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Hemstrom W, Grummer JA, Luikart G, Christie MR. Next-generation data filtering in the genomics era. Nat Rev Genet 2024; 25:750-767. [PMID: 38877133 DOI: 10.1038/s41576-024-00738-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
Abstract
Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology, evolution and human health. However, these datasets often contain noise or errors and are missing information that can affect the accuracy and reliability of subsequent computational analyses and conclusions. A key step in genomic data analysis is filtering - removing sequencing bases, reads, genetic variants and/or individuals from a dataset - to improve data quality for downstream analyses. Researchers are confronted with a multitude of choices when filtering genomic data; they must choose which filters to apply and select appropriate thresholds. To help usher in the next generation of genomic data filtering, we review and suggest best practices to improve the implementation, reproducibility and reporting standards for filter types and thresholds commonly applied to genomic datasets. We focus mainly on filters for minor allele frequency, missing data per individual or per locus, linkage disequilibrium and Hardy-Weinberg deviations. Using simulated and empirical datasets, we illustrate the large effects of different filtering thresholds on common population genetics statistics, such as Tajima's D value, population differentiation (FST), nucleotide diversity (π) and effective population size (Ne).
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Affiliation(s)
- William Hemstrom
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - Jared A Grummer
- Flathead Lake Biological Station, Wildlife Biology Program and Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Wildlife Biology Program and Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA.
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2
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Liu C, Liu P, Liu S, Guo H, Zhu T, Li W, Wang K, Kang X, Sun G. Genetic structure, selective characterization and specific molecular identity cards of high-yielding Houdan chickens based on genome-wide SNP. Poult Sci 2024; 103:104325. [PMID: 39316988 PMCID: PMC11462333 DOI: 10.1016/j.psj.2024.104325] [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: 05/29/2024] [Revised: 09/04/2024] [Accepted: 09/07/2024] [Indexed: 09/26/2024] Open
Abstract
The high-yielding Houdan chicken (GGF) is characterized by high egg production and disease resistance. This study conducted whole genome resequencing of the GGF population and compared it to data from other breeds. Genetic diversity analysis revealed higher observed heterozygosity (Ho), Polymorphism information content (PIC), number of runs of homozygosity (ROH), and inbreeding coefficient (FROH) in GGF. Linkage disequilibrium (LD) decay was slowest in GGF, indicating intensive inbreeding and strong selection. These findings suggest a need for appropriate strategies to enhance genetic diversity conservation in this breed. Population structure analysis demonstrated that GGF was genetically distinct from both the red jungle fowl (RJF) and Chinese indigenous chicken (CIC) populations, highlighting GGF as a unique genetic resource warranting intensive protection and utilization. Selective sweep analysis identified genes under selection in GGF, primarily enriched in signaling pathways related to oocyte meiosis and progesterone-mediated oocyte maturation. Key candidate genes included: CCNE1, SKP1, CDC20, CDK2, ADCY8, RPS6KA6, PPP3CB, PDE3B, HSP90AB1, and AKT3. These findings provide a theoretical foundation for their potential application in poultry breeding. Additionally, this study combined bioinformatics analysis with PCR amplification and Sanger sequencing to identify 4 SNPs that can serve as a molecular identity card (ID) for GGF: SNP1 (Chr2: 136130976), SNP3 (Chr4:11705164), SNP4 (Chr4: 63255588), and SNP5 (Chr24: 3271008). This study provides a scientific basis for effective management and conservation of GGF genetic resources, and establishes a simple, economical, and accurate set of molecular IDs to combat the proliferation of inferior breeds and protect genetic resources.
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Affiliation(s)
- Cong Liu
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China
| | - Pingquan Liu
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization of Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
| | - Shuangxing Liu
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization of Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
| | - Haishan Guo
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization of Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
| | - Tingqi Zhu
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization of Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
| | - Wenting Li
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization of Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
| | - Kejun Wang
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiangtao Kang
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China
| | - Guirong Sun
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization of Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China.
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3
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Laatri S, El Khayari S, Qriouet Z. Exploring the molecular aspect and updating evolutionary approaches to the DNA polymerase enzymes for biotechnological needs: A comprehensive review. Int J Biol Macromol 2024; 276:133924. [PMID: 39033894 DOI: 10.1016/j.ijbiomac.2024.133924] [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: 03/10/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
DNA polymerases are essential enzymes that play a key role in living organisms, as they participate in the synthesis and maintenance of the DNA molecule. The intrinsic properties of these enzymes have been widely observed and studied to understand their functions, activities, and behavior, which has allowed their natural power in DNA synthesis to be exploited in modern biotechnology, to the point of making them true pillars of the field. In this context, the laboratory evolution of these enzymes, either by directed evolution or rational design, has led to the generation of a wide range of new DNA polymerases with novel properties, suitable for a variety of biotechnological needs. In this review, we examine DNA polymerases at the molecular level, their biotechnological use, and their evolutionary methods in relation to the novel properties sought, providing a chronological selection of evolved DNA polymerases cited in the literature that we consider to be of great interest. To our knowledge, this work is the first to bring together the molecular, functional and evolutionary aspects of the DNA polymerase enzyme. We believe it will be of great interest to researchers whose aim is to produce new lines of evolved DNA polymerases.
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Affiliation(s)
- Said Laatri
- Microbiology and Molecular Biology Laboratory, Faculty of Sciences, Mohammed V-Souissi University, Rabat 10100, Morocco.
| | | | - Zidane Qriouet
- Pharmacology and Toxicology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V-Souissi University, Rabat 10100, Morocco
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Kumawat RL, Jena MK, Mittal S, Pathak B. Advancement of Next-Generation DNA Sequencing through Ionic Blockade and Transverse Tunneling Current Methods. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2401112. [PMID: 38716623 DOI: 10.1002/smll.202401112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/05/2024] [Indexed: 10/04/2024]
Abstract
DNA sequencing is transforming the field of medical diagnostics and personalized medicine development by providing a pool of genetic information. Recent advancements have propelled solid-state material-based sequencing into the forefront as a promising next-generation sequencing (NGS) technology, offering amplification-free, cost-effective, and high-throughput DNA analysis. Consequently, a comprehensive framework for diverse sequencing methodologies and a cross-sectional understanding with meticulous documentation of the latest advancements is of timely need. This review explores a broad spectrum of progress and accomplishments in the field of DNA sequencing, focusing mainly on electrical detection methods. The review delves deep into both the theoretical and experimental demonstrations of the ionic blockade and transverse tunneling current methods across a broad range of device architectures, nanopore, nanogap, nanochannel, and hybrid/heterostructures. Additionally, various aspects of each architecture are explored along with their strengths and weaknesses, scrutinizing their potential applications for ultrafast DNA sequencing. Finally, an overview of existing challenges and future directions is provided to expedite the emergence of high-precision and ultrafast DNA sequencing with ionic and transverse current approaches.
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Affiliation(s)
- Rameshwar L Kumawat
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
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5
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Hjelmen CE. Genome size and chromosome number are critical metrics for accurate genome assembly assessment in Eukaryota. Genetics 2024; 227:iyae099. [PMID: 38869251 DOI: 10.1093/genetics/iyae099] [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: 04/02/2024] [Revised: 04/02/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
The number of genome assemblies has rapidly increased in recent history, with NCBI databases reaching over 41,000 eukaryotic genome assemblies across about 2,300 species. Increases in read length and improvements in assembly algorithms have led to increased contiguity and larger genome assemblies. While this number of assemblies is impressive, only about a third of these assemblies have corresponding genome size estimations for their respective species on publicly available databases. In this paper, genome assemblies are assessed regarding their total size compared to their respective publicly available genome size estimations. These deviations in size are assessed related to genome size, kingdom, sequencing platform, and standard assembly metrics, such as N50 and BUSCO values. A large proportion of assemblies deviate from their estimated genome size by more than 10%, with increasing deviations in size with increased genome size, suggesting nonprotein coding and structural DNA may be to blame. Modest differences in performance of sequencing platforms are noted as well. While standard metrics of genome assessment are more likely to indicate an assembly approaching the estimated genome size, much of the variation in this deviation in size is not explained with these raw metrics. A new, proportional N50 metric is proposed, in which N50 values are made relative to the average chromosome size of each species. This new metric has a stronger relationship with complete genome assemblies and, due to its proportional nature, allows for a more direct comparison across assemblies for genomes with variation in sizes and architectures.
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Affiliation(s)
- Carl E Hjelmen
- Department of Biology, Utah Valley University, 800 W. University Parkway, Orem, UT 84058, USA
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6
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Sattler C, Ceylan B, Hoffmann L, Juric A, Kraus J, Marandi S, Shahnazari A, Rühl M. Sequence confirmation of synthetic DNA exceeding 100 nucleotides using restriction enzyme mediated digestion combined with high-resolution tandem mass spectrometry. J Pharm Biomed Anal 2024; 245:116180. [PMID: 38703748 DOI: 10.1016/j.jpba.2024.116180] [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: 12/21/2023] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024]
Abstract
Oligonucleotides have emerged as important therapeutic options for inherited diseases. In recent years, RNA therapeutics, especially mRNA, have been pushed to the market. Analytical methods for these molecules have been published extensively in the last few years. Notably, mass spectrometry has proven as a state-of-the-art quality control method. For RNA based therapeutics, numerous methods are available, while DNA therapeutics lack of suitable MS-based methods when it comes to molecules exceeding approximately 60 nucleotides. We present a method which combines the use of common restriction enzymes and short enzyme-directing oligonucleotides to generate DNA digestion products with the advantages of high-resolution tandem mass spectrometry. The instrumentation includes ion pair reverse phase chromatography coupled to a time-of-flight mass spectrometer with a collision induced dissociation (CID) for sequence analysis. Utilizing this approach, we increased the sequence coverage from 23.3% for a direct CID-MS/MS experiment of a 100 nucleotide DNA molecule to 100% sequence coverage using the restriction enzyme mediated approach presented in this work. This approach is suitable for research and development and quality control purposes in a regulated environment, which makes it a versatile tool for drug development.
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Affiliation(s)
| | - Burak Ceylan
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Luisa Hoffmann
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Andela Juric
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Julia Kraus
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Shima Marandi
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Aref Shahnazari
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Michael Rühl
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany.
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7
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Metz TO, Chang CH, Gautam V, Anjum A, Tian S, Wang F, Colby SM, Nunez JR, Blumer MR, Edison AS, Fiehn O, Jones DP, Li S, Morgan ET, Patti GJ, Ross DH, Shapiro MR, Williams AJ, Wishart DS. Introducing 'identification probability' for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605945. [PMID: 39131324 PMCID: PMC11312557 DOI: 10.1101/2024.07.30.605945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence - the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate approaches to communicate compound identification confidence also have been developed based on identification points schema. However, neither qualitative levels of identification confidence nor quantitative scoring systems address the degree of ambiguity in compound identifications in context of the chemical space being considered, are easily automated, or are transferable between analytical platforms. In this perspective, we propose that the metabolomics and related communities consider identification probability as an approach for automated and transferable assessment of compound identification and ambiguity in metabolomics and related studies. Identification probability is defined simply as 1/N, where N is the number of compounds in a reference library or chemical space that match to an experimentally measured molecule within user-defined measurement precision(s), for example mass measurement or retention time accuracy, etc. We demonstrate the utility of identification probability in an in silico analysis of multi-property reference libraries constructed from the Human Metabolome Database and computational property predictions, provide guidance to the community in transparent implementation of the concept, and invite the community to further evaluate this concept in parallel with their current preferred methods for assessing metabolite identification confidence.
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Affiliation(s)
- Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Christine H. Chang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Afia Anjum
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Siyang Tian
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Fei Wang
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
- Alberta Machine Intelligence Institute, Edmonton, AB, Canada
| | - Sean M. Colby
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Jamie R. Nunez
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Madison R. Blumer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Arthur S. Edison
- Department of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Dean P. Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Edward T. Morgan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gary J. Patti
- Center for Mass Spectrometry and Metabolic Tracing, Department of Chemistry, Department of Medicine, Washington University, Saint Louis, Missouri, USA
| | - Dylan H. Ross
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Madelyn R. Shapiro
- Artificial Intelligence & Data Analytics Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Antony J. Williams
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), Research Triangle Park, NC USA
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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8
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Odriozola I, Rasmussen JA, Gilbert MTP, Limborg MT, Alberdi A. A practical introduction to holo-omics. CELL REPORTS METHODS 2024; 4:100820. [PMID: 38986611 PMCID: PMC11294832 DOI: 10.1016/j.crmeth.2024.100820] [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: 12/14/2023] [Revised: 04/17/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024]
Abstract
Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main differences to generate and analyze the various types of omics, with a special focus on optimizing data generation and integration. We advocate for careful generation and distillation of data, followed by independent exploration and analyses of the single omic layers to obtain a better understanding of the study system, before the integration of multiple omic layers in a final model is attempted. We highlight critical decision points to achieve this aim and flag the main challenges to address complex biological questions regarding the integrative study of host-microbiota relationships.
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Affiliation(s)
- Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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Lim PK, Wang R, Mutwil M. LSTrAP-denovo: Automated Generation of Transcriptome Atlases for Eukaryotic Species Without Genomes. PHYSIOLOGIA PLANTARUM 2024; 176:e14407. [PMID: 38973613 DOI: 10.1111/ppl.14407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024]
Abstract
Despite the abundance of species with transcriptomic data, a significant number of species still lack sequenced genomes, making it difficult to study gene function and expression in these organisms. While de novo transcriptome assembly can be used to assemble protein-coding transcripts from RNA-sequencing (RNA-seq) data, the datasets used often only feature samples of arbitrarily selected or similar experimental conditions, which might fail to capture condition-specific transcripts. We developed the Large-Scale Transcriptome Assembly Pipeline for de novo assembled transcripts (LSTrAP-denovo) to automatically generate transcriptome atlases of eukaryotic species. Specifically, given an NCBI TaxID, LSTrAP-denovo can (1) filter undesirable RNA-seq accessions based on read data, (2) select RNA-seq accessions via unsupervised machine learning to construct a sample-balanced dataset for download, (3) assemble transcripts via over-assembly, (4) functionally annotate coding sequences (CDS) from assembled transcripts and (5) generate transcriptome atlases in the form of expression matrices for downstream transcriptomic analyses. LSTrAP-denovo is easy to implement, written in Python, and is freely available at https://github.com/pengkenlim/LSTrAP-denovo/.
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Affiliation(s)
- Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ruoxi Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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10
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Lamoureux CR, Phaneuf PV, Palsson B, Zielinski D. Escherichia coli non-coding regulatory regions are highly conserved. NAR Genom Bioinform 2024; 6:lqae041. [PMID: 38774514 PMCID: PMC11106028 DOI: 10.1093/nargab/lqae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/05/2024] [Accepted: 05/15/2024] [Indexed: 05/24/2024] Open
Abstract
Microbial genome sequences are rapidly accumulating, enabling large-scale studies of sequence variation. Existing studies primarily focus on coding regions to study amino acid substitution patterns in proteins. However, non-coding regulatory regions also play a distinct role in determining physiologic responses. To investigate intergenic sequence variation on a large-scale, we identified non-coding regulatory region alleles across 2350 Escherichia coli strains. This 'alleleome' consists of 117 781 unique alleles for 1169 reference regulatory regions (transcribing 1975 genes) at single base-pair resolution. We find that 64% of nucleotide positions are invariant, and variant positions vary in a median of just 0.6% of strains. Additionally, non-coding alleles are sufficient to recover E. coli phylogroups. We find that core promoter elements and transcription factor binding sites are significantly conserved, especially those located upstream of essential or highly-expressed genes. However, variability in conservation of transcription factor binding sites is significant both within and across regulons. Finally, we contrast mutations acquired during adaptive laboratory evolution with wild-type variation, finding that the former preferentially alter positions that the latter conserves. Overall, this analysis elucidates the wealth of information found in E. coli non-coding sequence variation and expands pangenomic studies to non-coding regulatory regions at single-nucleotide resolution.
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Affiliation(s)
- Cameron R Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Patrick V Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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11
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Domrazek K, Jurka P. Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals. Animals (Basel) 2024; 14:1578. [PMID: 38891625 PMCID: PMC11171117 DOI: 10.3390/ani14111578] [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: 04/24/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Next-Generation Sequencing (NGS) techniques have revolutionized veterinary medicine for cats and dogs, offering insights across various domains. In veterinary parasitology, NGS enables comprehensive profiling of parasite populations, aiding in understanding transmission dynamics and drug resistance mechanisms. In infectious diseases, NGS facilitates rapid pathogen identification, characterization of virulence factors, and tracking of outbreaks. Moreover, NGS sheds light on metabolic processes by elucidating gene expression patterns and metabolic pathways, essential for diagnosing metabolic disorders and designing tailored treatments. In autoimmune diseases, NGS helps identify genetic predispositions and molecular mechanisms underlying immune dysregulation. Veterinary oncology benefits from NGS through personalized tumor profiling, mutation analysis, and identification of therapeutic targets, fostering precision medicine approaches. Additionally, NGS plays a pivotal role in veterinary genetics, unraveling the genetic basis of inherited diseases and facilitating breeding programs for healthier animals. Physiological investigations leverage NGS to explore complex biological systems, unraveling gene-environment interactions and molecular pathways governing health and disease. Application of NGS in treatment planning enhances precision and efficacy by enabling personalized therapeutic strategies tailored to individual animals and their diseases, ultimately advancing veterinary care for companion animals.
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Affiliation(s)
- Kinga Domrazek
- Institute of Veterinary Medicine, Warsaw University of Life Sciences—SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland;
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12
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Wang T, Shi Y, Zheng M, Zheng J. Comparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among Bacillus subtilis Group. Microorganisms 2024; 12:986. [PMID: 38792815 PMCID: PMC11124052 DOI: 10.3390/microorganisms12050986] [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: 04/14/2024] [Revised: 05/04/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual genomes at the level of species, with few conducted within groups across different species. This study focused on Bacillus subtilis, the model of Gram-positive bacteria, and 14 other species with significant research value, employing comparative pangenomics as well as population enrichment analysis to ascertain the functional enrichment and diversity. Through the quantification of pangenome openness, this work revealed the underlying biological drivers and significant correlation between pangenome openness and various factors, including the distribution of toxin-antitoxin- and integrase-related genes, as well as the number of endonucleases, recombinases, repair system-related genes, prophages, integrases, and transfer mobile elements. Furthermore, the functional enrichment results indicated the potential for secondary metabolite, probiotic, and antibiotic exploration in Bacillus licheniformis, Bacillus paralicheniformis, and Bacillus spizizenii, respectively. In general, this work systematically exposed the quantification of pangenome openness, biological drivers, the pivotal role of genomic instability factors, and mobile elements, providing targeted exploration guidance for the Bs group.
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Affiliation(s)
- Taiquan Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiling Shi
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengzhuo Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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13
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Makalo MJR, Settypalli TBK, Meki IK, Bakhoum MT, Ahmed HO, Phalatsi MS, Ramatla T, Onyiche TE, Nionzima-Bohloa L, Metlin A, Dhingra M, Cattoli G, Lamien CE, Thekisoe OMM. Genetic Characterization of Lumpy Skin Disease Viruses Circulating in Lesotho Cattle. Viruses 2024; 16:762. [PMID: 38793643 PMCID: PMC11125814 DOI: 10.3390/v16050762] [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: 04/14/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Lumpy skin disease is one of the fast-spreading viral diseases of cattle and buffalo that can potentially cause severe economic impact. Lesotho experienced LSD for the first time in 1947 and episodes of outbreaks occurred throughout the decades. In this study, eighteen specimens were collected from LSD-clinically diseased cattle between 2020 and 2022 from Mafeteng, Leribe, Maseru, Berea, and Mohales' Hoek districts of Lesotho. A total of 11 DNA samples were analyzed by PCR and sequencing of the extracellular enveloped virus (EEV) glycoprotein, G-protein-coupled chemokine receptor (GPCR), 30 kDa RNA polymerase subunit (RPO30), and B22R genes. All nucleotide sequences of the above-mentioned genes confirmed that the PCR amplicons of clinical samples are truly LSDV, as they were identical to respective LSDV isolates on the NCBI GenBank. Two of the elevem samples were further characterized by whole-genome sequencing. The analysis, based on both CaPV marker genes and complete genome sequences, revealed that the LSDV isolates from Lesotho cluster with the NW-like LSDVs, which includes the commonly circulating LSDV field isolates from Africa, the Middle East, the Balkans, Turkey, and Eastern Europe.
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Affiliation(s)
- Mabusetsa Joseph Raporoto Makalo
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa; (T.R.); (T.E.O.); (O.M.M.T.)
- Department of Livestock Services, Ministry of Agriculture, Food Security, and Nutrition, Private A82, Maseru, Lesotho;
| | - Tirumala Bharani Kumar Settypalli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | - Irene Kasindi Meki
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | - Mame Thierno Bakhoum
- Laboratoire National de l’Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), BP 2057, Dakar, Senegal;
| | - Hatem Ouled Ahmed
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | | | - Tsepo Ramatla
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa; (T.R.); (T.E.O.); (O.M.M.T.)
| | - ThankGod Emmanuel Onyiche
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa; (T.R.); (T.E.O.); (O.M.M.T.)
- Department of Veterinary Parasitology and Entomology, University of Maiduguri, P. M. B. 1069, Maiduguri 600230, Nigeria
| | - Lineo Nionzima-Bohloa
- Department of Livestock Services, Ministry of Agriculture, Food Security, and Nutrition, Private A82, Maseru, Lesotho;
| | - Artem Metlin
- Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153 Rome, Italy; (A.M.); (M.D.)
| | - Madhur Dhingra
- Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153 Rome, Italy; (A.M.); (M.D.)
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | - Charles Euloge Lamien
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | - Oriel Matlhahane Molifi Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa; (T.R.); (T.E.O.); (O.M.M.T.)
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14
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Truong B, Ruan Y, Haidermota S, Patel A, Surakka I, Hornsby W, Koyama S, Lee SH, Natarajan P. Modification of coronary artery disease clinical risk factors by coronary artery disease polygenic risk score. MED 2024; 5:459-468.e3. [PMID: 38642556 PMCID: PMC11088498 DOI: 10.1016/j.medj.2024.02.015] [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: 04/12/2023] [Revised: 10/11/2023] [Accepted: 02/28/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND The extent to which the relationships between clinical risk factors and coronary artery disease (CAD) are altered by CAD polygenic risk score (PRS) is not well understood. Here, we determine whether the interactions between clinical risk factors and CAD PRS further explain risk for incident CAD. METHODS Participants were of European ancestry from the UK Biobank without prevalent CAD. An externally trained genome-wide CAD PRS was generated and then applied. Clinical risk factors were ascertained at baseline. Cox proportional hazards models were fitted to examine the incident CAD effects of CAD PRS, risk factors, and their interactions. Next, the PRS and risk factors were stratified to investigate the attributable risk of clinical risk factors. FINDINGS A total of 357,144 individuals of European ancestry without prevalent CAD were included. During a median of 11.1 years of follow-up (interquartile range 10.4-14.1 years), CAD PRS was associated with 1.35-fold (95% confidence interval [CI] 1.332-1.368) risk per SD for incident CAD. The prognostic relevance of the following risk factors was relatively diminished for those with high CAD PRS on a continuous scale: type 2 diabetes (hazard ratio [HR]interaction 0.91, 95% CIinteraction 0.88-0.94), increased body mass index (HRinteraction 0.97, 95% CIinteraction 0.96-0.98), and increased C-reactive protein (HRinteraction 0.98, 95% CIinteraction 0.96-0.99). However, a high CAD PRS yielded joint risk increases with low-density lipoprotein cholesterol (HRinteraction 1.05, 95% CIinteraction 1.04-1.06) and total cholesterol (HRinteraction 1.05, 95% CIinteraction 1.03-1.06). CONCLUSION The CAD PRS is associated with incident CAD, and its application improves the prognostic relevance of several clinical risk factors. FUNDING P.N. (R01HL127564, R01HL151152, and U01HG011719) is supported by the National Institutes of Health.
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Affiliation(s)
- Buu Truong
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Yunfeng Ruan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Sara Haidermota
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Aniruddh Patel
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Ida Surakka
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Whitney Hornsby
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Satoshi Koyama
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - S Hong Lee
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA 5000, Australia; UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA 5000, Australia
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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15
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Hogg CJ. Translating genomic advances into biodiversity conservation. Nat Rev Genet 2024; 25:362-373. [PMID: 38012268 DOI: 10.1038/s41576-023-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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16
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Steenwyk JL, King N. The promise and pitfalls of synteny in phylogenomics. PLoS Biol 2024; 22:e3002632. [PMID: 38768403 PMCID: PMC11105162 DOI: 10.1371/journal.pbio.3002632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Reconstructing the tree of life remains a central goal in biology. Early methods, which relied on small numbers of morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence in the results. Investigations based on phylogenomics, which use hundreds to thousands of loci for phylogenetic inquiry, have provided a clearer picture of life's history, but certain branches remain problematic. To resolve difficult nodes on the tree of life, 2 recent studies tested the utility of synteny, the conserved collinearity of orthologous genetic loci in 2 or more organisms, for phylogenetics. Synteny exhibits compelling phylogenomic potential while also raising new challenges. This Essay identifies and discusses specific opportunities and challenges that bear on the value of synteny data and other rare genomic changes for phylogenomic studies. Synteny-based analyses of highly contiguous genome assemblies mark a new chapter in the phylogenomic era and the quest to reconstruct the tree of life.
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Affiliation(s)
- Jacob L. Steenwyk
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Nicole King
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
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17
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Liu Z, Zhao J, Cui K, Guo H, Li Z, Zhou Z. Detection accuracy and clinical applications of DP-TOF mass spectrometry. J Int Med Res 2024; 52:3000605241255568. [PMID: 38819085 PMCID: PMC11143829 DOI: 10.1177/03000605241255568] [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: 12/07/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Abstract
OBJECTIVE Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently used in clinical microbiology laboratories. This study aimed to determine whether dual-polarity time-of-flight mass spectrometry (DP-TOF MS) could be applied to clinical nucleotide detection. METHODS This prospective study included 40 healthy individuals and 110 patients diagnosed with cardiovascular diseases. We used DP-TOF MS and Sanger sequencing to evaluate 17 loci across 11 genes associated with cardiovascular drug responses. In addition, we used DP-TOF MS to test 998 retrospectively collected clinical DNA samples with known results. RESULTS A, T, and G nucleotide detection by DP-TOF MS and Sanger sequencing revealed 100% concordance, whereas the C nucleotide concordance was 99.86%. Genotyping based on the results of the two methods showed 99.96% concordance. Regarding clinical applications, DP-TOF MS yielded a 99.91% concordance rate for known loci. The minimum detection limit for DNA was 0.4 ng; the inter-assay and intra-assay precision rates were both 100%. Anti-interference analysis showed that aerosol contamination greater than 1013 copies/µL in the laboratory environment could influence the results of DP-TOF MS. CONCLUSIONS The DP-TOF MS platform displayed good detection performance, as demonstrated by its 99.96% concordance rate with Sanger sequencing. Thus, it may be applied to clinical nucleotide detection.
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Affiliation(s)
- Zhaohui Liu
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Center of Laboratory Medicine, Fuwai Yunnan Cardiovascular Hospital, Kunming, Yunnan, China
| | - Juan Zhao
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Cui
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huimin Guo
- Zhejiang Digena Diagnosis Technology Co., Ltd., Hangzhou, Zhejiang, China
| | - Zhikai Li
- Zhejiang Digena Diagnosis Technology Co., Ltd., Hangzhou, Zhejiang, China
| | - Zhou Zhou
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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18
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Yang F, Jiang H, Ma K, Hegazy A, Wang X, Liang S, Chang G, Yu L, Tian B, Shi X. Genomic and phenotypic analyses reveal Paenibacillus polymyxa PJH16 is a potential biocontrol agent against cucumber fusarium wilt. Front Microbiol 2024; 15:1359263. [PMID: 38591040 PMCID: PMC11000672 DOI: 10.3389/fmicb.2024.1359263] [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: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain Paenibacillus polymyxa PJH16 in preventing Fusarium oxysporum f. sp. cucumerinum (Foc). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of β-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as P. polymyxa PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of P. polymyxa PJH16 with four closely related P. polymyxa strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in P. polymyxa PJH16. Therefore, P. polymyxa PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future.
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Affiliation(s)
- Fan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Huayan Jiang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Kai Ma
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Abeer Hegazy
- National Water Research Center, Shubra El Kheima, Egypt
| | - Xin Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Shen Liang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Gaozheng Chang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Liqin Yu
- Henan Natural Products Biotechnology Co., Ltd., Zhengzhou, China
| | - Baoming Tian
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xuanjie Shi
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [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: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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20
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Mathur S, Singh D, Ranjan R. Recent advances in plant translational genomics for crop improvement. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:335-382. [PMID: 38448140 DOI: 10.1016/bs.apcsb.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The growing population, climate change, and limited agricultural resources put enormous pressure on agricultural systems. A plateau in crop yields is occurring and extreme weather events and urbanization threaten the livelihood of farmers. It is imperative that immediate attention is paid to addressing the increasing food demand, ensuring resilience against emerging threats, and meeting the demand for more nutritious, safer food. Under uncertain conditions, it is essential to expand genetic diversity and discover novel crop varieties or variations to develop higher and more stable yields. Genomics plays a significant role in developing abundant and nutrient-dense food crops. An alternative to traditional breeding approach, translational genomics is able to improve breeding programs in a more efficient and precise manner by translating genomic concepts into practical tools. Crop breeding based on genomics offers potential solutions to overcome the limitations of conventional breeding methods, including improved crop varieties that provide more nutritional value and are protected from biotic and abiotic stresses. Genetic markers, such as SNPs and ESTs, contribute to the discovery of QTLs controlling agronomic traits and stress tolerance. In order to meet the growing demand for food, there is a need to incorporate QTLs into breeding programs using marker-assisted selection/breeding and transgenic technologies. This chapter primarily focuses on the recent advances that are made in translational genomics for crop improvement and various omics techniques including transcriptomics, metagenomics, pangenomics, single cell omics etc. Numerous genome editing techniques including CRISPR Cas technology and their applications in crop improvement had been discussed.
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Affiliation(s)
- Shivangi Mathur
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India
| | - Deeksha Singh
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India
| | - Rajiv Ranjan
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India.
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21
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Wang S, Mao X, Wang F, Zuo X, Fan C. Data Storage Using DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307499. [PMID: 37800877 DOI: 10.1002/adma.202307499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/01/2023] [Indexed: 10/07/2023]
Abstract
The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.
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Affiliation(s)
- Shaopeng Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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22
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Jern P, Greenwood AD. Wildlife endogenous retroviruses: colonization, consequences, and cooption. Trends Genet 2024; 40:149-159. [PMID: 37985317 DOI: 10.1016/j.tig.2023.10.014] [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: 09/11/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
Endogenous retroviruses (ERVs) are inherited genomic remains of past germline retroviral infections. Research on human ERVs has focused on medical implications of their dysregulation on various diseases. However, recent studies incorporating wildlife are yielding remarkable perspectives on long-term retrovirus-host interactions. These initial forays into broader taxonomic analysis, including sequencing of multiple individuals per species, show the incredible plasticity and variation of ERVs within and among wildlife species. This demonstrates that stochastic processes govern much of the vertebrate genome. In this review, we elaborate on discoveries pertaining to wildlife ERV origins and evolution, genome colonization, and consequences for host biology.
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Affiliation(s)
- Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany; School of Veterinary Medicine, Freie Unversität Berlin, Berlin, Germany.
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Costantini M, Esposito R, Ruocco N, Caramiello D, Cordella A, Ventola GM, Zupo V. De Novo Assembly of the Genome of the Sea Urchin Paracentrotus lividus (Lamarck 1816). Int J Mol Sci 2024; 25:1685. [PMID: 38338963 PMCID: PMC10855541 DOI: 10.3390/ijms25031685] [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: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The genome of P. lividus was sequenced using Illumina NextSeq 500 System (Illumina) in a 2 × 150 paired-end format. More than 30,000 open reading frames (ORFs), (more than 8000 are unique), were identified and analysed to provide molecular tools accessible for the scientific community. In particular, several genes involved in complex innate immune responses, oxidative metabolism, signal transduction, and kinome, as well as genes regulating the membrane receptors, were identified in the P. lividus genome. In this way, the employment of the Mediterranean sea urchin for investigations and comparative analyses was empowered, leading to the explanation of cis-regulatory networks and their evolution in a key developmental model occupying an important evolutionary position with respect to vertebrates and humans.
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Affiliation(s)
- Maria Costantini
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Via Ammiraglio Ferdinando Acton n. 55, 80133 Napoli, Italy;
| | - Roberta Esposito
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Via Ammiraglio Ferdinando Acton n. 55, 80133 Napoli, Italy;
| | - Nadia Ruocco
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Calabria Marine Centre, C.da Torre Spaccata, 87071 Amendolara, Italy;
| | - Davide Caramiello
- Stazione Zoologica Anton Dohrn, Department of Marine Animal Conservation and Public Engagement, Villa Comunale, 1, 80121 Naples, Italy;
| | - Angela Cordella
- Genomix4Life S.r.l., Baronissi, 84081 Salerno, Italy; (A.C.); (G.M.V.)
- Genome Research Center for Health-CRGS, Baronissi, 84081 Salerno, Italy
| | | | - Valerio Zupo
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Ischia Marine Centre, 80121 Naples, Italy
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24
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Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024; 22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [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: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024] Open
Abstract
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.
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Affiliation(s)
- Chankyung Kim
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Graduate Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Cancer and Inflammation, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Graduate Program in Geriatric and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
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25
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Mandal AK. Recent insights into crosstalk between genetic parasites and their host genome. Brief Funct Genomics 2024; 23:15-23. [PMID: 36307128 PMCID: PMC10799329 DOI: 10.1093/bfgp/elac032] [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: 08/04/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2024] Open
Abstract
The bulk of higher order organismal genomes is comprised of transposable element (TE) copies, i.e. genetic parasites. The host-parasite relation is multi-faceted, varying across genomic region (genic versus intergenic), life-cycle stages, tissue-type and of course in health versus pathological state. The reach of functional genomics though, in investigating genotype-to-phenotype relations, has been limited when TEs are involved. The aim of this review is to highlight recent progress made in understanding how TE origin biochemical activity interacts with the central dogma stages of the host genome. Such interaction can also bring about modulation of the immune context and this could have important repercussions in disease state where immunity has a role to play. Thus, the review is to instigate ideas and action points around identifying evolutionary adaptations that the host genome and the genetic parasite have evolved and why they could be relevant.
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Affiliation(s)
- Amit K Mandal
- Corresponding author: A.K. Mandal, Nuffield Department of Surgical Sciences (NDS), University of Oxford, Old Road Campus Research building (ORCRB), Oxford OX3 7DQ, UK. Tel: +44 (0)1865 617123; Fax: +44 (0)1865 768876; E-mail:
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26
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Nachtigall PG, Durham AM, Rokyta DR, Junqueira-de-Azevedo ILM. ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages. Gigascience 2024; 13:giad116. [PMID: 38241143 PMCID: PMC10797961 DOI: 10.1093/gigascience/giad116] [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: 07/14/2023] [Revised: 10/19/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The rapid development of sequencing technologies resulted in a wide expansion of genomics studies using venomous lineages. This facilitated research focusing on understanding the evolution of adaptive traits and the search for novel compounds that can be applied in agriculture and medicine. However, the toxin annotation of genomes is a laborious and time-consuming task, and no consensus pipeline is currently available. No computational tool currently exists to address the challenges specific to toxin annotation and to ensure the reproducibility of the process. RESULTS Here, we present ToxCodAn-Genome, the first software designed to perform automated toxin annotation in genomes of venomous lineages. This pipeline was designed to retrieve the full-length coding sequences of toxins and to allow the detection of novel truncated paralogs and pseudogenes. We tested ToxCodAn-Genome using 12 genomes of venomous lineages and achieved high performance on recovering their current toxin annotations. This tool can be easily customized to allow improvements in the final toxin annotation set and can be expanded to virtually any venomous lineage. ToxCodAn-Genome is fast, allowing it to run on any personal computer, but it can also be executed in multicore mode, taking advantage of large high-performance servers. In addition, we provide a guide to direct future research in the venomics field to ensure a confident toxin annotation in the genome being studied. As a case study, we sequenced and annotated the toxin repertoire of Bothrops alternatus, which may facilitate future evolutionary and biomedical studies using vipers as models. CONCLUSIONS ToxCodAn-Genome is suitable to perform toxin annotation in the genome of venomous species and may help to improve the reproducibility of further studies. ToxCodAn-Genome and the guide are freely available at https://github.com/pedronachtigall/ToxCodAn-Genome.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, 05503-900 SP, Brazil
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA
| | - Alan M Durham
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo (USP), São Paulo, 05508-090 SP, Brazil
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA
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27
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Akash A, Bencurova E, Dandekar T. How to make DNA data storage more applicable. Trends Biotechnol 2024; 42:17-30. [PMID: 37591721 DOI: 10.1016/j.tibtech.2023.07.006] [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: 01/27/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
The storage of digital data is becoming a worldwide problem. DNA has been recognized as a biological solution due to its ability to store genetic information without alteration over long periods. The first demonstrations of high-capacity long-lasting DNA digital data storage have been shown. However, high storage costs and slow retrieval of the data must be overcome to make DNA data storage more applicable and marketable. Herein, we discuss the issues and recent advances in DNA data storage methods and highlight pathways to make this technology more applicable to real-world digital data storage. We envision that a combination of molecular biology, nanotechnology, novel polymers, electronics, and automation with systematic development will allow DNA data storage sufficient for everyday use.
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Affiliation(s)
- Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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28
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Pokharel K, Weldenegodguad M, Dudeck S, Honkatukia M, Lindeberg H, Mazzullo N, Paasivaara A, Peippo J, Soppela P, Stammler F, Kantanen J. Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia. Sci Rep 2023; 13:23019. [PMID: 38155192 PMCID: PMC10754820 DOI: 10.1038/s41598-023-50253-7] [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: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Domestic reindeer (Rangifer tarandus) play a vital role in the culture and livelihoods of indigenous people across northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation and utilisation. In this study, we have generated a new genome assembly for the Fennoscandian domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilised to explore genetic diversity, population structure and selective sweeps in Eurasian Rangifer tarandus populations which was based on the largest population genomic dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct genetic clusters, with the Finnish wild forest reindeer (Rangifer tarandus fennicus) standing out as a unique subspecies. Divergence time estimates suggested a separation of ~ 52 thousand years ago (Kya) between the northern European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified four main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, the Finnish forest reindeer, and the Svalbard reindeer. Furthermore, two independent reindeer domestication processes were inferred, suggesting separate origins for the domestic Fennoscandian and eastern/northern Russian reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments.
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Affiliation(s)
- Kisun Pokharel
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Melak Weldenegodguad
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Stephan Dudeck
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Heli Lindeberg
- Natural Resources Institute Finland (Luke), 71750, Maaninka, Finland
| | - Nuccio Mazzullo
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | - Antti Paasivaara
- Natural Resources Institute Finland (Luke), Paavo Havaksentie 3, 90570, Oulu, Finland
| | - Jaana Peippo
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
- NordGen-Nordic Genetic Resource Center, 1432, Ås, Norway
| | - Päivi Soppela
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland.
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29
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Pronyk PM, de Alwis R, Rockett R, Basile K, Boucher YF, Pang V, Sessions O, Getchell M, Golubchik T, Lam C, Lin R, Mak TM, Marais B, Twee-Hee Ong R, Clapham HE, Wang L, Cahyorini Y, Polotan FGM, Rukminiati Y, Sim E, Suster C, Smith GJD, Sintchenko V. Advancing pathogen genomics in resource-limited settings. CELL GENOMICS 2023; 3:100443. [PMID: 38116115 PMCID: PMC10726422 DOI: 10.1016/j.xgen.2023.100443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Genomic sequencing has emerged as a powerful tool to enhance early pathogen detection and characterization with implications for public health and clinical decision making. Although widely available in developed countries, the application of pathogen genomics among low-resource, high-disease burden settings remains at an early stage. In these contexts, tailored approaches for integrating pathogen genomics within infectious disease control programs will be essential to optimize cost efficiency and public health impact. We propose a framework for embedding pathogen genomics within national surveillance plans across a spectrum of surveillance and laboratory capacities. We adopt a public health approach to genomics and examine its application to high-priority diseases relevant in resource-limited settings. For each grouping, we assess the value proposition for genomics to inform public health and clinical decision-making, alongside its contribution toward research and development of novel diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Paul Michael Pronyk
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore.
| | - Ruklanthi de Alwis
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore; Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Rebecca Rockett
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Yann Felix Boucher
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore 117549, Singapore; Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 117549, Singapore; Nanyang Technological University, Singapore 639798, Singapore
| | - Vincent Pang
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore
| | - October Sessions
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Marya Getchell
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Tanya Golubchik
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Connie Lam
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Raymond Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore 308442, Singapore
| | - Tze-Minn Mak
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore 138671, Singapore
| | - Ben Marais
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore
| | - Hannah Eleanor Clapham
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore
| | - Linfa Wang
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore; Programme for Research in Epidemic Preparedness and Response (PREPARE), Ministry of Health, Singapore 169854, Singapore
| | - Yorin Cahyorini
- Center for Health Resilience and Resource Policy, Ministry of Health, Jakarta 12950, Indonesia
| | - Francisco Gerardo M Polotan
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, Muntinlupa 1781, Metro Manila, Philippines
| | - Yuni Rukminiati
- Center for Health Resilience and Resource Policy, Ministry of Health, Jakarta 12950, Indonesia
| | - Eby Sim
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Carl Suster
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Gavin J D Smith
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Vitali Sintchenko
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia; Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
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30
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Xie Y, Chan LY, Cheung MY, Li MW, Lam HM. Current technical advancements in plant epitranscriptomic studies. THE PLANT GENOME 2023; 16:e20316. [PMID: 36890704 DOI: 10.1002/tpg2.20316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of plants are the result of the interplay between the internal developmental programming and plant-environment interactions. Gene expression regulations in plants are made up of multi-level networks. In the past few years, many studies were carried out on co- and post-transcriptional RNA modifications, which, together with the RNA community, are collectively known as the "epitranscriptome." The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third-generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant-environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi-omics investigations using the recent technical advancements.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Long-Yiu Chan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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31
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Pfeifer BA, Beitelshees M, Hill A, Bassett J, Jones CH. Harnessing synthetic biology for advancing RNA therapeutics and vaccine design. NPJ Syst Biol Appl 2023; 9:60. [PMID: 38036580 PMCID: PMC10689799 DOI: 10.1038/s41540-023-00323-3] [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: 06/01/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Recent global events have drawn into focus the diversity of options for combatting disease across a spectrum of prophylactic and therapeutic approaches. The recent success of the mRNA-based COVID-19 vaccines has paved the way for RNA-based treatments to revolutionize the pharmaceutical industry. However, historical treatment options are continuously updated and reimagined in the context of novel technical developments, such as those facilitated through the application of synthetic biology. When it comes to the development of genetic forms of therapies and vaccines, synthetic biology offers diverse tools and approaches to influence the content, dosage, and breadth of treatment with the prospect of economic advantage provided in time and cost benefits. This can be achieved by utilizing the broad tools within this discipline to enhance the functionality and efficacy of pharmaceutical agent sequences. This review will describe how synthetic biology principles can augment RNA-based treatments through optimizing not only the vaccine antigen, therapeutic construct, therapeutic activity, and delivery vector. The enhancement of RNA vaccine technology through implementing synthetic biology has the potential to shape the next generation of vaccines and therapeutics.
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Affiliation(s)
- Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | | | - Andrew Hill
- Pfizer, 66 Hudson Boulevard, New York, NY, 10001, USA
| | - Justin Bassett
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
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32
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H H, Mallajosyula SS. Unveiling DNA Translocation in Pristine Graphene Nanopores: Understanding Pore Clogging via Polarizable Simulations. ACS APPLIED MATERIALS & INTERFACES 2023; 15:55095-55108. [PMID: 37965826 DOI: 10.1021/acsami.3c12262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Graphene has garnered remarkable attention in recent years as an attractive nanopore membrane for rapid and accurate sequencing of DNA. The inherent characteristics of graphene offer exquisite experimental control over pore dimensions, encompassing both the width (pore diameter) and height. Despite these promising prospects, the practical deployment of pristine graphene nanopores for DNA sequencing has encountered a formidable challenge in the form of pore clogging, which is primarily attributed to hydrophobic interactions. However, a comprehensive understanding of the atomistic origins underpinning this clogging phenomenon and the nuanced impact of individual nucleobase identities on clogging dynamics remain an underexplored domain. Elucidating the atomistic intricacies governing pore clogging is pivotal to devising strategies for its mitigation and advancing our understanding of graphene nanopore behavior. We harness Drude polarizable simulations to systematically dissect the nucleobase-dependent mechanisms that play a pivotal role in nanopore clogging. We unveil nucleobase-specific interactions that illuminate the multifaceted roles played by both hydrophobic and electrostatic forces in driving nanopore clogging events. Notably, the Drude simulations also unveil the bias-dependent translocation dynamics and its pivotal role in alleviating pore clogging─a facet that remains significantly underestimated in conventional additive (nonpolarizable) simulations. Our findings underscore the indispensability of incorporating polarizability to faithfully capture the intricate dynamics governing graphene nanopore translocation phenomena, thus deepening our insights into this crucial field.
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Affiliation(s)
- Hemanth H
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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33
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Chen YL, Wang ZF, Jian SG, Liao HM, Liu DM. Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands. Int J Mol Sci 2023; 24:16273. [PMID: 38003462 PMCID: PMC10671804 DOI: 10.3390/ijms242216273] [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] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Cordia subcordata trees or shrubs, belonging to the Boraginaceae family, have strong resistance and have adapted to their habitat on a tropical coral island in China, but the lack of genome information regarding its genetic background is unclear. In this study, the genome was assembled using both short/long whole genome sequencing reads and Hi-C reads. The assembled genome was 475.3 Mb, with 468.7 Mb (99.22%) of the sequences assembled into 16 chromosomes. Repeat sequences accounted for 54.41% of the assembled genome. A total of 26,615 genes were predicted, and 25,730 genes were functionally annotated using different annotation databases. Based on its genome and the other 17 species, phylogenetic analysis using 336 single-copy genes obtained from ortholog analysis showed that C. subcordata was a sister to Coffea eugenioides, and the divergence time was estimated to be 77 MYA between the two species. Gene family evolution analysis indicated that the significantly expanded gene families were functionally related to chemical defenses against diseases. These results can provide a reference to a deeper understanding of the genetic background of C. subcordata and can be helpful in exploring its adaptation mechanism on tropical coral islands in the future.
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Affiliation(s)
- Yi-Lan Chen
- Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, China
- Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Zheng-Feng Wang
- Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shu-Guang Jian
- Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hai-Min Liao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Dong-Ming Liu
- Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Kwon D, Park N, Wy S, Lee D, Chai HH, Cho IC, Lee J, Kwon K, Kim H, Moon Y, Kim J, Park W, Kim J. A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa). Sci Data 2023; 10:761. [PMID: 37923776 PMCID: PMC10624824 DOI: 10.1038/s41597-023-02661-7] [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: 07/21/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
As plentiful high-quality genome assemblies have been accumulated, reference-guided genome assembly can be a good approach to reconstruct a high-quality assembly. Here, we present a chromosome-level genome assembly of the Korean crossbred pig called Nanchukmacdon (the NCMD assembly) using the reference-guided assembly approach with short and long reads. The NCMD assembly contains 20 chromosome-level scaffolds with a total size of 2.38 Gbp (N50: 138.77 Mbp). Its BUSCO score is 93.1%, which is comparable to the pig reference assembly, and a total of 20,588 protein-coding genes, 8,651 non-coding genes, and 996.14 Mbp of repetitive elements are annotated. The NCMD assembly was also used to close many gaps in the pig reference assembly. This NCMD assembly and annotation provide foundational resources for the genomic analyses of pig and related species.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngbeen Moon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Juyeon Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Shang L, Zhou Y, Wen S, Wang K, Li Y, Zhang M, Jian H, Lyu D. Construction of heat stress regulation networks based on Illumina and SMRT sequencing data in potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1271084. [PMID: 38023929 PMCID: PMC10651764 DOI: 10.3389/fpls.2023.1271084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
Potato (Solanum tuberosum L.) is one of the most important tuber food crops in the world; however, the cultivated potatoes are susceptible to high temperature, by which potato production is adversely affected. Understanding the coping mechanism of potato to heat stress is essential to secure yield and expand adaptability under environmental conditions with rising temperature. However, the lack of heat-related information has significantly limited the identification and application of core genes. To gain deeper insights into heat tolerance genes, next-generation sequencing and single-molecule real-time sequencing were used to learn the transcriptional response of potato to heat stress and 13,159 differentially expressed genes (DEGs) were identified in this study. All DEGs were grouped into 12 clusters using the K-means clustering algorithm. Gene Ontology enrichment analysis revealed that they were involved in temperature signaling, phytohormone, and protein modification. Among them, there were 950 differentially expressed transcription factors (DETFs). According to the network analysis of DETFs at the sixth hour under heat stress, we found some genes that were previously reported to be associated with photoperiodic tuberization, StCO (CONSTANS), tuber formation, StBEL11 (BEL1-LIKE 11), and earliness in potato, StCDF1 (CYCLING DOF FACTOR 1) responding to temperature. Furthermore, we verified the relative expression levels using quantitative real-time polymerase chain reaction, and the results were consistent with the inferences from transcriptomes. In addition, there were 22,125 alternative splicing events and 2,048 long non-coding RNAs. The database and network established in this study will extend our understanding of potato response to heat stress. It ultimately provided valuable resources for molecular analysis of heat stress response in potato and cultivation of potato varieties with heat tolerance.
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Affiliation(s)
- Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yonghong Zhou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ke Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yang Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Meihua Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
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Zhang K, Du M, Zhang H, Zhang X, Cao S, Wang X, Wang W, Guan X, Zhou P, Li J, Jiang W, Tang M, Zheng Q, Cao M, Zhou Y, Chen K, Liu Z, Fang Y. The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes. HORTICULTURE RESEARCH 2023; 10:uhad205. [PMID: 38046853 PMCID: PMC10689054 DOI: 10.1093/hr/uhad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/01/2023] [Indexed: 12/05/2023]
Abstract
Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value in red wine blending and nutrient-enriched foods developing. However, due to the lack of genome information, the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient. Here, the cultivar 'Yan73' was used for assembling the telomere-to-telomere (T2T) genome of teinturier grapes by combining the High Fidelity (HiFi), Hi-C and ultralong Oxford Nanopore Technologies (ONT) reads. Two haplotype genomes were assembled, at the sizes of 501.68 Mb and 493.38 Mb, respectively. In the haplotype 1 genome, the transposable elements (TEs) contained 32.77% of long terminal repeats (LTRs), while in the haplotype 2 genome, 31.53% of LTRs were detected in TEs. Furthermore, obvious inversions were identified in chromosome 18 between the two haplotypes. Transcriptome profiling suggested that the gene expression patterns in 'Cabernet Sauvignon' and 'Yan73' were diverse depending on tissues, developmental stages, and varieties. The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages, whereas the expression levels of numerous genes showed significant differences. Compared with other genes, the expression levels of VvMYBA1 and VvUFGT4 in all samples, VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of 'Yan73' were higher than those of 'Cabernet Sauvignon'. Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of 'Yan73' haplotype 2 genome. The 'Yan73' T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.
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Affiliation(s)
- Kekun Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Mengrui Du
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Hongyan Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Xiaoqian Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wenrui Wang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Xueqiang Guan
- Shandong Grape Research Institute, Shanda South Road, Jinan 250199, China
| | - Penghui Zhou
- Shandong Technology Innovation Center of Wine Grape and Wine, COFCO Great Wall Wine (Penglai) Co., Ltd., Yantai 265600, China
| | - Jin Li
- Shandong Technology Innovation Center of Wine Grape and Wine, COFCO Great Wall Wine (Penglai) Co., Ltd., Yantai 265600, China
| | | | - Meiling Tang
- Yantai Academy of Agricultural Sciences, Gangcheng West Street, Yantai 264000, China
| | - Qiuling Zheng
- Yantai Academy of Agricultural Sciences, Gangcheng West Street, Yantai 264000, China
| | - Muming Cao
- Viticulture and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
| | - Keqin Chen
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yulin Fang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
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Budassi J, Cho N, Del Valle A, Sokolov J. Microfluidic delivery of cutting enzymes for fragmentation of surface-adsorbed DNA molecules. PLoS One 2023; 18:e0250054. [PMID: 37672538 PMCID: PMC10482287 DOI: 10.1371/journal.pone.0250054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/24/2023] [Indexed: 09/08/2023] Open
Abstract
We describe a method for fragmenting, in-situ, surface-adsorbed and immobilized DNAs on polymethylmethacrylate(PMMA)-coated silicon substrates using microfluidic delivery of the cutting enzyme DNase I. Soft lithography is used to produce silicone elastomer (Sylgard 184) gratings which form microfluidic channels for delivery of the enzyme. Bovine serum albumin (BSA) is used to reduce DNase I adsorption to the walls of the microchannels and enable diffusion of the cutting enzyme to a distance of 10mm. Due to the DNAs being immobilized, the fragment order is maintained on the surface. Possible methods of preserving the order for application to sequencing are discussed.
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Affiliation(s)
- Julia Budassi
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
| | - NaHyun Cho
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
| | - Anthony Del Valle
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York, United States of America
| | - Jonathan Sokolov
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
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Narh Mensah DL, Wingfield BD, Coetzee MP. A practical approach to genome assembly and annotation of Basidiomycota using the example of Armillaria. Biotechniques 2023; 75:115-128. [PMID: 37681497 DOI: 10.2144/btn-2023-0023] [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: 09/09/2023] Open
Abstract
Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to further our understanding of the biology of phytopathogens, including Armillaria species. Most Armillaria species are facultative necrotrophs that cause root- and stem-rot, usually on woody plants, significantly impacting agriculture and forestry worldwide. Genome sequencing, assembly and annotation in terms of samples used and methods applied in Armillaria genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future Armillaria genome projects were developed. Knowledge gained from genomic studies of Armillaria species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.
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Affiliation(s)
- Deborah L Narh Mensah
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
- Council for Scientific and Industrial Research - Food Research Institute (CSIR-FRI), PO Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Martin Pa Coetzee
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
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Goes WM, Brasil CRF, Reis-Cunha JL, Coqueiro-Dos-Santos A, Grazielle-Silva V, de Souza Reis J, Souto TC, Laranjeira-Silva MF, Bartholomeu DC, Fernandes AP, Teixeira SMR. Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain. Genomics 2023; 115:110661. [PMID: 37263313 DOI: 10.1016/j.ygeno.2023.110661] [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: 11/22/2022] [Revised: 05/04/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023]
Abstract
We report the sequencing and assembly of the PH8 strain of Leishmania amazonensis one of the etiological agents of leishmaniasis. After combining data from long Pacbio reads, short Illumina reads and synteny with the Leishmania mexicana genome, the sequence of 34 chromosomes with 8317 annotated genes was generated. Multigene families encoding three virulence factors, A2, amastins and the GP63 metalloproteases, were identified and compared to their annotation in other Leishmania species. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we also identified 14 genes encoding proteins involved in parasite iron and heme metabolism and compared to genes from other Trypanosomatids. To follow these studies with a genetic approach to address the role of virulence factors, we tested two CRISPR-Cas9 protocols to generate L. amazonensis knockout cell lines, using the Miltefosine transporter gene as a proof of concept.
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Affiliation(s)
- Wanessa Moreira Goes
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Carlos Rodolpho Ferreira Brasil
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - João Luis Reis-Cunha
- Departamento de Veterinária Preventiva, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil; Departamento de Parasitologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Anderson Coqueiro-Dos-Santos
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Viviane Grazielle-Silva
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Júlia de Souza Reis
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Tatiane Cristina Souto
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Maria Fernanda Laranjeira-Silva
- Departamento de Fisiologia, Universidade de São Paulo, Rua do Matão 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil
| | - Daniella Castanheira Bartholomeu
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Ana Paula Fernandes
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil; Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, MG, CEP 31.210-360, Brazil
| | - Santuza Maria Ribeiro Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil; Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, MG, CEP 31.210-360, Brazil.
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Berres S, Gromoll J, Wöste M, Sandmann S, Laurentino S. OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations. BMC Bioinformatics 2023; 24:300. [PMID: 37496002 PMCID: PMC10369718 DOI: 10.1186/s12859-023-05422-w] [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: 04/19/2022] [Accepted: 07/18/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Modern genome sequencing leads to an ever-growing collection of genomic annotations. Combining these elements with a set of input regions (e.g. genes) would yield new insights in genomic associations, such as those involved in gene regulation. The required data are scattered across different databases making a manual approach tiresome, unpractical, and prone to error. Semi-automatic approaches require programming skills in data parsing, processing, overlap calculation, and visualization, which most biomedical researchers lack. Our aim was to develop an automated tool providing all necessary algorithms, benefiting both bioinformaticians and researchers without bioinformatic training. RESULTS We developed overlapping annotated genomic regions (OGRE) as a comprehensive tool to associate and visualize input regions with genomic annotations. It does so by parsing regions of interest, mining publicly available annotations, and calculating possible overlaps between them. The user can thus identify location, type, and number of associated regulatory elements. Results are presented as easy to understand visualizations and result tables. We applied OGRE to recent studies and could show high reproducibility and potential new insights. To demonstrate OGRE's performance in terms of running time and output, we have conducted a benchmark and compared its features with similar tools. CONCLUSIONS OGRE's functions and built-in annotations can be applied as a downstream overlap association step, which is compatible with most genomic sequencing outputs, and can thus enrich pre-existing analyses pipelines. Compared to similar tools, OGRE shows competitive performance, offers additional features, and has been successfully applied to two recent studies. Overall, OGRE addresses the lack of tools for automatic analysis, local genomic overlap calculation, and visualization by providing an easy to use, end-to-end solution for both biologists and computational scientists.
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Affiliation(s)
- Sven Berres
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany
| | - Jörg Gromoll
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1 Building A11, 48149, Munster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1 Building A11, 48149, Munster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany.
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Gable SM, Mendez JM, Bushroe NA, Wilson A, Byars MI, Tollis M. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order. Genes (Basel) 2023; 14:1387. [PMID: 37510292 PMCID: PMC10379679 DOI: 10.3390/genes14071387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
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Zürcher JF, Kleefeldt AA, Funke LFH, Birnbaum J, Fredens J, Grazioli S, Liu KC, Spinck M, Petris G, Murat P, Rehm FBH, Sale JE, Chin JW. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 2023; 619:555-562. [PMID: 37380776 PMCID: PMC7614783 DOI: 10.1038/s41586-023-06268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.
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Affiliation(s)
- Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Askar A Kleefeldt
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Jakob Birnbaum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Synthetic Biology for Clinical and Technological Innovation, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Simona Grazioli
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martin Spinck
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Pierre Murat
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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43
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Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546576. [PMID: 37425881 PMCID: PMC10327048 DOI: 10.1101/2023.06.28.546576] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).
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Affiliation(s)
- Delphine Larivière
- Dept. of Biochemistry and Molecular Biology, Pennsylvania State University, USA
| | - Linelle Abueg
- Vertebrate Genome Laboratory, The Rockefeller University, USA
| | | | - Cristóbal Gallardo-Alba
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Bjorn Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Alex Ostrovsky
- Departments of Biology and Computer Science, Johns Hopkins University, USA
| | - Marc Palmada-Flores
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain
| | - Brandon D Pickett
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keon Rabbani
- Department of Quantitative and Computational Biology, University of Southern California
| | | | - Mark Chaisson
- Department of Quantitative and Computational Biology, University of Southern California
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Joanna Collins
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Alexandra Denisova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, USA
| | | | | | | | - Nivesh Jain
- Vertebrate Genome Laboratory, The Rockefeller University, USA
| | - Cassidy Johnson
- Vertebrate Genome Laboratory, The Rockefeller University, USA
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, NY, 10065, USA
| | - Tomas Marques-Bonet
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Brian O'Toole
- Vertebrate Genome Laboratory, The Rockefeller University, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Simona Secomandi
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Marcella Sozzoni
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino (FI)
| | - Tatiana Tilley
- Vertebrate Genome Laboratory, The Rockefeller University, USA
| | | | - Marius van den Beek
- Dept. of Biochemistry and Molecular Biology, Pennsylvania State University, USA
| | - Robert M Waterhouse
- Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, USA
| | - Michael C Schatz
- Departments of Biology and Computer Science, Johns Hopkins University, USA
| | - Anton Nekrutenko
- Dept. of Biochemistry and Molecular Biology, Pennsylvania State University, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, USA
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44
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Shi X, Cao S, Wang X, Huang S, Wang Y, Liu Z, Liu W, Leng X, Peng Y, Wang N, Wang Y, Ma Z, Xu X, Zhang F, Xue H, Zhong H, Wang Y, Zhang K, Velt A, Avia K, Holtgräwe D, Grimplet J, Matus JT, Ware D, Wu X, Wang H, Liu C, Fang Y, Rustenholz C, Cheng Z, Xiao H, Zhou Y. The complete reference genome for grapevine ( Vitis vinifera L.) genetics and breeding. HORTICULTURE RESEARCH 2023; 10:uhad061. [PMID: 37213686 PMCID: PMC10199708 DOI: 10.1093/hr/uhad061] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/02/2023] [Indexed: 05/23/2023]
Abstract
Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres, limiting the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the study of inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) is 69 Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.
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Affiliation(s)
- Xiaoya Shi
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuo Cao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Siyang Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yue Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China
| | - Zhongjie Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenwen Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanling Peng
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Nan Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yiwen Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiyao Ma
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaodong Xu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Fan Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hui Xue
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Haixia Zhong
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Kekun Zhang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Amandine Velt
- SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
| | - Komlan Avia
- SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jérôme Grimplet
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Systems Biotech Program, Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Xinyu Wu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Haibo Wang
- Fruit Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit Tree, Liaoning Province, Xingcheng 125100, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450004, China
| | - Yuling Fang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | | | - Zongming Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Xiao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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45
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Ueno S, Hasegawa Y, Kato S, Mori H, Tsukada H, Ohira H, Kaneko S. Rapid survey of de novo mutations in naturally growing tree species following the March 2011 disaster in Fukushima: The effect of low-dose-rate radiation. ENVIRONMENT INTERNATIONAL 2023; 174:107893. [PMID: 37058973 DOI: 10.1016/j.envint.2023.107893] [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: 12/11/2022] [Revised: 02/13/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
The impact of low-dose-rate radiation on genetics is largely unknown, particularly in natural environments. The Fukushima Dai-ich Nuclear Power Plant disaster resulted in the creation of contaminated natural lands. In this study, de novo mutations (DNMs) in germ line cells were surveyed from double-digest RADseq fragments in Japanese cedar and flowering cherry trees exposed to ambient dose rates ranging from 0.08 to 6.86 μGy h-1. These two species are among the most widely cultivated Japanese gymnosperm and angiosperm trees for forestry and horticultural purpose, respectively. For Japanese flowering cherry, open crossings were performed to produce seedlings, and only two candidate DNMs were detected from uncontaminated area. For Japanese cedar, the haploid megagametophytes were used as next generation samples. The use of megagametophytes from open crossing for next generation mutation screening had many advantages such as reducing exposure to radiation in contaminated areas because artificial crossings are not needed and the ease of data analysis owing to the haploid nature of megagametophytes. A direct comparison of the nucleotide sequences of parents and megagametophytes revealed an average of 1.4 candidate DNMs per megagametophyte sample (range: 0-40) after filtering procedures were optimized based on the validation of DNMs via Sanger sequencing. There was no relationship between the observed mutations and the ambient dose rate in the growing area or the concentration of 137Cs in cedar branches. The present results also suggest that mutation rates differ among lineages and that the growing environment has a relatively large influence on these mutation rates. These results suggested there was no significant increase in the mutation rate of the germplasm of Japanese cedar and flowering cherry trees growing in the contaminated areas.
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Affiliation(s)
- Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan.
| | - Yoichi Hasegawa
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Shuri Kato
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan; Tama Forest Science Garden, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1833-81 Todori, Hachioji, Tokyo 193-0843, Japan
| | - Hideki Mori
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Hirofumi Tsukada
- Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan
| | - Hajime Ohira
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan.
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46
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Jeon MS, Jeong DM, Doh H, Kang HA, Jung H, Eyun SI. A practical comparison of the next-generation sequencing platform and assemblers using yeast genome. Life Sci Alliance 2023; 6:e202201744. [PMID: 36746534 PMCID: PMC9902641 DOI: 10.26508/lsa.202201744] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
Assembling fragmented whole-genomic information from the sequencing data is an inevitable process for further genome-wide research. However, it is intricate to select the appropriate assembly pipeline for unknown species because of the species-specific genomic properties. Therefore, our study focused on relatively more static proclivities of sequencing platforms and assembly algorithms than the fickle genome sequences. A total of 212 draft and polished de novo assemblies were constructed under the different sequencing platforms and assembly algorithms with the repetitive yeast genome. Our comprehensive data indicated that sequencing reads from Oxford Nanopore with R7.3 flow cells generated more continuous assemblies than those derived from the PacBio Sequel, although the homopolymer-based assembly errors and chimeric contigs exist. In addition, the comparison between two second-generation sequencing platforms showed that Illumina NovaSeq 6000 provides more accurate and continuous assembly in the second-generation-sequencing-first pipeline, but MGI DNBSEQ-T7 provides a cheap and accurate read in the polishing process. Furthermore, our insight into the relationship among the computational time, read length, and coverage depth provided clues to the optimal pipelines of yeast assembly.
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Affiliation(s)
- Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Da Min Jeong
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Huijeong Doh
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyungtaek Jung
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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47
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Leeb T, Bannasch D, Schoenebeck JJ. Identification of Genetic Risk Factors for Monogenic and Complex Canine Diseases. Annu Rev Anim Biosci 2023; 11:183-205. [PMID: 36322969 DOI: 10.1146/annurev-animal-050622-055534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Advances in DNA sequencing and other technologies have greatly facilitated the identification of genetic risk factors for inherited diseases in dogs. We review recent technological developments based on selected examples from canine disease genetics. The identification of disease-causing variants in dogs with monogenic diseases may become a widely employed diagnostic approach in clinical veterinary medicine in the not-too-distant future. Diseases with complex modes of inheritance continue to pose challenges to researchers but have also become much more tangible than in the past. In addition to strategies for identifying genetic risk factors, we provide some thoughts on the interpretation of sequence variants that are largely inspired by developments in human clinical genetics.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland;
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California, Davis, California, USA;
| | - Jeffrey J Schoenebeck
- The Roslin Institute and Royal (Dick) School for Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom;
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48
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Hayashi K, Alseekh S, Fernie AR. Genetic and epigenetic control of the plant metabolome. Proteomics 2023:e2200104. [PMID: 36781168 DOI: 10.1002/pmic.202200104] [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: 11/29/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by changing the enzyme's catalytic activity or abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect transcription and ultimately metabolite content. In addition to genetic mutations, transgenerational epigenetic variations have also been found to affect metabolic content by controlling the transcription of metabolism-related genes. However, the majority of cases reported so far, in which epigenetic mechanisms are associated with metabolism, are non-transgenerational, and are triggered by developmental signals or environmental stress. Although, accumulating research has provided evidence of strong genetic control of the metabolome, epigenetic control has been largely untouched. Here, we provide a review of the genetic and epigenetic control of metabolism with a focus on epigenetics. We discuss both transgenerational and non-transgenerational epigenetic marks regulating metabolism as well as prospects of the field of metabolic control where intricate interactions between genetics and epigenetics are involved.
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Affiliation(s)
- Koki Hayashi
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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49
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Nishida Y, Kodama K, Sengoku S. The gap between development and manufacturing in gene therapy: Strategic options for overcoming traps. Drug Discov Today 2023; 28:103429. [PMID: 36334648 DOI: 10.1016/j.drudis.2022.103429] [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: 07/31/2022] [Revised: 10/22/2022] [Accepted: 10/29/2022] [Indexed: 11/08/2022]
Abstract
Gene therapy has been one of the most promising therapeutic approaches in recent years. This study analyzed a research and development (R&D) system for adeno-associated virus (AAV)-based gene therapies, and confirmed that there was a gap between the development and manufacturing capabilities. Although a start-up company that has no academic or manufacturing facilities can begin the clinical development process, it cannot successfully continue development activities without forming alliances and capital investment or, at a certain stage, without appropriate manufacturing and marketing strategies. We reviewed a series of case studies to categorize the acquisition patterns of pharmaceutical companies that are engaged in AAV gene therapy. These results provide insights into the R&D structures for AAV gene therapies from a technological management perspective.
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Affiliation(s)
- Yu Nishida
- Department of Innovation Science, School of Environment and Society, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Kota Kodama
- Graduate School of Technology Management, Ritsumeikan Uuniversity, Ibaraki-shi, Osaka, Japan
| | - Shintaro Sengoku
- Department of Innovation Science, School of Environment and Society, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
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Nguyen TV, Vander Jagt CJ, Wang J, Daetwyler HD, Xiang R, Goddard ME, Nguyen LT, Ross EM, Hayes BJ, Chamberlain AJ, MacLeod IM. In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants. Genet Sel Evol 2023; 55:9. [PMID: 36721111 PMCID: PMC9887926 DOI: 10.1186/s12711-023-00783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/23/2023] [Indexed: 02/02/2023] Open
Abstract
Studies have demonstrated that structural variants (SV) play a substantial role in the evolution of species and have an impact on Mendelian traits in the genome. However, unlike small variants (< 50 bp), it has been challenging to accurately identify and genotype SV at the population scale using short-read sequencing. Long-read sequencing technologies are becoming competitively priced and can address several of the disadvantages of short-read sequencing for the discovery and genotyping of SV. In livestock species, analysis of SV at the population scale still faces challenges due to the lack of resources, high costs, technological barriers, and computational limitations. In this review, we summarize recent progress in the characterization of SV in the major livestock species, the obstacles that still need to be overcome, as well as the future directions in this growing field. It seems timely that research communities pool resources to build global population-scale long-read sequencing consortiums for the major livestock species for which the application of genomic tools has become cost-effective.
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Affiliation(s)
- Tuan V. Nguyen
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | | | - Jianghui Wang
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia
| | - Ruidong Xiang
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, VIC 3052 Australia
| | - Michael E. Goddard
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, VIC 3052 Australia
| | - Loan T. Nguyen
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD 4072 Australia
| | - Elizabeth M. Ross
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD 4072 Australia
| | - Ben J. Hayes
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD 4072 Australia
| | - Amanda J. Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia
| | - Iona M. MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
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