-18, StLiter can build the graph 5-9 times faster than TwoPaCo using less maximal memory cost. For k-mer length larger than 18, given the graph of a short (k- x)-mer, such as x= 1-2, compared with TwoPaCo building the graph directly, StLiter can also build the graph more efficiently. The source codes of StLiter can be downloaded from web site https://github.com/BioLab-cz/StLiter.
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20
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Goussarov G, Mysara M, Vandamme P, Van Houdt R. Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. Microbiologyopen 2022; 11:e1298. [PMID: 35765182 PMCID: PMC9179125 DOI: 10.1002/mbo3.1298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome‐assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation.
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Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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21
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Jiang F, Mao AP, Liu YY, Liu FZ, Li YL, Li J, Zhou JY, Tang XW, Ju AP, Li FT, Wan JH, Zuo LD, Li DZ. Detection of rare thalassemia mutations using long-read single-molecule real-time sequencing. Gene 2022; 825:146438. [PMID: 35306112 DOI: 10.1016/j.gene.2022.146438] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Abstract
Gap- polymerase chain reaction (PCR), reverse dot-blot assay (RDB), real-time PCR based multicolor melting curve analysis (MMCA assay), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing are conventional methods to diagnose thalassemia but all of them have limitations. In this study, we applied single-molecule real-time (SMRT) sequencing following multiplex long-range PCR to uncover rare mutations in nine patients and their family members. The patients with different results between Gap-PCR and MMCA assay or with phenotype not matching genotype were included. Using SMRT sequencing, we first identified the carriers with αααanti3.7/HKαα, -α762bpα/αα (chr16:172,648-173,409), ααfusion/αQSα (in a trans configuration), two cases with novel gene rearrangements and another case with a novel 341 bp insertion in α-globin gene cluster, respectively. One carrier with --SEA/αααanti4.2, and two carriers with the coexistence of globin variant and an α-globin gene duplication were also found. Most importantly, we could determine two defects in α-globin gene cluster being a cis or trans configuration in a single test. Our results showed that SMRT has great advantages in detection of α-globin gene triplications, rare deletions and determination of a cis or trans configuration. SMRT is a comprehensive and one-step method for thalassemia screening and diagnosis, especially for detection of rare thalassemia mutations.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ai-Ping Mao
- Berry Genomics Corporation, Beijing, 102200, China
| | - Yin-Yin Liu
- Berry Genomics Corporation, Beijing, 102200, China
| | - Feng-Zhi Liu
- Medical Genetics Laboratory, Foshan Maternal and Child Health Hospital, Foshan, Guangdong, China
| | - Yan-Lin Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Xue-Wei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ai-Ping Ju
- Clinical Laboratory, Huadu District Maternal and Neonatal Healthcare Hospital of Guangzhou, Hu Zhong Hospital, Guangzhou, Guangdong, China
| | - Fa-Tao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jun-Hui Wan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Lian-Dong Zuo
- Scientific Research Department, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China.
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22
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Xian S, Zhong H, Yi B, Liu X, Shen G, Li M, Zhang Z, Luo Q, Li S, Zhou M, Xu F, Chen A. Identification of pellicle formation related microorganisms in traditional Sichuan paocai through metagenomic sequence and the effects of Baijiu/Salt on pellicle and volatile components. Food Res Int 2022; 159:111130. [DOI: 10.1016/j.foodres.2022.111130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022]
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23
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Li M, Sun C, Xu N, Bian P, Tian X, Wang X, Wang Y, Jia X, Heller R, Wang M, Wang F, Dai X, Luo R, Guo Y, Wang X, Yang P, Hu D, Liu Z, Fu W, Zhang S, Li X, Wen C, Lan F, Siddiki AZ, Suwannapoom C, Zhao X, Nie Q, Hu X, Jiang Y, Yang N. De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on micro-chromosomes and sub-telomeric regions. Mol Biol Evol 2022; 39:6553873. [PMID: 35325213 PMCID: PMC9021737 DOI: 10.1093/molbev/msac066] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.
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Affiliation(s)
- Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Naiyi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaomeng Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.,National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China
| | - Xinzheng Jia
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.,School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Mingshan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95064, USA
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Rongsong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiangnan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhenyu Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shunjin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaochang Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Chaoliang Wen
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Fangren Lan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Amam Zonaed Siddiki
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chittagong Veterinary and Animal Sciences University, Chittagong-4202, Bangladesh
| | | | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, Quebec, Canada
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
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24
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Smirnov DN, Shekhovtsov SV, Shipova AA, Gazizova GR, Shagimardanova EI, Bulakhova NA, Meshcheryakova EN, Poluboyarova TV, Khrameeva EE, Peltek SE, Berman DI. De novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensis. Vavilovskii Zhurnal Genet Selektsii 2022; 26:109-116. [PMID: 35342853 PMCID: PMC8894097 DOI: 10.18699/vjgb-22-07] [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: 08/10/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
The Siberian wood frog Rana amurensis Boulenger, 1886 is the most hypoxia-tolerant amphibian. It can survive for several months in an almost complete absence of oxygen. Little is known about the mechanisms of this remarkable resilience, in part because studies of amphibian genomes are impeded by their large size. To make the Siberian wood frog more amenable for genetic analysis, we performed transcriptome sequencing and de novo assembly for the R. amurensis brain under hypoxia and normoxia, as well as for the normoxic heart. In order to build a de novo transcriptome assembly of R. amurensis, we utilized 125-bp paired-end reads obtained from the brain under normoxia and hypoxia conditions, and from the heart under normoxia. In the transcriptome assembled from about 100,000,000 reads, 81.5 % of transcripts were annotated as complete, 5.3 % as fragmented, and 13.2 % as missing. We detected 59,078 known transcripts that clustered into 22,251 genes; 11,482 of them were assigned to specific GO categories. Among them, we found 6696 genes involved in protein binding, 3531 genes involved in catalytic activity, and 576 genes associated with transporter activity. A search for genes encoding receptors of the most important neurotransmitters, which may participate in the response to hypoxia, resulted in a set of expressed receptors of dopamine, serotonin, GABA, glutamate, acetylcholine, and norepinephrine. Unexpectedly, no transcripts for histamine receptors were found. The data obtained in this study create a valuable resource for studying the mechanisms of hypoxia tolerance in the Siberian wood frog, as well as for amphibian studies in general.
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Affiliation(s)
- D. N. Smirnov
- Center of Life Sciences, Skolkovo Institute of Science and Technology; Ben-Gurion University of the Negev, Department of Life Sciences
| | - S. V. Shekhovtsov
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. A. Shipova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - G. R. Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University
| | | | - N. A. Bulakhova
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
| | - E. N. Meshcheryakova
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
| | - T. V. Poluboyarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. E. Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology
| | - S. E. Peltek
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - D. I. Berman
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
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25
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Regueira-Iglesias A, Vázquez-González L, Balsa-Castro C, Blanco-Pintos T, Martín-Biedma B, Arce VM, Carreira MJ, Tomás I. In-Silico Detection of Oral Prokaryotic Species With Highly Similar 16S rRNA Sequence Segments Using Different Primer Pairs. Front Cell Infect Microbiol 2022; 11:770668. [PMID: 35223533 PMCID: PMC8863748 DOI: 10.3389/fcimb.2021.770668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
Although clustering by operational taxonomic units (OTUs) is widely used in the oral microbial literature, no research has specifically evaluated the extent of the limitations of this sequence clustering-based method in the oral microbiome. Consequently, our objectives were to: 1) evaluate in-silico the coverage of a set of previously selected primer pairs to detect oral species having 16S rRNA sequence segments with ≥97% similarity; 2) describe oral species with highly similar sequence segments and determine whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain the in-silico amplicons from the complete genomes of 186 bacterial and 135 archaeal species. Each fasta file for the same primer pair was inserted as subject and query in BLASTN for obtaining the similarity percentage between amplicons belonging to different oral species. Amplicons with 100% alignment coverage of the query sequences and with an amplicon similarity value ≥97% (ASI97) were selected. For each primer, the species coverage with no ASI97 (SC-NASI97) was calculated. Based on the SC-NASI97 parameter, the best primer pairs were OP_F053-KP_R020 for bacteria (region V1-V3; primer pair position for Escherichia coli J01859.1: 9-356); KP_F018-KP_R002 for archaea (V4; undefined-532); and OP_F114-KP_R031 for both (V3-V5; 340-801). Around 80% of the oral-bacteria and oral-archaea species analyzed had an ASI97 with at least one other species. These very similar species play different roles in the oral microbiota and belong to bacterial genera such as Campylobacter, Rothia, Streptococcus and Tannerella, and archaeal genera such as Halovivax, Methanosarcina and Methanosalsum. Moreover, ~20% and ~30% of these two-by-two similarity relationships were established between species from different bacterial and archaeal genera, respectively. Even taxa from distinct families, orders, and classes could be grouped in the same possible OTU. Consequently, regardless of the primer pair used, sequence clustering with a 97% similarity provides an inaccurate description of oral-bacterial and oral-archaeal species, which can greatly affect microbial diversity parameters. As a result, OTU clustering conditions the credibility of associations between some oral species and certain health and disease conditions. This significantly limits the comparability of the microbial diversity findings reported in oral microbiome literature.
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Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Lara Vázquez-González
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Benjamín Martín-Biedma
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Víctor M. Arce
- Department of Physiology and Center for Disease in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria J. Carreira
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
- *Correspondence: Inmaculada Tomás, ; Maria J. Carreira,
| | - Inmaculada Tomás
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
- *Correspondence: Inmaculada Tomás, ; Maria J. Carreira,
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26
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Hurgobin B. Annotation of Protein-Coding Genes in Plant Genomes. Methods Mol Biol 2022; 2443:309-326. [PMID: 35037214 DOI: 10.1007/978-1-0716-2067-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Advances in next-generation sequencing technologies and the lower sequencing costs are paving the way to more plant genome sequencing, assembly, and annotation projects. While genome assembly is the first step toward elucidating the genome structure of a species, it is the annotation of the protein-coding genes that provide meaningful information to biologists. However, genome annotation is not a trivial task. Therefore, the aim of this chapter is to provide a detailed view of this important process, including tools and commands that can be used to carry out such a process.
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Affiliation(s)
- Bhavna Hurgobin
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, AgriBio Building, La Trobe University, Bundoora, VIC, Australia.
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC, Australia.
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27
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28
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Wolf E, Gaquerel E, Scharmann M, Yant L, Koch MA. Evolutionary footprints of a cold relic in a rapidly warming world. eLife 2021; 10:e71572. [PMID: 34930524 PMCID: PMC8741218 DOI: 10.7554/elife.71572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here, we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This sudden change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified Arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed central carbon metabolism responses to cold in diverse species and ecotypes, likely due to continuous connections to cold habitats that may have facilitated widespread adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in the adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.
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Affiliation(s)
- Eva Wolf
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
| | - Mathias Scharmann
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, the University of NottinghamNottinghamUnited Kingdom
| | - Marcus A Koch
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
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29
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Comparative genomics of Leishmania isolates from Brazil confirms the presence of Leishmania major in the Americas. Int J Parasitol 2021; 51:1047-1057. [PMID: 34329650 DOI: 10.1016/j.ijpara.2021.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 11/22/2022]
Abstract
Leishmania (Leishmania) major is an important agent of cutaneous leishmaniasis, having as a vector sandflies belonging to the genus Phlebotomus. Although this species has been described as restricted to the Old World, parasites similar to L. major have been isolated from South American patients who have never travelled abroad. These parasites were named "L. major-like", and several studies have been carried out to characterise them biochemically, molecularly, and biologically. However, the phylogenetic origin of these isolates is still unknown. In the present study we characterised three L. major-like isolates, named BH49, BH121 and BH129, using comparative genomics approaches. We evaluated the presence of gene and segmental duplications/deletions and the presence of aneuploidies that could explain the differences in infectivity observed in the BH49 and BH121 isolates. All isolates presented a pattern of mosaic aneuploidy and gene copy number variation, which are common in the genus Leishmania. Virulence factors such as phosphatases and peptidases were found to have increased gene copy numbers in the infective isolate, which could explain the difference in infectivity previously observed between BH121 and BH49. Phylogenetic analyses revealed that BH49, BH121 and BH129 L. major-like grouped with L. major isolates, and suggest they were imported from the Old World in at least two independent events. We suggest that new epidemiological inquiries should also evaluate L. major infections in South America, to assess the epidemiological importance of this species in the New World.
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30
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Fritz A, Bremges A, Deng ZL, Lesker TR, Götting J, Ganzenmueller T, Sczyrba A, Dilthey A, Klawonn F, McHardy AC. Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biol 2021; 22:212. [PMID: 34281604 PMCID: PMC8287296 DOI: 10.1186/s13059-021-02426-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
AbstractWith viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a deBruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assess Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. We show Haploflow reconstructs viral strain genomes from patient HCMV samples and SARS-CoV-2 wastewater samples identical to clinical isolates.
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Affiliation(s)
- Adrian Fritz
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Andreas Bremges
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Zhi-Luo Deng
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till Robin Lesker
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Jasper Götting
- German Centre for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tina Ganzenmueller
- German Centre for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute for Medical Virology, University Hospital Tuebingen, Tuebingen, Germany
| | - Alexander Sczyrba
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Frank Klawonn
- Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbuettel, Germany
- Biostatistics Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Alice Carolyn McHardy
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- German Centre for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany.
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31
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Zhao L, Wang H, Li P, Sun K, Guan DL, Xu SQ. Genome Size Estimation and Full-Length Transcriptome of Sphingonotus tsinlingensis: Genetic Background of a Drought-Adapted Grasshopper. Front Genet 2021; 12:678625. [PMID: 34322153 PMCID: PMC8313316 DOI: 10.3389/fgene.2021.678625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/14/2021] [Indexed: 11/25/2022] Open
Abstract
Sphingonotus Fieber, 1852 (Orthoptera: Acrididae), is a grasshopper genus comprising approximately 170 species, all of which prefer dry environments such as deserts, steppes, and stony benchlands. In this study, we aimed to examine the adaptation of grasshopper species to arid environments. The genome size of Sphingonotus tsinlingensis was estimated using flow cytometry, and the first high-quality full-length transcriptome of this species was produced. The genome size of S. tsinlingensis is approximately 12.8 Gb. Based on 146.98 Gb of PacBio sequencing data, 221.47 Mb full-length transcripts were assembled. Among these, 88,693 non-redundant isoforms were identified with an N50 value of 2,726 bp, which was markedly longer than previous grasshopper transcriptome assemblies. In total, 48,502 protein-coding sequences were identified, and 37,569 were annotated using public gene function databases. Moreover, 36,488 simple tandem repeats, 12,765 long non-coding RNAs, and 414 transcription factors were identified. According to gene functions, 61 cytochrome P450 (CYP450) and 66 heat shock protein (HSP) genes, which may be associated with drought adaptation of S. tsinlingensis, were identified. We compared the transcriptomes of S. tsinlingensis and two other grasshopper species which were less tolerant to drought, namely Mongolotettix japonicus and Gomphocerus licenti. We observed the expression of CYP450 and HSP genes in S. tsinlingensis were higher. We produced the first full-length transcriptome of a Sphingonotus species that has an ultra-large genome. The assembly characteristics were better than those of all known grasshopper transcriptomes. This full-length transcriptome may thus be used to understand the genetic background and evolution of grasshoppers.
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Affiliation(s)
- Lu Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Ping Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Kuo Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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Dida F, Yi G. Empirical evaluation of methods for de novo genome assembly. PeerJ Comput Sci 2021; 7:e636. [PMID: 34307867 PMCID: PMC8279138 DOI: 10.7717/peerj-cs.636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/19/2021] [Indexed: 06/12/2023]
Abstract
Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms. A drastic reduction in the costs of generating short reads on the genomes of new organisms is attributable to recent advances in NGS technologies such as Ion Torrent, Illumina, and PacBio. Genome research has led to the creation of high-quality reference genomes for several organisms, and de novo assembly is a key initiative that has facilitated gene discovery and other studies. More powerful analytical algorithms are needed to work on the increasing amount of sequence data. We make a thorough comparison of the de novo assembly algorithms to allow new users to clearly understand the assembly algorithms: overlap-layout-consensus and de-Bruijn-graph, string-graph based assembly, and hybrid approach. We also address the computational efficacy of each algorithm's performance, challenges faced by the assem- bly tools used, and the impact of repeats. Our results compare the relative performance of the different assemblers and other related assembly differences with and without the reference genome. We hope that this analysis will contribute to further the application of de novo sequences and help the future growth of assembly algorithms.
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Affiliation(s)
- Firaol Dida
- Department of Multimedia Engineering, Dongguk University, Seoul, South Korea
| | - Gangman Yi
- Department of Multimedia Engineering, Dongguk University, Seoul, South Korea
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Li XY, Tan ZJ. Advances in research technology of regulation of intestinal microecology by traditional Chinese medicine. Shijie Huaren Xiaohua Zazhi 2021; 29:479-487. [DOI: 10.11569/wcjd.v29.i9.479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The intestine is a diversified microecosystem whose structure and function are research hotspots in the fields of life sciences and medicine. The research on the regulation of intestinal microecology by traditional Chinese medicine is of great significance to the elucidation of the basic theories and the mechanism of therapeutic effects of traditional Chinese medicine. The micro-ecological research technology is very important for the research in this field. We, by reviewing the relevant literature, summarize the related technologies for the intestinal micro-ecological research of traditional Chinese medicine, such as microbial culture counting method, molecular biology techniques (denaturing/temperature gradient gel electrophoresis (DGGE/TGGE), gene chip, real-time quantitative polymerase chain reaction (PT-PCR), terminal-restriction fragment length polymorphism (T-RFLP), amplified ribosomal DNA restriction analysis (ARDRA), fluorescent in situ hybridization (FISH), high-throughput sequencing (HTS), metabolic level analysis techniques, and proteomics), intestinal enzyme activity detection, microbial activity detection technology, and in vitro simulated gastrointestinal environment experiments, with an aim to provide reference for the intestinal micro-ecological research of traditional Chinese medicine and the application of related technologies.
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Affiliation(s)
- Xiao-Ya Li
- Hunan University of Chinese Medicine, Changsha 410208, Hunan Province, China
| | - Zhou-Jin Tan
- Hunan University of Chinese Medicine, Changsha 410208, Hunan Province, China
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Gómez-Muñoz C, García-Ortega LF, Montalvo-Arredondo J, Pérez-Ortega E, Damas-Buenrostro LC, Riego-Ruiz L. Long insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast. G3-GENES GENOMES GENETICS 2021; 11:6188626. [PMID: 33768233 PMCID: PMC8495930 DOI: 10.1093/g3journal/jkab088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022]
Abstract
Lager beer is made with the hybrid Saccharomyces pastorianus. Many publicly available S. pastorianus genome assemblies are highly fragmented due to the difficulties of assembling hybrid genomes, such as the presence of homeologous chromosomes from both parental types, and translocations between them. To improve the assembly of a previously sequenced lager yeast hybrid Saccharomyces sp. 790 and elucidate its genome structure, we proposed the use of alternative experimental evidence. We determined the phylogenetic position of Saccharomyces sp. 790 and established it as S. pastorianus 790. Then, we obtained from this yeast a bacterial artificial chromosome (BAC) genomic library with its BAC-end sequences (BESs). To analyze these data, we developed a pipeline (applicable to other assemblies) that classifies BES pairs alignments according to their orientation. For the case of S. pastorianus 790, paired-end BESs alignments validated parts of the assembly and unpaired-end ones suggested contig joins or misassemblies. Importantly, the BACs library was preserved and used for verification experiments. Unpaired-end alignments were used to upgrade the previous assembly and provided an improved detection of translocations. With this, we proposed a genome structure of S. pastorianus 790, which was similar to that of other lager yeasts; however, when we estimated chromosome copy number and experimentally measured its genome size, we discovered that one key difference is the outstanding S. pastorianus 790 ploidy level (allopentaploid). Altogether, our results show the value of combining bioinformatic analyses with experimental data such as long-insert clone information to improve a short-read assembly of a hybrid genome.
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Affiliation(s)
- Cintia Gómez-Muñoz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216
| | - Luis Fernando García-Ortega
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216.,Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico, 36824
| | - Javier Montalvo-Arredondo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216.,Dirección General Académica, Universidad Autónoma Agraria Antonio Narro, Saltillo, Mexico, 25315
| | | | | | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216
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Fritz A, Bremges A, Deng ZL, Lesker TR, Götting J, Ganzenmüller T, Sczyrba A, Dilthey A, Klawonn F, McHardy A. Haploflow: Strain-resolved de novo assembly of viral genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.25.428049. [PMID: 33532769 PMCID: PMC7852260 DOI: 10.1101/2021.01.25.428049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assessed Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. Haplotype reconstructed high-quality strain-resolved assemblies from clinical HCMV samples and SARS-CoV-2 genomes from wastewater metagenomes identical to genomes from clinical isolates.
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Affiliation(s)
- A. Fritz
- BIFO, Department of Computational Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- DZIF, German Centre for Infection Research
| | - A. Bremges
- BIFO, Department of Computational Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- DZIF, German Centre for Infection Research
| | - Z.-L. Deng
- BIFO, Department of Computational Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - T.-R. Lesker
- BIFO, Department of Computational Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - J. Götting
- DZIF, German Centre for Infection Research
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - T. Ganzenmüller
- DZIF, German Centre for Infection Research
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute for Medical Virology, University Hospital Tuebingen, Tuebingen, Germany
| | - A. Sczyrba
- BIFO, Department of Computational Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - A. Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - F. Klawonn
- Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbuettel, Germany
- Biostatistics Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - A.C. McHardy
- BIFO, Department of Computational Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- DZIF, German Centre for Infection Research
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Xavier MJ, Salas-Huetos A, Oud MS, Aston KI, Veltman JA. Disease gene discovery in male infertility: past, present and future. Hum Genet 2021; 140:7-19. [PMID: 32638125 PMCID: PMC7864819 DOI: 10.1007/s00439-020-02202-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022]
Abstract
Identifying the genes causing male infertility is important to increase our biological understanding as well as the diagnostic yield and clinical relevance of genetic testing in this disorder. While significant progress has been made in some areas, mainly in our knowledge of the genes underlying rare qualitative sperm defects, the same cannot be said for the genetics of quantitative sperm defects. Technological advances and approaches in genomics are critical for the process of disease gene identification. In this review we highlight the impact of various technological developments on male infertility gene discovery as well as functional validation, going from the past to the present and the future. In particular, we draw attention to the use of unbiased genomics approaches, the development of increasingly relevant functional assays and the importance of large-scale international collaboration to advance disease gene identification in male infertility.
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Affiliation(s)
- M J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - A Salas-Huetos
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah, Salt Lake City, USA
| | - M S Oud
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - K I Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah, Salt Lake City, USA.
| | - J A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK.
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38
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Cechova M. Probably Correct: Rescuing Repeats with Short and Long Reads. Genes (Basel) 2020; 12:48. [PMID: 33396198 PMCID: PMC7823596 DOI: 10.3390/genes12010048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Ever since the introduction of high-throughput sequencing following the human genome project, assembling short reads into a reference of sufficient quality posed a significant problem as a large portion of the human genome-estimated 50-69%-is repetitive. As a result, a sizable proportion of sequencing reads is multi-mapping, i.e., without a unique placement in the genome. The two key parameters for whether or not a read is multi-mapping are the read length and genome complexity. Long reads are now able to span difficult, heterochromatic regions, including full centromeres, and characterize chromosomes from "telomere to telomere". Moreover, identical reads or repeat arrays can be differentiated based on their epigenetic marks, such as methylation patterns, aiding in the assembly process. This is despite the fact that long reads still contain a modest percentage of sequencing errors, disorienting the aligners and assemblers both in accuracy and speed. Here, I review the proposed and implemented solutions to the repeat resolution and the multi-mapping read problem, as well as the downstream consequences of reference choice, repeat masking, and proper representation of sex chromosomes. I also consider the forthcoming challenges and solutions with regards to long reads, where we expect the shift from the problem of repeat localization within a single individual to the problem of repeat positioning within pangenomes.
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Affiliation(s)
- Monika Cechova
- Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Central European Institute of Technology (CEITEC), 621 00 Brno, Czech Republic
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39
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Larson MA, Abdalhamid B, Puniya BL, Helikar T, Kelley DW, Iwen PC. Differences in Blood-derived Francisella tularensis Type B Strains from Clinical Cases of Tularemia. Microorganisms 2020; 8:microorganisms8101515. [PMID: 33019689 PMCID: PMC7600085 DOI: 10.3390/microorganisms8101515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/26/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
Francisella tularensis can cause the zoonotic disease tularemia and is partitioned into subspecies due to differences in chromosomal organization and virulence. The subspecies holarctica (type B) is generally considered more clonal than the other subpopulations with moderate virulence compared to the hypervirulent A.I clade. We performed whole genome sequencing (WGS) on six type B strains isolated from the blood of patients with tularemia within a one-year period from the same United States region, to better understand the associated pathogenicity. The WGS data were compared to the prototype strain for this subspecies, specifically FSC200, which was isolated from a patient with tularemia in Europe. These findings revealed 520–528 single nucleotide polymorphisms (SNPs) between the six United States type B strains compared to FSC200, with slightly higher A+T content in the latter strain. In contrast, comparisons between the six type B isolates showed that five of the six type B isolates had only 4–22 SNPs, while one of the strains had 47–53 SNPs. Analysis of SNPs in the core genome for the six United States type B isolates and the FSC200 strain gave similar results, suggesting that some of these mutations may have been nonsynonymous, resulting in altered protein function and pathogenicity.
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Affiliation(s)
- Marilynn A. Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.); (D.W.K.); (P.C.I.)
- Correspondence: ; Tel.: +1-402-559-9115
| | - Baha Abdalhamid
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.); (D.W.K.); (P.C.I.)
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (B.L.P.); (T.H.)
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (B.L.P.); (T.H.)
| | - David W. Kelley
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.); (D.W.K.); (P.C.I.)
| | - Peter C. Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.); (D.W.K.); (P.C.I.)
- Nebraska Public Health Laboratory, Omaha, NE 68198, USA
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Alonge M, Shumate A, Puiu D, Zimin AV, Salzberg SL. Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies. Genetics 2020; 216:599-608. [PMID: 32796007 PMCID: PMC7536849 DOI: 10.1534/genetics.120.303501] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/10/2020] [Indexed: 11/18/2022] Open
Abstract
Bread wheat (Triticum aestivum) is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, genomic resources are limited compared to other major crops. The IWGSC recently published a reference genome and associated annotation (IWGSC CS v1.0, Chinese Spring) that has been widely adopted and utilized by the wheat community. Although this reference assembly represents all three wheat subgenomes at chromosome-scale, it was derived from short reads, and thus is missing a substantial portion of the expected 16 Gbp of genomic sequence. We earlier published an independent wheat assembly (Triticum_aestivum_3.1, Chinese Spring) that came much closer in length to the expected genome size, although it was only a contig-level assembly lacking gene annotations. Here, we describe a reference-guided effort to scaffold those contigs into chromosome-length pseudomolecules, add in any missing sequence that was unique to the IWGSC CS v1.0 assembly, and annotate the resulting pseudomolecules with genes. Our updated assembly, Triticum_aestivum_4.0, contains 15.07 Gbp of nongap sequence anchored to chromosomes, which is 1.2 Gbps more than the previous reference assembly. It includes 108,639 genes unambiguously localized to chromosomes, including over 2000 genes that were previously unplaced. We also discovered >5700 additional gene copies, facilitating the accurate annotation of functional gene duplications including at the Ppd-B1 photoperiod response locus.
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Affiliation(s)
- Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21211
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21211
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21211
| | - Steven L Salzberg
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21211
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
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41
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Zhao H, Chen Y, Shen C, Li L, Li Q, Tan K, Huang H, Hu G. Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient with e14a3 BCR-ABL1 transcript using Nanopore sequencing. J Gene Med 2020; 23:e3276. [PMID: 32949441 DOI: 10.1002/jgm.3276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The genetic changes in chronic myeloid leukaemia (CML) have been well established, although challenges persist in cases with rare fusion transcripts or complex variant translocations. Here, we present a CML patient with e14a3 BCR-ABL1 transcript and t(9;22;12) variant Philadelphia (Ph) chromosome. METHODS Cytogenetic analysis and fluorescence in situ hybridization (FISH) was performed to identify the chromosomal aberrations and gene fusions. Rare fusion transcript was verified by a reverse transcription-polymerase chain reaction (RT-PCR). Breakpoints were characterized and validated using Oxford Nanopore Technologies (ONT) (Oxford, UK) and Sanger sequencing, respectively. RESULTS The karyotype showed the translocation t(9;22;12)(q34;q11.2;q24) [20] and FISH indicated 40% positive BCR-ABL1 fusion signals. The RT-PCR suggested e14a3 type fusion transcript. The ONT sequencing analysis identified specific positions of translocation breakpoints: chr22:23633040-chr9:133729579, chr12:121567595-chr22:24701405, which were confirmed using Sanger sequencing. The patient achieved molecular remission 3 months after imatinib therapy. CONCLUSIONS The present study indicates Nanopore sequencing as a valid strategy, which can characterize breakpoints precisely in special clinical cases with atypical structural variations. CML patients with e14a3 transcripts may have good clinical course in the tyrosine kinase inhibitor era, as reviewed here.
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Affiliation(s)
- Hu Zhao
- Department of Haematology, The Affiliated Zhuzhou Hospital, XiangYa Medical College, Central South University, Zhuzhou, Hunan, China
| | - Yuan Chen
- Department of Haematology, The Affiliated Zhuzhou Hospital, XiangYa Medical College, Central South University, Zhuzhou, Hunan, China
| | - Chanjuan Shen
- Department of Haematology, The Affiliated Zhuzhou Hospital, XiangYa Medical College, Central South University, Zhuzhou, Hunan, China
| | - Lingshu Li
- Department of Haematology, The Affiliated Zhuzhou Hospital, XiangYa Medical College, Central South University, Zhuzhou, Hunan, China
| | - Qingzhao Li
- Department of Haematology, The Affiliated Zhuzhou Hospital, XiangYa Medical College, Central South University, Zhuzhou, Hunan, China
| | - Kui Tan
- Department of Haematology, The Affiliated Zhuzhou Hospital, XiangYa Medical College, Central South University, Zhuzhou, Hunan, China
| | - Huang Huang
- Department of Haematology, The Affiliated Zhuzhou Hospital, XiangYa Medical College, Central South University, Zhuzhou, Hunan, China
| | - Guoyu Hu
- Department of Haematology, The Affiliated Zhuzhou Hospital, XiangYa Medical College, Central South University, Zhuzhou, Hunan, China
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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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43
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Chen G, Xie X. Exon sequencing mutation detection algorithm based on PCR matching. PLoS One 2020; 15:e0236709. [PMID: 32790736 PMCID: PMC7425927 DOI: 10.1371/journal.pone.0236709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/13/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND With the development of second-generation sequencing technology, more and more DNA sequence variations have been detected. Exon sequencing is the first choice for sequencing many cancer genes, and it can be better used to identify disease status by detecting gene variants. PCR sequence is an effective method to capture that sequence of an exon in the process of sequencing. Exon sequencing sequence contains PCR primer sequence, the correct position of the sequence can be determined by PCR primer sequence, which can be found in SNP, Indel mutation point by comparing the sequence of PCR primer sequence. RESULTS In this paper, a matching algorithm based on the PCR primer sequence is proposed, which can effectively sequence the position of PCR primer sequence and find out the key position sequence. Then the sequencing sequence is sorted and the number of the same sequence is counted to reduce the matching times. Then, the sequenced sequence was matched with PCR primer sequence, so that the DNA position could be accurately matched and the variation in the sequenced sequence could be found more quickly. CONCLUSIONS Compared with the traditional sequence matching method, PCR primer sequence matching method can match many sequences and find more variation. It also showed a high recall rate in the recall rate.
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Affiliation(s)
- Guobin Chen
- College of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, PR China
- Chongqing Key Laboratory of Spatial Data Mining and Big Data Integration for Ecology and Environment, Rongzhi College of Chongqing Technology and Business University, Chongqing, PR China
| | - Xianzhong Xie
- College of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, PR China
- * E-mail:
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Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum. BMC Genomics 2020; 21:470. [PMID: 32640982 PMCID: PMC7346634 DOI: 10.1186/s12864-020-06814-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 06/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome sequencing technologies have been improved at an exponential pace but precise chromosome-scale genome assembly still remains a great challenge. The draft genome of cultivated G. arboreum was sequenced and assembled with shotgun sequencing approach, however, it contains several misassemblies. To address this issue, we generated an improved reassembly of G. arboreum chromosome 12 using genetic mapping and reference-assisted approaches and evaluated this reconstruction by comparing with homologous chromosomes of G. raimondii and G. hirsutum. RESULTS In this study, we generated a high quality assembly of the 94.64 Mb length of G. arboreum chromosome 12 (A_A12) which comprised of 144 scaffolds and contained 3361 protein coding genes. Evaluation of results using syntenic and collinear analysis of reconstructed G. arboreum chromosome A_A12 with its homologous chromosomes of G. raimondii (D_D08) and G. hirsutum (AD_A12 and AD_D12) confirmed the significant improved quality of current reassembly as compared to previous one. We found major misassemblies in previously assembled chromosome 12 (A_Ca9) of G. arboreum particularly in anchoring and orienting of scaffolds into a pseudo-chromosome. Further, homologous chromosomes 12 of G. raimondii (D_D08) and G. arboreum (A_A12) contained almost equal number of transcription factor (TF) related genes, and showed good collinear relationship with each other. As well, a higher rate of gene loss was found in corresponding homologous chromosomes of tetraploid (AD_A12 and AD_D12) than diploid (A_A12 and D_D08) cotton, signifying that gene loss is likely a continuing process in chromosomal evolution of tetraploid cotton. CONCLUSION This study offers a more accurate strategy to correct misassemblies in sequenced draft genomes of cotton which will provide further insights towards its genome organization.
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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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Park SY, Jeon J, Kim JA, Jeon MJ, Jeong MH, Kim Y, Lee Y, Chung H, Lee YH, Kim S. Draft Genome Sequence of Alternaria alternata JS-1623, a Fungal Endophyte of Abies koreana. MYCOBIOLOGY 2020; 48:240-244. [PMID: 37970559 PMCID: PMC10635108 DOI: 10.1080/12298093.2020.1756134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2023]
Abstract
Alternaria alternata JS-1623 is an endophytic fungus isolated from a stem tissue of Korean fir, Abies koreana. Ethyl acetate extracts of culture filtrates exhibited anti-inflammatory activity in LPS induced microglia BV-2 cell without cytotoxicity. Here we report a 33.67 Mb sized genome assembly of JS-1623 comprised of 13 scaffolds with N50 of 4.96 Mb, and 92.41% of BUSCO completeness. GC contents were 50.97%. Of the 11,197 genes annotated, gene families related to the biosynthesis of secondary metabolites or transcription factors were identified.
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Affiliation(s)
- Sook-Young Park
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Jongbum Jeon
- Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Jung A. Kim
- Microbiology Resources Division, National Institute of Biological Resources, Incheon, Korea
| | - Mi Jin Jeon
- Microbiology Resources Division, National Institute of Biological Resources, Incheon, Korea
| | - Min-Hye Jeong
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Youngmin Kim
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Yerim Lee
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Hyunjung Chung
- Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Soonok Kim
- Microbiology Resources Division, National Institute of Biological Resources, Incheon, Korea
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Lal Gupta C, Kumar Tiwari R, Cytryn E. Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes. ENVIRONMENT INTERNATIONAL 2020; 138:105667. [PMID: 32234679 DOI: 10.1016/j.envint.2020.105667] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios.
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Affiliation(s)
- Chhedi Lal Gupta
- Institute of Soil, Water and Environmental Sciences, Volcani Research Center, Agriculture Research Organization, Rishon Lezion 7528809, Israel
| | - Rohit Kumar Tiwari
- Department of Biosciences, Integral University, Lucknow 226026, UP, India
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Research Center, Agriculture Research Organization, Rishon Lezion 7528809, Israel.
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Norrell AE, Jones KL, Saillant EA. Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis. PLoS One 2020; 15:e0232402. [PMID: 32348345 PMCID: PMC7190162 DOI: 10.1371/journal.pone.0232402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/15/2020] [Indexed: 11/19/2022] Open
Abstract
The red snapper Lutjanus campechanus is an exploited reef fish of major economic importance in the Gulf of Mexico region. Studies of genome wide genetic variation are needed to understand the structure of wild populations and develop breeding programs for aquaculture but interpretation of these genome scans is limited by the absence of reference genome. In this work, the first draft of a reference genome was developed and characterized for the red snapper. P-454 and Illumina sequencing were conducted to produce paired-end reads that were assembled into reference contigs and scaffolds. The current assembly spans over 770 Mb, representing an estimated 69% of the red snapper genome in 67,254 scaffolds (N50 = 16,803 bp). The genome contigs were applied to map double digest Restriction-Site Associated DNA Tags and characterize Single Nucleotide Polymorphisms (SNPs) in five outbred full-sib families. The identified SNPs and 97 microsatellite loci were used to generate a high-density linkage map that includes 7,420 markers distributed across 24 linkage groups and spans 1,346.64 cM with an average inter–marker distance of 0.18 cM. Sex-specific maps revealed a 1.10:1 female to male map length ratio. A total of 4,422 genome contigs (10.5% of the assembly) were anchored to the map and used in a comparative genomic analysis of the red snapper and two model teleosts. Red snapper showed a high degree of chromosome level syntenic conservation with both medaka and spotted green puffer and a near one to one correspondence between the 24 red snapper linkage groups and corresponding medaka chromosomes was observed. This work established the first draft of a reference genome for a lutjanid fish. The obtained genomic resources will serve as a framework for the interpretation of genome scans during studies of wild populations and captive breeding programs.
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Affiliation(s)
- Adrienne E. Norrell
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, United States of America
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Eric A. Saillant
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, United States of America
- * E-mail:
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Medvedev P. Modeling biological problems in computer science: a case study in genome assembly. Brief Bioinform 2020; 20:1376-1383. [PMID: 29394324 DOI: 10.1093/bib/bby003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/07/2017] [Indexed: 11/14/2022] Open
Abstract
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. We show the modeling process step-by-step, including all the intermediate failed attempts. Please note this is not an introduction to how genome assembly algorithms work and, if treated as such, would be incomplete and unnecessarily long-winded.
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50
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Tang L, Li M, Wu FX, Pan Y, Wang J. MAC: Merging Assemblies by Using Adjacency Algebraic Model and Classification. Front Genet 2020; 10:1396. [PMID: 32082361 PMCID: PMC7005248 DOI: 10.3389/fgene.2019.01396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022] Open
Abstract
With the generation of a large amount of sequencing data, different assemblers have emerged to perform de novo genome assembly. As a single strategy is hard to fit various biases of datasets, none of these tools outperforms the others on all species. The process of assembly reconciliation is to merge multiple assemblies and generate a high-quality consensus assembly. Several assembly reconciliation tools have been proposed. However, the existing reconciliation tools cannot produce a merged assembly which has better contiguity and contains less errors simultaneously, and the results of these tools usually depend on the ranking of input assemblies. In this study, we propose a novel assembly reconciliation tool MAC, which merges assemblies by using the adjacency algebraic model and classification. In order to solve the problem of uneven sequencing depth and sequencing errors, MAC identifies consensus blocks between contig sets to construct an adjacency graph. To solve the problem of repetitive region, MAC employs classification to optimize the adjacency algebraic model. What’s more, MAC designs an overall scoring function to solve the problem of unknown ranking of input assembly sets. The experimental results from four species of GAGE-B demonstrate that MAC outperforms other assembly reconciliation tools.
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Affiliation(s)
- Li Tang
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Fang-Xiang Wu
- School of Computer Science and Engineering, Central South University, Changsha, China.,Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yi Pan
- School of Computer Science and Engineering, Central South University, Changsha, China.,Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, China
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