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Song B, Buckler ES, Stitzer MC. New whole-genome alignment tools are needed for tapping into plant diversity. TRENDS IN PLANT SCIENCE 2024; 29:355-369. [PMID: 37749022 DOI: 10.1016/j.tplants.2023.08.013] [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: 04/24/2023] [Revised: 07/19/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023]
Abstract
Genome alignment is one of the most foundational methods for genome sequence studies. With rapid advances in sequencing and assembly technologies, these newly assembled genomes present challenges for alignment tools to meet the increased complexity and scale. Plant genome alignment is technologically challenging because of frequent whole-genome duplications (WGDs) as well as chromosome rearrangements and fractionation, high nucleotide diversity, widespread structural variation, and high transposable element (TE) activity causing large proportions of repeat elements. We summarize classical pairwise and multiple genome alignment (MGA) methods, and highlight techniques that are widely used or are being developed by the plant research community. We also outline the remaining challenges for precise genome alignment and the interpretation of alignment results in plants.
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Affiliation(s)
- Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China; Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA; Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Michelle C Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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2
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Kudron M, Gevirtzman L, Victorsen A, Lear BC, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Huynh C, Vafeados D, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker SE, Reinke V, Waterston RH. Binding profiles for 954 Drosophila and C. elegans transcription factors reveal tissue specific regulatory relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576242. [PMID: 38293065 PMCID: PMC10827215 DOI: 10.1101/2024.01.18.576242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the modERN (model organism Encyclopedia of Regulatory Networks) consortium that systematically assayed TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). We describe key features of these datasets, comprising 604 TFs identifying 3.6M sites in the fly and 350 TFs identifying 0.9 M sites in the worm. Applying a machine learning model to these data identifies sets of TFs with a prominent role in promoting target gene expression in specific cell types. TF binding data are available through the ENCODE Data Coordinating Center and at https://epic.gs.washington.edu/modERNresource, which provides access to processed and summary data, as well as widgets to probe cell type-specific TF-target relationships. These data are a rich resource that should fuel investigations into TF function during development.
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Affiliation(s)
- Michelle Kudron
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Louis Gevirtzman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Alec Victorsen
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN 55455
| | - Bridget C. Lear
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Jiahao Gao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Jinrui Xu
- Department of Biology, Howard University, Washington, District of Columbia 20059, USA
- Center for Applied Data Science and Analytics, Howard University, Washington, District of Columbia 20059, USA
| | - Swapna Samanta
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Emily Frink
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Adri Tran-Pearson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Chau Huynh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Dionne Vafeados
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Ann Hammonds
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - William Fisher
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Martha Wall
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637
| | - Greg Wesseling
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Vanessa Hernandez
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Zhichun Lin
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Mary Kasparian
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Kevin White
- Department of Biochemistry and Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Ravi Allada
- Department of Neurobiology, Northwestern University, Evanston IL 60208
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
- Department of Statistics and Data Science, Yale University, New Haven, Connecticut 06520, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Susan E. Celniker
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Valerie Reinke
- Department of Genetics, Yale University, New Haven, Connecticut 06520
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
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3
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Vu TN, Clark JR, Jang E, D'Souza R, Nguyen LP, Pinto NA, Yoo S, Abadie R, Maresso AW, Yong D. Appelmans protocol - A directed in vitro evolution enables induction and recombination of prophages with expanded host range. Virus Res 2024; 339:199272. [PMID: 37981215 PMCID: PMC10730860 DOI: 10.1016/j.virusres.2023.199272] [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: 07/31/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
Infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) present significant healthcare challenges due to limited treatment options. Bacteriophage (phage) therapy offers potential as an alternative treatment. However, the high host specificity of phages poses challenges for their therapeutic application. To broaden the phage spectrum, laboratory-based phage training using the Appelmans protocol was employed in this study. As a result, the protocol successfully expanded the host range of a phage cocktail targeting CRAB. Further analysis revealed that the expanded host range phages isolated from the output cocktail were identified as recombinant derivatives originating from prophages induced from encountered bacterial strains. These findings provide valuable genetic insights into the protocol's mechanism when applied to phages infecting A. baumannii strains that have never been investigated before. However, it is noteworthy that the expanded host range phages obtained from this protocol exhibited limited stability, raising concerns about their suitability for therapeutic purposes.
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Affiliation(s)
- Thao Nguyen Vu
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Justin Ryan Clark
- Tailored Antibacterials and Innovative Laboratories for Phage Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, US
| | - Eris Jang
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; University of Georgia Terry College of Business, Athens, GA, US
| | - Roshan D'Souza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Le Phuong Nguyen
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, US
| | - Naina Adren Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seongjun Yoo
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Ricardo Abadie
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Anthony William Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, US
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.
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Puritz JB, Guo X, Hare M, He Y, Hillier LW, Jin S, Liu M, Lotterhos KE, Minx P, Modak T, Proestou D, Rice ES, Tomlinson C, Warren WC, Witkop E, Zhao H, Gomez-Chiarri M. A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference. Mol Ecol Resour 2024; 24:e13801. [PMID: 37186213 DOI: 10.1111/1755-0998.13801] [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: 09/29/2022] [Revised: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.
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Affiliation(s)
- Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Matthew Hare
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Yan He
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Shubo Jin
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Ming Liu
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - Pat Minx
- Donald Danforth Plant Science Center, Olivette, Missouri, USA
| | - Tejashree Modak
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Dina Proestou
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, Kingston, Rhode Island, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA
| | - Wesley C Warren
- Departments of Animal Sciences and Surgery, Institute of Informatics and Data Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Erin Witkop
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Honggang Zhao
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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5
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Kang JS, Giang VNL, Park HS, Park YS, Cho W, Nguyen VB, Shim H, Waminal NE, Park JY, Kim HH, Yang TJ. Evolution of the Araliaceae family involved rapid diversification of the Asian Palmate group and Hydrocotyle specific mutational pressure. Sci Rep 2023; 13:22325. [PMID: 38102332 PMCID: PMC10724125 DOI: 10.1038/s41598-023-49830-7] [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: 04/04/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
The Araliaceae contain many valuable species in medicinal and industrial aspects. We performed intensive phylogenomics using the plastid genome (plastome) and 45S nuclear ribosomal DNA sequences. A total of 66 plastome sequences were used, 13 of which were newly assembled in this study, 12 from new sequences, and one from existing data. While Araliaceae plastomes showed conserved genome structure, phylogenetic reconstructions based on four different plastome datasets revealed phylogenetic discordance within the Asian Palmate group. The divergence time estimation revealed that splits in two Araliaceae subfamilies and the clades exhibiting phylogenetic discordances in the Asian Palmate group occurred at two climatic optima, suggesting that global warming events triggered species divergence, particularly the rapid diversification of the Asian Palmate group during the Middle Miocene. Nucleotide substitution analyses indicated that the Hydrocotyloideae plastomes have undergone accelerated AT-biased mutations (C-to-T transitions) compared with the Aralioideae plastomes, and the acceleration may occur in their mitochondrial and nuclear genomes as well. This implies that members of the genus Hydrocotyle, the only aquatic plants in the Araliaceae, have experienced a distinct evolutionary history from the other species. We also discussed the intercontinental disjunction in the genus Panax and proposed a hypothesis to complement the previously proposed hypothesis. Our results provide the evolutionary trajectory of Araliaceae and advance our current understanding of the evolution of Araliaceae species.
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Affiliation(s)
- Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Vo Ngoc Linh Giang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, South Korea
| | - Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Woohyeon Cho
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Van Binh Nguyen
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Biology, Dalat University, Dalat, 670000, Vietnam
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Nomar Espinosa Waminal
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Gatersleben, Germany
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea.
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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6
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Mi J, He T, Hu X, Wang Z, Wang T, Qi X, Li K, Gao L, Liu C, Zhang Y, Wang S, Qiu Y, Liu Z, Song J, Wang X, Gao Y, Cui H. Enterococcus faecium C171: Modulating the Immune Response to Acute Lethal Viral Challenge. Int J Antimicrob Agents 2023; 62:106969. [PMID: 37758064 DOI: 10.1016/j.ijantimicag.2023.106969] [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: 01/31/2023] [Revised: 08/08/2023] [Accepted: 09/09/2023] [Indexed: 10/03/2023]
Abstract
Commensal bacteria modulate acute immune responses to infection in hosts. In this study, Enterococcus faecium C171 was screened and isolated. This strain has similar basic characteristics to the reference probiotic, including strong anti-inflammatory and anti-infective effects. E. faecium C171 inhibits the production of pro-Caspase-1 and significantly reduces the production of interleukin-1β (IL-1β) in vitro. These reactions were confirmed using the Transwell system. Live E. faecium C171 mainly exerted an inhibitory effect on acute inflammation, whereas the anti-infective and immune-activating effects were primarily mediated by the E. faecium C171-produced bacterial extracellular vesicles (Efm-C171-BEVs). Furthermore, in the specific pathogen-free (SPF) chicken model, oral administration of E. faecium C171 increased the relative abundance of beneficial microbiota (Enterococcus and Lactobacillus), particularly Enterococcus, the most important functional bacteria of the gut microbiota. E. faecium C171 significantly inhibited the acute inflammatory response induced by a highly virulent infectious disease, and reduced mortality in SPF chickens by 75%. In addition, E. faecium C171 induced high levels of CD3+, CD4-, and CD8- immunoregulatory cells and CD8+ killer T cells, and significantly improved the proliferative activity of T cells in peripheral blood mononuclear cells, and the secretion of interferon-γ. These findings indicate that E. faecium C171 and Efm-C171-BEVs are promising candidates for adjuvant treatment of acute inflammatory diseases and acute viral infections.
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Affiliation(s)
- Jielan Mi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Tana He
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Xinyun Hu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Zhihao Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Tingting Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Xiaole Qi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Kai Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Li Gao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Changjun Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Yanping Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Suyan Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Yu Qiu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Zengqi Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Jie Song
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Xiaomei Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Yulong Gao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Hongyu Cui
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
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Paparella A, L’Abbate A, Palmisano D, Chirico G, Porubsky D, Catacchio CR, Ventura M, Eichler EE, Maggiolini FAM, Antonacci F. Structural Variation Evolution at the 15q11-q13 Disease-Associated Locus. Int J Mol Sci 2023; 24:15818. [PMID: 37958807 PMCID: PMC10648317 DOI: 10.3390/ijms242115818] [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: 10/09/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The impact of segmental duplications on human evolution and disease is only just starting to unfold, thanks to advancements in sequencing technologies that allow for their discovery and precise genotyping. The 15q11-q13 locus is a hotspot of recurrent copy number variation associated with Prader-Willi/Angelman syndromes, developmental delay, autism, and epilepsy and is mediated by complex segmental duplications, many of which arose recently during evolution. To gain insight into the instability of this region, we characterized its architecture in human and nonhuman primates, reconstructing the evolutionary history of five different inversions that rearranged the region in different species primarily by accumulation of segmental duplications. Comparative analysis of human and nonhuman primate duplication structures suggests a human-specific gain of directly oriented duplications in the regions flanking the GOLGA cores and HERC segmental duplications, representing potential genomic drivers for the human-specific expansions. The increasing complexity of segmental duplication organization over the course of evolution underlies its association with human susceptibility to recurrent disease-associated rearrangements.
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Affiliation(s)
- Annalisa Paparella
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Alberto L’Abbate
- Institute of Biomembranes, Bioenergetics, and Molecular Biotechnology (IBIOM), 70125 Bari, Italy
| | - Donato Palmisano
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Gerardina Chirico
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Claudia R. Catacchio
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute (HHMI), University of Washington, Seattle, WA 98195, USA
| | - Flavia A. M. Maggiolini
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA), 70010 Bari, Italy
| | - Francesca Antonacci
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
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8
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Li J, Zhao T, Guan D, Pan Z, Bai Z, Teng J, Zhang Z, Zheng Z, Zeng J, Zhou H, Fang L, Cheng H. Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits. CELL GENOMICS 2023; 3:100390. [PMID: 37868039 PMCID: PMC10589632 DOI: 10.1016/j.xgen.2023.100390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/25/2023] [Accepted: 08/02/2023] [Indexed: 10/24/2023]
Abstract
Assessment of genomic conservation between humans and pigs at the functional level can improve the potential of pigs as a human biomedical model. To address this, we developed a deep learning-based approach to learn the genomic conservation at the functional level (DeepGCF) between species by integrating 386 and 374 functional profiles from humans and pigs, respectively. DeepGCF demonstrated better prediction performance compared with the previous method. In addition, the resulting DeepGCF score captures the functional conservation between humans and pigs by examining chromatin states, sequence ontologies, and regulatory variants. We identified a core set of genomic regions as functionally conserved that plays key roles in gene regulation and is enriched for the heritability of complex traits and diseases in humans. Our results highlight the importance of cross-species functional comparison in illustrating the genetic and evolutionary basis of complex phenotypes.
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Affiliation(s)
- Jinghui Li
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Tianjing Zhao
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Dailu Guan
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Zhonghao Bai
- Center for Quantitative Genetics and Genomics (QGG), Aarhus University, 8000 Aarhus, Denmark
| | - Jinyan Teng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhe Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics (QGG), Aarhus University, 8000 Aarhus, Denmark
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
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9
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Li G, Jiang D, Wang J, Liao Y, Zhang T, Zhang H, Dai X, Ren H, Chen C, Zheng Y. A High-Continuity Genome Assembly of Chinese Flowering Cabbage ( Brassica rapa var. parachinensis) Provides New Insights into Brassica Genome Structure Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:2498. [PMID: 37447059 DOI: 10.3390/plants12132498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
Chinese flowering cabbage (Brassica rapa var. parachinensis) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality de novo assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chinese flowering cabbage with an integrated approach using PacBio, Illumina, and Hi-C technology. We modeled 47,598 protein-coding genes in this analysis and annotated 52% (205.9/384) of its genome as repetitive sequences including 17% in DNA transposons and 22% in long terminal retrotransposons (LTRs). Phylogenetic analysis reveals the genome of the Chinese flowering cabbage has a closer evolutionary relationship with the AA diploid progenitor of the allotetraploid species, Brassica juncea. Comparative genomic analysis of Brassica species with different subgenome types (A, B and C) reveals that the pericentromeric regions on chromosome 5 and 6 of the AA genome have been significantly expanded compared to the orthologous genomic regions in the BB and CC genomes, largely driven by LTR-retrotransposon amplification. Furthermore, we identified a large number of structural variations (SVs) within the B. rapa lines that could impact coding genes, suggesting the functional significance of SVs on Brassica genome evolution. Overall, our high-quality genome assembly of the Chinese flowering cabbage provides a valuable genetic resource for deciphering the genome evolution of Brassica species and it can potentially serve as the reference genome guiding the molecular breeding practice of B. rapa crops.
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Affiliation(s)
- Guangguang Li
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Ding Jiang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Juntao Wang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yi Liao
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Xiuchun Dai
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Hailong Ren
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
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10
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Zhou W, Furey NM, Soisook P, Thong VD, Lim BK, Rossiter SJ, Mao X. Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group. Mol Phylogenet Evol 2023; 183:107784. [PMID: 37040825 DOI: 10.1016/j.ympev.2023.107784] [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: 12/09/2022] [Revised: 03/11/2023] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
Abstract
Chromosomal variation among closely related taxa is common in both plants and animals, and can reduce rates of introgression as well as promote reproductive isolation and speciation. In mammals, studies relating introgression to chromosomal variation have tended to focus on a few model systems and typically characterized levels of introgression using small numbers of loci. Here we took a genome-wide approach to examine how introgression rates vary among four closely related horseshoe bats (Rhinolophus pearsoni group) that possess different diploid chromosome numbers (2n = 42, 44, 46, and 60) resulting from Robertsonian (Rb) changes (fissions/fusions). Using a sequence capture we obtained orthologous loci for thousands of nuclear loci, as well as mitogenomes, and performed phylogenetic and population genetic analyses. We found that the taxon with 2n = 60 was the first to diverge in this group, and that the relationships among the three other taxa (2n = 42, 44 and 46) showed discordance across our different analyses. Our results revealed signatures of multiple ancient introgression events between the four taxa, with evidence of mitonuclar discordance in phylogenetic trees and reticulation events in their evolutionary history. Despite this, we found no evidence of recent and/or ongoing introgression between taxa. Overall, our results indicate that the effects of Rb changes on the reduction of introgression are complicated and that these may contribute to reproductive isolation and speciation in concert with other factors (e.g. phenotypic and genic divergence).
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Affiliation(s)
- Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Neil M Furey
- Fauna & Flora International (Cambodia), PO Box 1380, No. 19, Street 360, Boeng Keng Kong 1, Phnom Penh 12000, Cambodia
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Vu D Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam; Graduate University of Science and Technology, VAST, Viet Nam
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China.
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11
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Chang G, Yuan X, Guo Q, Bai H, Cao X, Liu M, Wang Z, Li B, Wang S, Jiang Y, Wang Z, Zhang Y, Xu Q, Song Q, Pan R, Qiu L, Gu T, Wu X, Bi Y, Cao Z, Zhang Y, Chen Y, Li H, Liu J, Dai W, Chen G. The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:483-500. [PMID: 37652165 PMCID: PMC10787023 DOI: 10.1016/j.gpb.2023.08.002] [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: 01/26/2021] [Revised: 07/05/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assemblies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.
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Affiliation(s)
- Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Xiaoya Yuan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qixin Guo
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Xiaofang Cao
- Novogene Bioinformatics Institute, Beijing 100080, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing 100080, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Bichun Li
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shasha Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhiquan Wang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Yang Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qi Xu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qianqian Song
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Rui Pan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Lingling Qiu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tiantian Gu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xinsheng Wu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yulin Bi
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhengfeng Cao
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yu Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yang Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing 100080, China
| | - Jianfeng Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100091, China
| | - Wangcheng Dai
- Zhenjiang Tiancheng Agricultural Science and Technology Co., Ltd, Zhenjiang 210034, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
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12
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Lin TS, Chiu SH, Chen CC, Lin CH. Investigation of monacolin K, yellow pigments, and citrinin production capabilities of Monascus purpureus and Monascus ruber (Monascus pilosus). J Food Drug Anal 2023; 31:85-94. [PMID: 37224553 PMCID: PMC10208672 DOI: 10.38212/2224-6614.3438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/12/2022] [Indexed: 09/07/2023] Open
Abstract
Red mold rice (RMR) is a traditional Chinese medicine prepared using Monascus fermentation. Monascus ruber ( pilosus) and Monascus purpureus have a long history of use as food and medicine. As an economically important starter culture, the relationship between the taxonomy of Monascus and production capabilities of secondary metabolites is crucial for the Monascus food industry. In this study, monacolin K, monascin, ankaflavin, and citrinin production by M. purpureus and M. ruber were genomically and chemically investigated. Our findings suggest that M. purpureus can produce monascin and ankaflavin in a correlated manner, whereas M. ruber produces monascin with minimum ankaflavin. M. purpureus is capable of producing citrinin; however, it is unlikely able to produce monacolin K. In contrast, M. ruber produces monacolin K, but not citrinin. We suggest that the current monacolin K content-related regulation of Monascus food should be revised, and labeling of Monascus species should be considered.
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Affiliation(s)
- Tzu-shing Lin
- Department of Life Science, National Taitung University,
Taiwan
| | - Shih-Hau Chiu
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute (FIRDI),
Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute (FIRDI),
Taiwan
| | - Chih-Hui Lin
- Department of Life Science, National Taitung University,
Taiwan
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13
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Peters DL, Davis CM, Harris G, Zhou H, Rather PN, Hrapovic S, Lam E, Dennis JJ, Chen W. Characterization of Virulent T4-Like Acinetobacter baumannii Bacteriophages DLP1 and DLP2. Viruses 2023; 15:v15030739. [PMID: 36992448 PMCID: PMC10051250 DOI: 10.3390/v15030739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
The world is currently facing a global health crisis due to the rapid increase in antimicrobial-resistant bacterial infections. One of the most concerning pathogens is Acinetobacter baumannii, which is listed as a Priority 1 pathogen by the World Health Organization. This Gram-negative bacterium has many intrinsic antibiotic resistance mechanisms and the ability to quickly acquire new resistance determinants from its environment. A limited number of effective antibiotics against this pathogen complicates the treatment of A. baumannii infections. A potential treatment option that is rapidly gaining interest is “phage therapy”, or the clinical application of bacteriophages to selectively kill bacteria. The myoviruses DLP1 and DLP2 (vB_AbaM-DLP_1 and vB_AbaM-DLP_2, respectively) were isolated from sewage samples using a capsule minus variant of A. baumannii strain AB5075. Host range analysis of these phages against 107 A. baumannii strains shows a limited host range, infecting 15 and 21 for phages DLP1 and DLP2, respectively. Phage DLP1 has a large burst size of 239 PFU/cell, a latency period of 20 min, and virulence index of 0.93. In contrast, DLP2 has a smaller burst size of 24 PFU/cell, a latency period of 20 min, and virulence index of 0.86. Both phages show potential for use as therapeutics to combat A. baumannii infections.
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Affiliation(s)
- Danielle L. Peters
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Correspondence:
| | - Carly M. Davis
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Greg Harris
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Hongyan Zhou
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Philip N. Rather
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
- Research Service, Atlanta VA Medical Center, Decatur, GA 30033, USA
| | - Sabahudin Hrapovic
- Aquatic and Crop Resource Development (ACRD) Research Center, National Research Council Canada, Montreal, QC H4P 2R2, Canada
| | - Edmond Lam
- Aquatic and Crop Resource Development (ACRD) Research Center, National Research Council Canada, Montreal, QC H4P 2R2, Canada
| | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Wangxue Chen
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Department of Biology, Brock University, St. Catharines, ON L2S 3A1, Canada
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14
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Firtina C, Park J, Alser M, Kim JS, Cali D, Shahroodi T, Ghiasi N, Singh G, Kanellopoulos K, Alkan C, Mutlu O. BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis. NAR Genom Bioinform 2023; 5:lqad004. [PMID: 36685727 PMCID: PMC9853099 DOI: 10.1093/nargab/lqad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/16/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding exact-matching seeds as the conventional hashing methods assign distinct hash values for different seeds, including highly similar seeds. Finding only exact-matching seeds causes either (i) increasing the use of the costly sequence alignment or (ii) limited sensitivity. We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches. BLEND (i) utilizes a technique called SimHash, that can generate the same hash value for similar sets, and (ii) provides the proper mechanisms for using seeds as sets with the SimHash technique to find fuzzy seed matches efficiently. We show the benefits of BLEND when used in read overlapping and read mapping. For read overlapping, BLEND is faster by 2.4×-83.9× (on average 19.3×), has a lower memory footprint by 0.9×-14.1× (on average 3.8×), and finds higher quality overlaps leading to accurate de novo assemblies than the state-of-the-art tool, minimap2. For read mapping, BLEND is faster by 0.8×-4.1× (on average 1.7×) than minimap2. Source code is available at https://github.com/CMU-SAFARI/BLEND.
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Affiliation(s)
- Can Firtina
- To whom correspondence should be addressed. Tel: +41 44 632 64 29;
| | - Jisung Park
- ETH Zurich, Zurich 8092, Switzerland,POSTECH, Pohang 37673, Republic of Korea
| | | | | | | | | | | | | | | | - Can Alkan
- Bilkent University, Ankara 06800, Turkey
| | - Onur Mutlu
- Correspondence may also be addressed to Onur Mutlu. Tel: +41 44 632 64 29;
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15
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Chen J, Jiang T, Jiang J, Deng L, Liu Y, Zhong Z, Fu H, Yang B, Zhang L. The chloroplast GATA-motif of Mahonia bealei participates in alkaloid-mediated photosystem inhibition during dark to light transition. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153894. [PMID: 36525836 DOI: 10.1016/j.jplph.2022.153894] [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: 05/14/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Mahonia bealei and Mahonia fortunei are important plant resources in Traditional Chinese Medicine that are valued for their high levels of benzylisoquinoline alkaloids (BIAs). Although the phytotoxic activity of BIAs has been recognized, information is limited on the mechanism of action by which these compounds regulate photosynthetic activity. Here, we performed comparative chloroplast genome analysis to examine insertions and deletions in the two species. We found a GATA-motif located in the promoter region of the ndhF gene of only M. bealei. K-mer frequency-based diversity analysis illustrated the close correlation between the GATA-motif and leaf phenotype. We found that the GATA-motif significantly inhibits GUS gene expression in tobacco during the dark-light transition (DLT). The expression of ndhF was downregulated in M. bealei and upregulated in M. fortunei during the DLT. NDH-F activity was remarkably decreased and exhibited a significant negative correlation with BIA levels in M. bealei during the DLT. Furthermore, the NADPH produced through photosynthetic metabolism was found to decrease in M. bealei during the DLT. Taken together, our results indicate that this GATA-motif might act as the functional site by which BIAs inhibit photosynthetic metabolism through downregulating ndhF expression during the DLT.
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Affiliation(s)
- Jiaqi Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Tianfu Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jiajun Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Linfang Deng
- The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310005, China
| | - Yiting Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Zhuoheng Zhong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Hongwei Fu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Bingxian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Lin Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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16
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Park TH. Complete chloroplast genome sequence of Solanum iopetalum, one of the tuber-bearing wild potato relatives. Mitochondrial DNA B Resour 2023; 8:347-351. [PMID: 36876142 PMCID: PMC9980020 DOI: 10.1080/23802359.2023.2183720] [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] [Indexed: 03/06/2023] Open
Abstract
Solanum iopetalum belongs to the Solanaceae family and is one of the tuber-bearing wild Solanum species. In this study, chloroplast genome sequencing of the species, completed with Illumina sequencing technology, is presented. The length of the chloroplast genome is 155,625 bp with a GC content of 37.86%. It comprises a large single copy (LSC) region of 86,057 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,593 bp. Additionally, 158 functional genes in the genome are identified, including 105 protein-coding genes, 8 ribosomal RNAs, and 45 transfer RNAs. Phylogenetic analysis revealed that S. iopetalum is grouped into a large clade with other Solanum species, including cultivated potatoes (S. tuberosum) and is closely related to Mexican Solanum species (S. stoloniferum, S. verrucosum, S. hougasii, S. hjertingii, and S. demissum). This study provides useful genomic information for future breeding and evolutionary studies of S. iopetalum and other Solanum species.
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Affiliation(s)
- Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
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17
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A novel broad spectrum venom metalloproteinase autoinhibitor in the rattlesnake Crotalus atrox evolved via a shift in paralog function. Proc Natl Acad Sci U S A 2022; 119:e2214880119. [PMID: 36508672 PMCID: PMC9907073 DOI: 10.1073/pnas.2214880119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The complexity of snake venom composition reflects adaptation to the diversity of prey and may be driven at times by a coevolutionary arms race between snakes and venom-resistant prey. However, many snakes are also resistant to their own venom due to serum-borne inhibitors of venom toxins, which raises the question of how snake autoinhibitors maintain their efficacy as venom proteins evolve. To investigate this potential three-way arms race among venom, prey, and autoinhibitors, we have identified and traced the evolutionary origin of serum inhibitors of snake venom metalloproteinases (SVMPs) in the Western Diamondback rattlesnake Crotalus atrox which possesses the largest known battery of SVMP genes among crotalids examined. We found that C. atrox expresses five members of a Fetuin A-related metalloproteinase inhibitor family but that one family member, FETUA-3, is the major SVMP inhibitor that binds to approximately 20 different C. atrox SVMPs and inhibits activities of all three SVMP classes. We show that the fetua-3 gene arose deep within crotalid evolution before the origin of New World species but, surprisingly, fetua-3 belongs to a different paralog group than previously identified SVMP inhibitors in Asian and South American crotalids. Conversely, the C. atrox FETUA-2 ortholog of previously characterized crotalid SVMP inhibitors shows limited activity against C. atrox SVMPs. These results reveal that there has been a functional evolutionary shift in the major SVMP inhibitor in the C. atrox lineage as the SVMP family expanded and diversified in the Crotalus lineage. This broad-spectrum inhibitor may be of potential therapeutic interest.
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18
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Hijazi H, Reis LM, Pehlivan D, Bernstein JA, Muriello M, Syverson E, Bonner D, Estiar MA, Gan-Or Z, Rouleau GA, Lyulcheva E, Greenhalgh L, Tessarech M, Colin E, Guichet A, Bonneau D, van Jaarsveld R, Lachmeijer A, Ruaud L, Levy J, Tabet AC, Ploski R, Rydzanicz M, Kępczyński Ł, Połatyńska K, Li Y, Fatih JM, Marafi D, Rosenfeld JA, Coban-Akdemir Z, Bi W, Gibbs RA, Hobson GM, Hunter JV, Carvalho CM, Posey JE, Semina EV, Lupski JR. TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 deletions. Am J Hum Genet 2022; 109:2270-2282. [PMID: 36368327 PMCID: PMC9748253 DOI: 10.1016/j.ajhg.2022.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022] Open
Abstract
An Xq22.2 region upstream of PLP1 has been proposed to underly a neurological disease trait when deleted in 46,XX females. Deletion mapping revealed that heterozygous deletions encompassing the smallest region of overlap (SRO) spanning six Xq22.2 genes (BEX3, RAB40A, TCEAL4, TCEAL3, TCEAL1, and MORF4L2) associate with an early-onset neurological disease trait (EONDT) consisting of hypotonia, intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. None of the genes within the SRO have been associated with monogenic disease in OMIM. Through local and international collaborations facilitated by GeneMatcher and Matchmaker Exchange, we have identified and herein report seven de novo variants involving TCEAL1 in seven unrelated families: three hemizygous truncating alleles; one hemizygous missense allele; one heterozygous TCEAL1 full gene deletion; one heterozygous contiguous deletion of TCEAL1, TCEAL3, and TCEAL4; and one heterozygous frameshift variant allele. Variants were identified through exome or genome sequencing with trio analysis or through chromosomal microarray. Comparison with previously reported Xq22 deletions encompassing TCEAL1 identified a more-defined syndrome consisting of hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features include strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies. An additional maternally inherited hemizygous missense allele of uncertain significance was identified in a male with hypertonia and spasticity without syndromic features. These data provide evidence that TCEAL1 loss of function causes a neurological rare disease trait involving significant neurological impairment with features overlapping the EONDT phenotype in females with the Xq22 deletion.
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Affiliation(s)
- Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linda M. Reis
- Department of Pediatrics and Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Jonathan A. Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Michael Muriello
- Department of Pediatrics and Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI, USA
| | - Erin Syverson
- Department of Pediatrics and Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI, USA
| | - Devon Bonner
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Mehrdad A. Estiar
- Department of Human Genetics, McGill University, Montreal, QC, Canada,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montreal, QC, Canada,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada,Department of Neurology & Neurosurgery, McGill University, Montreal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montreal, QC, Canada,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada,Department of Neurology & Neurosurgery, McGill University, Montreal, QC, Canada
| | - Ekaterina Lyulcheva
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | - Lynn Greenhalgh
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | - Marine Tessarech
- Department of Medical Genetics, Angers University Hospital, Angers, France,Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Estelle Colin
- Department of Medical Genetics, Angers University Hospital, Angers, France,Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Agnès Guichet
- Department of Medical Genetics, Angers University Hospital, Angers, France,Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Dominique Bonneau
- Department of Medical Genetics, Angers University Hospital, Angers, France,Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - R.H. van Jaarsveld
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - A.M.A. Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lyse Ruaud
- INSERM UMR1141, Neurodiderot, University of Paris, 75019 Paris, France,APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Jonathan Levy
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Anne-Claude Tabet
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Łukasz Kępczyński
- Department of Genetics, Polish Mother’s Memorial Hospital – Research Institute, Łódź, Poland
| | - Katarzyna Połatyńska
- Department of Developmental Neurology an Epileptology, Polish Mother’s Memorial Hospital – Research Institute, Łódź, Poland
| | - Yidan Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Baylor Genetics, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Baylor Genetics, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Grace M. Hobson
- Department of Research, Nemours Children’s Health, Wilmington, DE, USA
| | - Jill V. Hunter
- E.B. Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, TX, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elena V. Semina
- Department of Pediatrics and Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI, USA,Departments of Ophthalmology and Visual Sciences and Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA,Corresponding author
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA,Texas Children’s Hospital, Houston, TX, USA,Corresponding author
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19
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Bajic M, Ravishankar S, Sheth M, Rowe LA, Pacheco MA, Patel DS, Batra D, Loparev V, Olsen C, Escalante AA, Vannberg F, Udhayakumar V, Barnwell JW, Talundzic E. The first complete genome of the simian malaria parasite Plasmodium brasilianum. Sci Rep 2022; 12:19802. [PMID: 36396703 PMCID: PMC9671904 DOI: 10.1038/s41598-022-20706-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022] Open
Abstract
Naturally occurring human infections by zoonotic Plasmodium species have been documented for P. knowlesi, P. cynomolgi, P. simium, P. simiovale, P. inui, P. inui-like, P. coatneyi, and P. brasilianum. Accurate detection of each species is complicated by their morphological similarities with other Plasmodium species. PCR-based assays offer a solution but require prior knowledge of adequate genomic targets that can distinguish the species. While whole genomes have been published for P. knowlesi, P. cynomolgi, P. simium, and P. inui, no complete genome for P. brasilianum has been available. Previously, we reported a draft genome for P. brasilianum, and here we report the completed genome for P. brasilianum. The genome is 31.4 Mb in size and comprises 14 chromosomes, the mitochondrial genome, the apicoplast genome, and 29 unplaced contigs. The chromosomes consist of 98.4% nucleotide sites that are identical to the P. malariae genome, the closest evolutionarily related species hypothesized to be the same species as P. brasilianum, with 41,125 non-synonymous SNPs (0.0722% of genome) identified between the two genomes. Furthermore, P. brasilianum had 4864 (82.1%) genes that share 80% or higher sequence similarity with 4970 (75.5%) P. malariae genes. This was demonstrated by the nearly identical genomic organization and multiple sequence alignments for the merozoite surface proteins msp3 and msp7. We observed a distinction in the repeat lengths of the circumsporozoite protein (CSP) gene sequences between P. brasilianum and P. malariae. Our results demonstrate a 97.3% pairwise identity between the P. brasilianum and the P. malariae genomes. These findings highlight the phylogenetic proximity of these two species, suggesting that P. malariae and P. brasilianum are strains of the same species, but this could not be fully evaluated with only a single genomic sequence for each species.
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Affiliation(s)
- Marko Bajic
- grid.422961.a0000 0001 0029 6188Association of Public Health Laboratories, Silver Spring, MD USA ,grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | | | - Mili Sheth
- grid.416738.f0000 0001 2163 0069Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Lori A. Rowe
- grid.416738.f0000 0001 2163 0069Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA USA ,grid.265219.b0000 0001 2217 8588Virus Characterization Isolation Production and Sequencing Core, Tulane National Primate Research Center, Covington, LA USA
| | - M. Andreina Pacheco
- grid.264727.20000 0001 2248 3398Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA USA
| | - Dhruviben S. Patel
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Dhwani Batra
- grid.416738.f0000 0001 2163 0069Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Vladimir Loparev
- grid.416738.f0000 0001 2163 0069Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Christian Olsen
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Ananias A. Escalante
- grid.264727.20000 0001 2248 3398Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA USA
| | - Fredrik Vannberg
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics at Georgia Tech, Georgia Institute of Technology, Atlanta, GA USA
| | - Venkatachalam Udhayakumar
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - John W. Barnwell
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Eldin Talundzic
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
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20
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Haddock J, Domyan ET. A DNA Replication Mechanism Can Explain Structural Variation at the Pigeon Recessive Red Locus. Biomolecules 2022; 12:1509. [PMID: 36291717 PMCID: PMC9599118 DOI: 10.3390/biom12101509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 08/08/2023] Open
Abstract
For species to adapt to their environment, evolution must act upon genetic variation that is present in the population. Elucidating the molecular mechanisms that give rise to this variation is thus of crucial importance for understanding how organisms evolve. In addition to variation caused by point mutations, structural variation (deletions, duplications, inversions, translocations) is also an important source of variety. Mechanisms involving recombination, transposition and retrotransposition, and replication have been proposed for generating structural variation, and each are capable of explaining certain rearrangements. In this study, we conduct a detailed analysis of two partially overlapping rearrangements (e1 and e2 allele) in domestic rock pigeon (Columba livia) which are both associated with the recessive red phenotype. We find that a replicative mechanism is best able to explain the complex architecture of the e1 allele, and is also compatible with the simpler architecture of the e2 allele as well.
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Affiliation(s)
| | - Eric T. Domyan
- Department of Biology, Utah Valley University, Orem, UT 84058, USA
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21
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Park YS, Kang JS, Park JY, Shim H, Yang HO, Kang JH, Yang TJ. Analysis of the complete plastomes and nuclear ribosomal DNAs from Euonymus hamiltonianus and its relatives sheds light on their diversity and evolution. PLoS One 2022; 17:e0275590. [PMID: 36197898 PMCID: PMC9534445 DOI: 10.1371/journal.pone.0275590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Euonymus hamiltonianus and its relatives (Celastraceae family) are used for ornamental and medicinal purposes. However, species identification in Euonymus is difficult due to their morphological diversity. Using plastid genome (plastome) data, we attempt to reveal phylogenetic relationship among Euonymus species and develop useful markers for molecular identification. We assembled the plastome and nuclear ribosomal DNA (nrDNA) sequences from five Euonymus lines collected from South Korea: three Euonymus hamiltonianus accessions, E. europaeus, and E. japonicus. We conducted an in-depth comparative analysis using ten plastomes, including other publicly available plastome data for this genus. The genome structures, gene contents, and gene orders were similar in all Euonymus plastomes in this study. Analysis of nucleotide diversity revealed six divergence hotspots in their plastomes. We identified 339 single nucleotide polymorphisms and 293 insertion or deletions among the four E. hamiltonianus plastomes, pointing to abundant diversity even within the same species. Among 77 commonly shared genes, 9 and 33 were identified as conserved genes in the genus Euonymus and E. hamiltonianus, respectively. Phylogenetic analysis based on plastome and nrDNA sequences revealed the overall consensus and relationships between plastomes and nrDNAs. Finally, we developed six barcoding markers and successfully applied them to 31 E. hamiltonianus lines collected from South Korea. Our findings provide the molecular basis for the classification and molecular taxonomic criteria for the genus Euonymus (at least in Korea), which should aid in more objective classification within this genus. Moreover, the newly developed markers will be useful for understanding the species delimitation of E. hamiltonianus and closely related species.
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Affiliation(s)
- Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Hyun Ok Yang
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Korea
| | | | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
- * E-mail:
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22
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Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biol 2022; 23:182. [PMID: 36038949 PMCID: PMC9421119 DOI: 10.1186/s13059-022-02735-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/21/2022] [Indexed: 01/22/2023] Open
Abstract
With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. By identifying nucleotides across genomes which share a common ancestor, multiple genome alignments commonly serve as the bedrock for comparative genomics studies. In this review, we provide an overview of the algorithmic template that most multiple genome alignment methods follow. We also discuss prospective areas of improvement of multiple genome alignment for keeping up with continuously arriving high-quality T2T assembled genomes and for unlocking clinically-relevant insights.
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Affiliation(s)
- Bryce Kille
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Advait Balaji
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael Nute
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA.
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23
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Milián-García Y, Hempel CA, Janke LAA, Young RG, Furukawa-Stoffer T, Ambagala A, Steinke D, Hanner RH. Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae). BMC Genomics 2022; 23:584. [PMID: 35962326 PMCID: PMC9375341 DOI: 10.1186/s12864-022-08743-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial genomes are the most sequenced genomes after bacterial and fungal genomic DNA. However, little information on mitogenomes is available for multiple metazoan taxa, such as Culicoides, a globally distributed, megadiverse genus containing 1,347 species. AIM Generating novel mitogenomic information from single Culicoides sonorensis and C. biguttatus specimens, comparing available mitogenome mapping and de novo assembly tools, and identifying the best performing strategy and tools for Culicoides species. RESULTS We present two novel and fully annotated mitochondrial haplotypes for two Culicoides species, C. sonorensis and C. biguttatus. We also annotated or re-annotated the only available reference mitogenome for C. sonorensis and C. arakawae. All species present a high similarity in mitogenome organization. The general gene arrangement for all Culicoides species was identical to the ancestral insect mitochondrial genome. Only short spacers were found in C. sonorensis (up to 30 bp), contrary to C. biguttatus (up to 114 bp). The mitochondrial genes ATP8, NAD2, NAD6, and LSU rRNA exhibited the highest nucleotide diversity and pairwise interspecific p genetic distance, suggesting that these genes might be suitable and complementary molecular barcodes for Culicoides identification in addition to the commonly utilized COI gene. We observed performance differences between the compared mitogenome generation strategies. The mapping strategy outperformed the de novo assembly strategy, but mapping results were partially biased in the absence of species-specific reference mitogenome. Among the utilized tools, BWA performed best for C. sonorensis while SPAdes, MEGAHIT, and MitoZ were among the best for C. biguttatus. The best-performing mitogenome annotator was MITOS2. Additionally, we were able to recover exogenous mitochondrial DNA from Bos taurus (biting midges host) from a C. biguttatus blood meal sample. CONCLUSIONS Two novel annotated mitogenome haplotypes for C. sonorensis and C. biguttatus using High-Throughput Sequencing are presented. Current results are useful as the baseline for mitogenome reconstruction of the remaining Culicoides species from single specimens to HTS and genome annotation. Mapping to a species-specific reference mitogenome generated better results for Culicoides mitochondrial genome reconstruction than de novo assembly, while de novo assembly resulted better in the absence of a closely related reference mitogenome. These results have direct implications for molecular-based identification of these vectors of human and zoonotic diseases, setting the basis for using the whole mitochondrial genome as a marker in Culicoides identification.
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Affiliation(s)
- Yoamel Milián-García
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Christopher A Hempel
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Lauren A A Janke
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.,John H. Daniels Faculty of Architecture, Landscape, and Design, University of Toronto, 33 Willcocks Street, Toronto, ON, M5S 3B3, Canada
| | - Robert G Young
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Tara Furukawa-Stoffer
- Canadian Food Inspection Agency, National Centre for Animal Disease, 225090 Township Road 9-1, Lethbridge LaboratoryLethbridge, AB, T1J 0P3, Canada
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, 1015, Arlington Street, Winnipeg, MB, R3E 3M4, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
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24
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An accurate alignment-free protein sequence comparator based on physicochemical properties of amino acids. Sci Rep 2022; 12:11158. [PMID: 35778592 PMCID: PMC9247937 DOI: 10.1038/s41598-022-15266-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/21/2022] [Indexed: 11/08/2022] Open
Abstract
Bio-sequence comparators are one of the most basic and significant methods for assessing biological data, and so, due to the importance of proteins, protein sequence comparators are particularly crucial. On the other hand, the complexity of the problem, the growing number of extracted protein sequences, and the growth of studies and data analysis applications addressing protein sequences have necessitated the development of a rapid and accurate approach to account for the complexities in this field. As a result, we propose a protein sequence comparison approach, called PCV, which improves comparison accuracy by producing vectors that encode sequence data as well as physicochemical properties of the amino acids. At the same time, by partitioning the long protein sequences into fix-length blocks and providing encoding vector for each block, this method allows for parallel and fast implementation. To evaluate the performance of PCV, like other alignment-free methods, we used 12 benchmark datasets including classes with homologous sequences which may require a simple preprocessing search tool to select the homologous data. And then, we compared the protein sequence comparison outcomes to those of alternative alignment-based and alignment-free methods, using various evaluation criteria. These results indicate that our method provides significant improvement in sequence classification accuracy, compared to the alternative alignment-free methods and has an average correlation of about 94% with the ClustalW method as our reference method, while considerably reduces the processing time.
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25
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Neumann B, Lippmann N, Wendt S, Karlas T, Lübbert C, Werner G, Pfeifer Y, Schuster CF. Recurrent bacteremia with a hypermucoviscous Escherichia coli isolated from a patient with perihilar cholangiocarcinoma: insights from a comprehensive genome-based analysis. Ann Clin Microbiol Antimicrob 2022; 21:28. [PMID: 35751078 PMCID: PMC9233328 DOI: 10.1186/s12941-022-00521-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 02/07/2023] Open
Abstract
Background Escherichia coli (E. coli) is a common human pathogen, responsible for a broad spectrum of infections. Sites of infection can vary, but the hepato-biliary system is of particular concern due to the infection-associated formation of gallstones and the spread of pathogens from the bile ducts into the bloodstream. Case presentation The presented case is striking, as the detected isolate showed a positive string test. This hypermucoviscous phenotype is atypical for E. coli and a particular feature of hypervirulent Klebsiella pneumoniae (K. pneumoniae) variants. Objectives To provide new insights into the genomic background of an E. coli strain with an unusual hypermucoviscous phenotype using hybrid short- and long-read sequencing approaches. Results Complete hybrid assemblies of the E. coli genome and plasmids were done and used for genome based typing. Isolate 537–20 was assigned to the multilocus sequence type ST88 and serotype O8:H4. The strain showed a close relationship to avian pathogenic strains. Analysis of the chromosome and plasmids revealed the presence of several virulence factors, such as the Conserved Virulence Plasmidic (CVP) region on plasmid 537-20_1, including several iron acquisition genes (sitABCD, iroABCDEN, iucABCD, hbd) and the iutA gene encoding the receptor of the siderophore aerobactin. The hypermucoviscous phenotype could be caused by encapsulation of putative K. pneumoniae origin. Conclusions Hybrid sequencing enabled detailed genomic characterization of the hypermucoviscous E. coli strain, revealing virulence factors that have their putative origin in K. pneumoniae. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-022-00521-7.
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Affiliation(s)
- Bernd Neumann
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany. .,Institute for Hospital Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg General Hospital, 90419, Nuremberg, Germany.
| | - Norman Lippmann
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Sebastian Wendt
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany.,Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Thomas Karlas
- Division of Gastroenterology, Department of Medicine II, Leipzig University Medical Center, 04103, Leipzig, Germany
| | - Christoph Lübbert
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany.,Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Guido Werner
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany
| | - Yvonne Pfeifer
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany
| | - Christopher F Schuster
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany. .,Current Address: Center for Pandemic Vaccines and Therapeutics (ZEPAI), Paul-Ehrlich-Institute, 63225, Langen, Germany.
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26
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Ebel M, Migliorelli G, Stanke M. Global, highly specific and fast filtering of alignment seeds. BMC Bioinformatics 2022; 23:225. [PMID: 35689182 PMCID: PMC9188137 DOI: 10.1186/s12859-022-04745-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background An important initial phase of arguably most homology search and alignment methods such as required for genome alignments is seed finding. The seed finding step is crucial to curb the runtime as potential alignments are restricted to and anchored at the sequence position pairs that constitute the seed. To identify seeds, it is good practice to use sets of spaced seed patterns, a method that locally compares two sequences and requires exact matches at certain positions only. Results We introduce a new method for filtering alignment seeds that we call geometric hashing. Geometric hashing achieves a high specificity by combining non-local information from different seeds using a simple hash function that only requires a constant and small amount of additional time per spaced seed. Geometric hashing was tested on the task of finding homologous positions in the coding regions of human and mouse genome sequences. Thereby, the number of false positives was decreased about million-fold over sets of spaced seeds while maintaining a very high sensitivity. Conclusions An additional geometric hashing filtering phase could improve the run-time, accuracy or both of programs for various homology-search-and-align tasks. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04745-4.
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Affiliation(s)
- Matthis Ebel
- Institute for Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489, Greifswald, Germany.,Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Giovanna Migliorelli
- Institute for Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489, Greifswald, Germany.,Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Mario Stanke
- Institute for Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489, Greifswald, Germany. .,Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany.
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27
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Identification of Two Diamondback Moth Parasitoids, Diadegma fenestrale and Diadegma semiclausum, Using LAMP for Application in Biological Control. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The diamondback moth, Plutella xylostella L., is a lepidopteran pest that damages various vegetable plants belonging to the genus Brassica worldwide. Various biological controls, such as parasitoid wasps, have been used to control this pest. Among these, Diadegma semiclausum and Diadegmafenestrale are widely used globally. In field-based biological control research, the investigation of the population dynamics of parasitoids and the rate of parasitism within the pest population is very important. However, achieving profundity in research is difficult when morphologically similar species coexist in the field. The morphological characteristics of D. semiclausum and D. fenestrale are very similar, and they both parasitize P. xylostella larvae. Therefore, to accurately identify these species, in this study, we developed a molecular diagnostic method by using loop-mediated isothermal amplification (LAMP). The mitochondrial genome of D. fenestrale and partial nucleotide sequences, including the ITS region of D. semiclausum, were analyzed for use as species diagnosis markers. The results showed that the homology of D. fenestrale to D. semiclausum was 94%, due to the excessively low homology of the D loop, but the actual homology was higher than 94%, particularly in the coding region. D. fenestrale species-specific primers for LAMP were designed based on the region encoding COX3, and the optimal diagnostic reaction condition for the four primers (F3, B3, FIP, and BIP) was 63 °C for 35 min. A species-specific primer capable of classifying D. semiclausum was developed based on the ITS2 region, and the optimal reaction condition for diagnosis was 63 °C for 40 min. Under optimal conditions for both species, upon addition of the loop primer LB, the reaction efficiency increased, and the reaction time was shortened by more than 5 min. The diagnostic limit concentration was up to 10 pg under both optimal conditions; therefore, it was possible to detect even very low concentrations. For both species, diagnosis was possible by using LAMP assay with a DNA-releasing technique, without a DNA extraction process, and by incubating a tissue sample or the homogenized whole body at 95 °C for 5 min. In the case of D. fenestrale, it was possible to diagnose the parasitoid in P. xylostella larvae. Therefore, the developed LAMP diagnostic method can be used in a variety of ways to determine whether P. xylostella has been parasitized in the process of field research and mass breeding, and to accurately distinguish the species that are parasitic to P. xylostella larvae. This LAMP-based diagnostic method can be applied to identify various parasitoids that are used for the biological control of P. xylostella.
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28
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Park TH. Complete chloroplast genome sequence of Solanum hjertingii, one of the wild potato relatives. Mitochondrial DNA B Resour 2022; 7:715-717. [PMID: 35493716 PMCID: PMC9045759 DOI: 10.1080/23802359.2022.2068983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Solanum hjertingii is a wild tuber-bearing species classified in the Solanaceae family. The chloroplast genome of S. hjertingii was completed via de novo assembly using Illumina paired-end sequencing data. Total length of the chloroplast genome of S. hjertingii is 155,545 bp consisting of 85,976 bp in a large single copy, 18,383 bp in a small single copy, and 25,593 bp in a pair of inverted repeat regions. Its structure is circular and typically quadripartite. It contains 158 predicted genes in total, including 105 protein-coding, 45 tRNA, and eight rRNA genes. Maximum likelihood phylogenetic analysis of the sequence along with 33 species in the Solanaceae family revealed that S. hjertingii belongs to a large clade with other Solanum species including S. tuberosum and is most closely grouped in the clade with S. hougasii and S. stoloniferum in the clade.
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Affiliation(s)
- Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
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29
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Ha D, Kim D, Kim I, Oh Y, Kong J, Han S, Kim S. OUP accepted manuscript. Nucleic Acids Res 2022; 50:1849-1863. [PMID: 35137181 PMCID: PMC8887464 DOI: 10.1093/nar/gkac050] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Mouse models have been engineered to reveal the biological mechanisms of human diseases based on an assumption. The assumption is that orthologous genes underlie conserved phenotypes across species. However, genetically modified mouse orthologs of human genes do not often recapitulate human disease phenotypes which might be due to the molecular evolution of phenotypic differences across species from the time of the last common ancestor. Here, we systematically investigated the evolutionary divergence of regulatory relationships between transcription factors (TFs) and target genes in functional modules, and found that the rewiring of gene regulatory networks (GRNs) contributes to the phenotypic discrepancies that occur between humans and mice. We confirmed that the rewired regulatory networks of orthologous genes contain a higher proportion of species-specific regulatory elements. Additionally, we verified that the divergence of target gene expression levels, which was triggered by network rewiring, could lead to phenotypic differences. Taken together, a careful consideration of evolutionary divergence in regulatory networks could be a novel strategy to understand the failure or success of mouse models to mimic human diseases. To help interpret mouse phenotypes in human disease studies, we provide quantitative comparisons of gene expression profiles on our website (http://sbi.postech.ac.kr/w/RN).
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Affiliation(s)
- Doyeon Ha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | | | - Youngchul Oh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - JungHo Kong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Seong Kyu Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Sanguk Kim
- To whom correspondence should be addressed. Tel: +82 54 279 2348; Fax: +82 54 279 2199;
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30
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The long noncoding RNA H19 regulates tumor plasticity in neuroendocrine prostate cancer. Nat Commun 2021; 12:7349. [PMID: 34934057 PMCID: PMC8692330 DOI: 10.1038/s41467-021-26901-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
Neuroendocrine (NE) prostate cancer (NEPC) is a lethal subtype of castration-resistant prostate cancer (PCa) arising either de novo or from transdifferentiated prostate adenocarcinoma following androgen deprivation therapy (ADT). Extensive computational analysis has identified a high degree of association between the long noncoding RNA (lncRNA) H19 and NEPC, with the longest isoform highly expressed in NEPC. H19 regulates PCa lineage plasticity by driving a bidirectional cell identity of NE phenotype (H19 overexpression) or luminal phenotype (H19 knockdown). It contributes to treatment resistance, with the knockdown of H19 re-sensitizing PCa to ADT. It is also essential for the proliferation and invasion of NEPC. H19 levels are negatively regulated by androgen signaling via androgen receptor (AR). When androgen is absent SOX2 levels increase, driving H19 transcription and facilitating transdifferentiation. H19 facilitates the PRC2 complex in regulating methylation changes at H3K27me3/H3K4me3 histone sites of AR-driven and NEPC-related genes. Additionally, this lncRNA induces alterations in genome-wide DNA methylation on CpG sites, further regulating genes associated with the NEPC phenotype. Our clinical data identify H19 as a candidate diagnostic marker and predictive marker of NEPC with elevated H19 levels associated with an increased probability of biochemical recurrence and metastatic disease in patients receiving ADT. Here we report H19 as an early upstream regulator of cell fate, plasticity, and treatment resistance in NEPC that can reverse/transform cells to a treatable form of PCa once therapeutically deactivated. Elevated expression of long noncoding RNA H19 is seen in clinical samples of neuroendocrine prostate cancer (PCa). Here the authors show H19 promotes plasticity from luminal to neuroendocrine by epigenetic reprogramming.
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31
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G Ribeiro P, Torres Jiménez MF, Andermann T, Antonelli A, Bacon CD, Matos-Maraví P. A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics. Mol Ecol 2021; 30:6021-6035. [PMID: 34674330 PMCID: PMC9298010 DOI: 10.1111/mec.16240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 09/24/2021] [Accepted: 10/16/2021] [Indexed: 11/28/2022]
Abstract
The increasing availability of short‐read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extraction strategies and implement them into secapr, a pipeline that processes short‐read data into multilocus alignments for phylogenetics and molecular ecology analyses. We integrate the processing of data from low‐coverage WGS (<30×) and target sequence capture into a flexible framework, while optimizing de novo contig assembly and loci extraction. Specifically, we test different assembly strategies by contrasting their ability to recover loci from targeted butterfly protein‐coding genes, using four data sets: a WGS data set across different average coverages (10×, 5× and 2×) and a data set for which these loci were enriched prior to sequencing via target sequence capture. Using the resulting de novo contigs, we account for potential errors within contigs and infer phylogenetic trees to evaluate the ability of each assembly strategy to recover species relationships. We demonstrate that choosing multiple sizes of kmer simultaneously for assembly results in the highest yield of extracted loci from de novo assembled contigs, while data sets derived from sequencing read depths as low as 5× recovers the expected species relationships in phylogenetic trees. By making the tested assembly approaches available in the secapr pipeline, we hope to inspire future studies to incorporate complementary data and make an informed choice on the optimal assembly strategy.
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Affiliation(s)
- Pedro G Ribeiro
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - María Fernanda Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.,Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.,Royal Botanical Gardens Kew, Richmond, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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32
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Development of a LAMP-Based Molecular Species Diagnosis Method for Four Major Agricultural Pests in the Genus Spodoptera (Lepidoptera: Noctuidae). INSECTS 2021; 12:insects12100883. [PMID: 34680652 PMCID: PMC8541213 DOI: 10.3390/insects12100883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Four major Spodoptera pests, S. exigua, S. frugiperda, S. litura, and S. littoralis, are widely distributed polyphagous pests affecting various crops. Despite different distribution areas, these four species cause serious damage to agriculture worldwide. As these species are morphologically similar at the larval stage, diagnostic methods have been developed and utilized for their identification. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for rapid and effective species diagnosis, along with PCR, to identify Korean field-collected or overseas samples. The optimal conditions for the LAMP assay were 61 °C for 60 min with four LAMP primers. Additional loop primers increased the amplification efficiency in S. exigua, whereas increased non-specific amplification was found in other species. A broad range of DNA concentrations was observed in the LAMP assay, and the minimum detectable DNA concentration was 1 pg. The DNA release method for LAMP involved incubation of larval or adult tissue samples for 5 min at 95 °C, without a DNA extraction step. Considering the gradual diversification invasive pest incidence, this simple and accurate LAMP assay can be used for intensive field monitoring of invasive pests and integrated management of these species. Abstract Molecular-based species identification tools are helpful to identify tiny insect and lepidopteran pests that show morphological similarities in the larval stage and are essential for quarantine as well as agricultural research. Here, we focused on four major Spodoptera pests: S. exigua, S. frugiperda, S. litura, and S. littoralis. S. exigua and S. litura mitochondrial genome sequences were newly identified and species-specific sequence regions were identified in the cytochrome c oxidase subunit II and III regions. Species primers were designed and applied in loop-mediated isothermal amplification (LAMP) and PCR to identify Korean field-collected or overseas samples. The optimal incubation conditions for LAMP were 61 °C for 60 min with four LAMP primers. Additional loop primers increased the amplification efficiency for S. exigua, and the nonspecific amplification for other species. The LAMP assay could detect a wide range of DNA concentrations, with the range 1 ng–1 pg in dependence of four LAMP primers. The DNA-releasing technique, without DNA extraction, in the LAMP assay involved larval or adult tissue sample incubation at 95 °C for 5 min. The entire process takes approximately 70 min. This new molecular diagnostic method is simple and accurate, with application in the field and laboratory and for monitoring and ecological studies.
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33
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Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal PI, Yang HT, Xue V, Knyazev S, Singer BD, Balliu B, Koslicki D, Skums P, Zelikovsky A, Alkan C, Mutlu O, Mangul S. Technology dictates algorithms: recent developments in read alignment. Genome Biol 2021; 22:249. [PMID: 34446078 PMCID: PMC8390189 DOI: 10.1186/s13059-021-02443-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today's diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.
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Affiliation(s)
- Mohammed Alser
- Computer Science Department, ETH Zürich, 8092, Zürich, Switzerland
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Information Technology and Electrical Engineering Department, ETH Zürich, Zürich, 8092, Switzerland
| | - Jeremy Rotman
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Dhrithi Deshpande
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Kodi Taraszka
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Huwenbo Shi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pelin Icer Baykal
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Harry Taegyun Yang
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Ph.D. Program, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Victor Xue
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sergey Knyazev
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Brunilda Balliu
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - David Koslicki
- Computer Science and Engineering, Pennsylvania State University, University Park, PA, 16801, USA
- Biology Department, Pennsylvania State University, University Park, PA, 16801, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16801, USA
| | - Pavel Skums
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
- The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Can Alkan
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Bilkent-Hacettepe Health Sciences and Technologies Program, Ankara, Turkey
| | - Onur Mutlu
- Computer Science Department, ETH Zürich, 8092, Zürich, Switzerland
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Information Technology and Electrical Engineering Department, ETH Zürich, Zürich, 8092, Switzerland
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA.
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34
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Dong C, Simonett SP, Shin S, Stapleton DS, Schueler KL, Churchill GA, Lu L, Liu X, Jin F, Li Y, Attie AD, Keller MP, Keleş S. INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants. Genome Biol 2021; 22:241. [PMID: 34425882 PMCID: PMC8381555 DOI: 10.1186/s13059-021-02450-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 08/02/2021] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies reveal many non-coding variants associated with complex traits. However, model organism studies largely remain as an untapped resource for unveiling the effector genes of non-coding variants. We develop INFIMA, Integrative Fine-Mapping, to pinpoint causal SNPs for diversity outbred (DO) mice eQTL by integrating founder mice multi-omics data including ATAC-seq, RNA-seq, footprinting, and in silico mutation analysis. We demonstrate INFIMA's superior performance compared to alternatives with human and mouse chromatin conformation capture datasets. We apply INFIMA to identify novel effector genes for GWAS variants associated with diabetes. The results of the application are available at http://www.statlab.wisc.edu/shiny/INFIMA/ .
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Affiliation(s)
- Chenyang Dong
- Department of Statistics, University of Wisconsin-Madison, Madison, WI USA
| | - Shane P. Simonett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Sunyoung Shin
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX USA
| | - Donnie S. Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Kathryn L. Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | | | - Leina Lu
- Case Western University, Cleveland, OH USA
| | | | - Fulai Jin
- Case Western University, Cleveland, OH USA
| | - Yan Li
- Case Western University, Cleveland, OH USA
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI USA
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35
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Pseudogenes: Four Decades of Discovery. Methods Mol Biol 2021. [PMID: 34165705 DOI: 10.1007/978-1-0716-1503-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
A pseudogene is defined as a genomic DNA sequence that looks like a mutated or truncated version of a known functional gene. Nearly four decades since their first discovery it has been estimated that between ~12,000 and ~20,000 pseudogenes exist in the human genome. Early efforts to characterize functions for pseudogenes were unsuccessful, thus they were considered functionless relics of evolutionary selection, junk DNA or genetic fossils. Remarkably, an increasing number of pseudogenes have been reported to be expressed as RNA transcripts above and beyond levels considered accidental or spurious transcription. There is emerging evidence that some expressed pseudogene transcripts have biological functions and should be defined as a subclass of functional long noncoding RNAs (lncRNA). In this introductory chapter, I briefly summarize the history and the current knowledge of pseudogenes, and highlight the emerging functions of some pseudogenes in human biology and disease. This second iteration of Pseudogenes in Methods in Molecular Biology highlights new methodological approaches to investigate this intriguing family of lncRNAs and the extent of their biological function.
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36
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Ramanathan N, Ramamurthy J, Natarajan G. Numerical Characterization of DNA Sequences for Alignment-free Sequence Comparison - A Review. Comb Chem High Throughput Screen 2021; 25:365-380. [PMID: 34382516 DOI: 10.2174/1386207324666210811101437] [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: 12/30/2020] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Biological macromolecules namely, DNA, RNA, and protein have their building blocks organized in a particular sequence and the sequential arrangement encodes evolutionary history of the organism (species). Hence, biological sequences have been used for studying evolutionary relationships among the species. This is usually carried out by multiple sequence algorithms (MSA). Due to certain limitations of MSA, alignment-free sequence comparison methods were developed. The present review is on alignment-free sequence comparison methods carried out using numerical characterization of DNA sequences. <P> Discussion: The graphical representation of DNA sequences by chaos game representation and other 2-dimesnional and 3-dimensional methods are discussed. The evolution of numerical characterization from the various graphical representations and the application of the DNA invariants thus computed in phylogenetic analysis is presented. The extension of computing molecular descriptors in chemometrics to the calculation of new set of DNA invariants and their use in alignment-free sequence comparison in a N-dimensional space and construction of phylogenetic tress is also reviewed. <P> Conclusion: The phylogenetic tress constructed by the alignment-free sequence comparison methods using DNA invariants were found to be better than those constructed using alignment-based tools such as PHLYIP and ClustalW. One of the graphical representation methods is now extended to study viral sequences of infectious diseases for the identification of conserved regions to design peptide-based vaccine by combining numerical characterization and graphical representation.
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Affiliation(s)
- Natarajan Ramanathan
- Department of Chemistry, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu. India
| | - Jayalakshmi Ramamurthy
- Department of Computer Science, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu. India
| | - Ganapathy Natarajan
- Department of Mechanical Engineering and Industrial Engineering, University of Wisconsin, Platteville, WI 53818. United States
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37
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Complete Closed Genome Sequence of the Extremely Heat-Resistant Strain Escherichia coli AW1.7. Microbiol Resour Announc 2021; 10:e0050221. [PMID: 34292065 PMCID: PMC8297447 DOI: 10.1128/mra.00502-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli isolate AW1.7 is an extremely heat-resistant bacterium and has been widely used as a reference strain in extreme heat resistance studies for almost a decade. Here, we report its complete closed genome sequence.
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38
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Wang X, Kokabee L, Kokabee M, Conklin DS. Bruton's Tyrosine Kinase and Its Isoforms in Cancer. Front Cell Dev Biol 2021; 9:668996. [PMID: 34307353 PMCID: PMC8297165 DOI: 10.3389/fcell.2021.668996] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
Bruton’s tyrosine kinase (BTK) is a soluble tyrosine kinase with central roles in the development, maturation, and signaling of B cells. BTK has been found to regulate cell proliferation, survival, and migration in various B-cell malignancies. Targeting BTK with recently developed BTK inhibitors has been approved by the Food and Drug Administration (FDA) for the treatment of several hematological malignancies and has transformed the treatment of several B-cell malignancies. The roles that BTK plays in B cells have been appreciated for some time. Recent studies have established that BTK is expressed and plays pro-tumorigenic roles in several epithelial cancers. In this review, we focus on novel isoforms of the BTK protein expressed in epithelial cancers. We review recent work on the expression, function, and signaling of these isoforms and their value as potential therapeutic targets in epithelial tumors.
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Affiliation(s)
- Xianhui Wang
- Department of Biomedical Sciences, Cancer Research Center, State University of New York, Rensselaer, NY, United States
| | - Leila Kokabee
- Department of Biomedical Sciences, Cancer Research Center, State University of New York, Rensselaer, NY, United States
| | - Mostafa Kokabee
- Department of Biomedical Sciences, Cancer Research Center, State University of New York, Rensselaer, NY, United States
| | - Douglas S Conklin
- Department of Biomedical Sciences, Cancer Research Center, State University of New York, Rensselaer, NY, United States
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39
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Wang R, Yang Y, Jing Y, Segar ST, Zhang Y, Wang G, Chen J, Liu QF, Chen S, Chen Y, Cruaud A, Ding YY, Dunn DW, Gao Q, Gilmartin PM, Jiang K, Kjellberg F, Li HQ, Li YY, Liu JQ, Liu M, Machado CA, Ming R, Rasplus JY, Tong X, Wen P, Yang HM, Yang JJ, Yin Y, Zhang XT, Zhang YY, Yu H, Yue Z, Compton SG, Chen XY. Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association. Nat Ecol Evol 2021; 5:974-986. [PMID: 34002050 DOI: 10.1038/s41559-021-01469-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Many insects metamorphose from antagonistic larvae into mutualistic adult pollinators, with reciprocal adaptation leading to specialized insect-plant associations. It remains unknown how such interactions are established at molecular level. Here we assemble high-quality genomes of a fig species, Ficus pumila var. pumila, and its specific pollinating wasp, Wiebesia pumilae. We combine multi-omics with validation experiments to reveal molecular mechanisms underlying this specialized interaction. In the plant, we identify the specific compound attracting pollinators and validate the function of several key genes regulating its biosynthesis. In the pollinator, we find a highly reduced number of odorant-binding protein genes and an odorant-binding protein mainly binding the attractant. During antagonistic interaction, we find similar chemical profiles and turnovers throughout the development of galled ovules and seeds, and a significant contraction of detoxification-related gene families in the pollinator. Our study identifies some key genes bridging coevolved mutualists, establishing expectations for more diffuse insect-pollinator systems.
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Affiliation(s)
- Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Yang Yang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yi Jing
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, UK
| | - Yu Zhang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Gang Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jin Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | | | - Shan Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yan Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | | | - Yuan-Yuan Ding
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Derek W Dunn
- College of Life Sciences, Northwest University, Xi'an, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Philip M Gilmartin
- Department of Biological and Marine Science, University of Hull, Hull, UK
| | - Kai Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Finn Kjellberg
- CEFE, CNRS, University of Montpellier, Paul Valéry University Montpellier, EPHE, IRD, Montpellier, France
| | - Hong-Qing Li
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuan-Yuan Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Jian-Quan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Min Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Xin Tong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ping Wen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | | | - Jing-Jun Yang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xing-Tan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,School of Life Sciences, Qufu Normal University, Qufu, China.
| | - Zhen Yue
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.
| | | | - Xiao-Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China. .,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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Kim J, Nam HY, Kwon M, Kim HJ, Yi HJ, Haenniger S, Unbehend M, Heckel DG. Development of a simple and accurate molecular tool for Spodoptera frugiperda species identification using LAMP. PEST MANAGEMENT SCIENCE 2021; 77:3145-3153. [PMID: 33644961 DOI: 10.1002/ps.6350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/28/2020] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The fall armyworm, Spodoptera frugiperda is a native species of the Americas. First detected in western and central Africa in early 2016, it has become one of the most serious invasive lepidopteran pests in many African and Asian countries. S. frugiperda has spread very quickly; however, there are no molecular-based, simple and accurate diagnostic tools for identification of this species in the field. Methods to identify invasive S. frugiperda are urgently needed because farmers and agricultural managers have no prior experience with this pest. RESULTS Based on mitochondrial genome sequence alignment, a S. frugiperda-specific sequence region was identified in the transfer RNA-coding region between NADH dehydrogenase, ND3, and ND5. Using this unique region, species-diagnostic primers were designed and applied in a loop-mediated isothermal amplification (LAMP) assay and a conventional polymerase chain reaction to identify field-collected samples of S. frugiperda. The optimal incubation conditions for the LAMP assay were 61°C for 90 min with four LAMP primers; an additional loop primer increased the amplification efficiency. A response was obtained for a wide range of DNA concentrations in the LAMP assay and the minimum detectable DNA concentration was 10 pg. CONCLUSIONS We developed a new LAMP-based molecular diagnostic method that it is easy to use and accurate. The LAMP assay was used with a DNA-releasing technique for larval and adult samples, without a DNA extraction step, by incubating the tissue sample at 95°C for 5 min. This method can be applied in intensive field monitoring of S. frugiperda and its ecological studies. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Juil Kim
- Program of Applied Biology, Division of Bio-resource Sciences, College of Agriculture and Life Science, Kangwon National University, Chuncheon, Republic of Korea
- Highland Agriculture Research Institute, National Institute of Crop Science, RDA, Pyeongchang, Republic of Korea
| | - Hwa Y Nam
- Program of Applied Biology, Division of Bio-resource Sciences, College of Agriculture and Life Science, Kangwon National University, Chuncheon, Republic of Korea
- Highland Agriculture Research Institute, National Institute of Crop Science, RDA, Pyeongchang, Republic of Korea
| | - Min Kwon
- Highland Agriculture Research Institute, National Institute of Crop Science, RDA, Pyeongchang, Republic of Korea
| | - Hyun J Kim
- Crop foundation Division, National Institute of Crop Science, RDA, Wanju, Republic of Korea
| | - Hwi J Yi
- Crop Production Technology Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Sabine Haenniger
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Melanie Unbehend
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
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41
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Li J, Bian C, Yi Y, Yu H, You X, Shi Q. Temporal dynamics of teleost populations during the Pleistocene: a report from publicly available genome data. BMC Genomics 2021; 22:490. [PMID: 34193045 PMCID: PMC8247217 DOI: 10.1186/s12864-021-07816-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 06/14/2021] [Indexed: 12/04/2022] Open
Abstract
Background Global climate oscillation, as a selection dynamic, is an ecologically important element resulting in global biodiversity. During the glacial geological periods, most organisms suffered detrimental selection pressures (such as food shortage and habitat loss) and went through population declines. However, during the mild interglacial periods, many species re-flourished. These temporal dynamics of effective population sizes (Ne) provide essential information for understanding and predicting evolutionary outcomes during historical and ongoing global climate changes. Results Using high-quality genome assemblies and corresponding sequencing data, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) method to quantify Ne changes of twelve representative teleost species from approximately 10 million years ago (mya) to 10 thousand years ago (kya). These results revealed multiple rounds of population contraction and expansion in most of the examined teleost species during the Neogene and the Quaternary periods. We observed that 83% (10/12) of the examined teleosts had experienced a drastic decline in Ne before the last glacial period (LGP, 110–12 kya), slightly earlier than the reported pattern of Ne changes in 38 avian species. In comparison with the peaks, almost all of the examined teleosts maintained long-term lower Ne values during the last few million years. This is consistent with increasingly dramatic glaciation during this period. Conclusion In summary, these findings provide a more comprehensive understanding of the historical Ne changes in teleosts. Results presented here could lead to the development of appropriate strategies to protect species in light of ongoing global climate changes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07816-7.
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Affiliation(s)
- Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China.
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China.,Center of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China
| | - Yunhai Yi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Hui Yu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China. .,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China. .,Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China.
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Dall'Agnol B, Webster A, Souza UA, Barbieri A, Mayer FQ, Cardoso GA, Torres TT, Machado RZ, Ferreira CAS, Reck J. Genomic analysis on Brazilian strains of Anaplasma marginale. ACTA ACUST UNITED AC 2021; 30:e000421. [PMID: 34076044 DOI: 10.1590/s1984-29612021043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/15/2021] [Indexed: 11/21/2022]
Abstract
Anaplasma marginale is a vector-borne pathogen that causes a disease known as anaplasmosis. No sequenced genomes of Brazilian strains are yet available. The aim of this work was to compare whole genomes of Brazilian strains of A. marginale (Palmeira and Jaboticabal) with genomes of strains from other regions (USA and Australia strains). Genome sequencing of Brazilian strains was performed by means of next-generation sequencing. Reads were mapped using the genome of the Florida strain of A. marginale as a reference sequence. Single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) were identified. The data showed that two Brazilian strains grouped together in one particular clade, which grouped in a larger American group together with North American strains. Moreover, some important differences in surface proteins between the two Brazilian isolates can be discerned. These results shed light on the evolutionary history of A. marginale and provide the first genome information on South American isolates. Assessing the genome sequences of strains from different regions is essential for increasing knowledge of the pan-genome of this bacteria.
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Affiliation(s)
- Bruno Dall'Agnol
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor - IPVDF, Eldorado do Sul, RS, Brasil
| | - Anelise Webster
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor - IPVDF, Eldorado do Sul, RS, Brasil
| | - Ugo Araújo Souza
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor - IPVDF, Eldorado do Sul, RS, Brasil
| | - Antonela Barbieri
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor - IPVDF, Eldorado do Sul, RS, Brasil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor - IPVDF, Eldorado do Sul, RS, Brasil
| | | | | | - Rosangela Zacarias Machado
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Jaboticabal, SP, Brasil
| | | | - José Reck
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor - IPVDF, Eldorado do Sul, RS, Brasil
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43
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Kwon SB, Ernst J. Learning a genome-wide score of human-mouse conservation at the functional genomics level. Nat Commun 2021; 12:2495. [PMID: 33941776 PMCID: PMC8093196 DOI: 10.1038/s41467-021-22653-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/24/2021] [Indexed: 01/06/2023] Open
Abstract
Identifying genomic regions with functional genomic properties that are conserved between human and mouse is an important challenge in the context of mouse model studies. To address this, we develop a method to learn a score of evidence of conservation at the functional genomics level by integrating information from a compendium of epigenomic, transcription factor binding, and transcriptomic data from human and mouse. The method, Learning Evidence of Conservation from Integrated Functional genomic annotations (LECIF), trains neural networks to generate this score for the human and mouse genomes. The resulting LECIF score highlights human and mouse regions with shared functional genomic properties and captures correspondence of biologically similar human and mouse annotations. Analysis with independent datasets shows the score also highlights loci associated with similar phenotypes in both species. LECIF will be a resource for mouse model studies by identifying loci whose functional genomic properties are likely conserved.
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Affiliation(s)
- Soo Bin Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, CA, USA. .,Computer Science Department, University of California, Los Angeles, CA, USA. .,Department of Computational Medicine, University of California, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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44
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Vitamin D decreases silencer methylation to downregulate renin gene expression. Gene 2021; 786:145623. [PMID: 33798678 DOI: 10.1016/j.gene.2021.145623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/18/2021] [Accepted: 03/26/2021] [Indexed: 01/21/2023]
Abstract
Renin, encoded by REN, is an essential enzyme in the renin-angiotensin aldosterone system (RAAS) which is responsible for the maintenance of blood pressure homeostasis. Transcriptional regulation of REN has been linked to enhancer-promoter crosstalk, cAMP response element-binding protein (CREB), the active metabolite of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), and a less well-characterized intronic silencer element. We hypothesized that in addition to these, differential DNA methylation is linked to REN expression and influenced by 1,25(OH)2D3. REN expressing cells (HEK293) were used to elucidate the effect of 1,25(OH)2D3 on REN methylation and expression as quantified by methylation-sensitive qPCR and RT-qPCR, respectively. In vitro 1,25(OH)2D3 supplementation (10 nM) induced significant hypomethylation of the REN silencer (P < 0.050), which was linked to a significant reduction in REN expression (P < 0.010) but had no effect on enhancer methylation. In addition, 1,25(OH)2D3 increased VDR (P < 0.05), as well as TET1 (P < 0.05) expression, suggesting an association between 1,25(OH)2D3 and DNA methylation. Thus, it appears that the silencer element, which is controlled by DNA methylation and influenced by 1,25(OH)2D3, plays an essential role in regulating REN expression.
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45
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Park TH. Complete chloroplast genome sequence of the wild diploid potato relative, Solanum acaule. Mitochondrial DNA B Resour 2021; 6:1189-1191. [PMID: 33829083 PMCID: PMC8008929 DOI: 10.1080/23802359.2021.1902414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Affiliation(s)
- Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
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46
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Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ. Evolution of genome structure in the Drosophila simulans species complex. Genome Res 2021; 31:380-396. [PMID: 33563718 PMCID: PMC7919458 DOI: 10.1101/gr.263442.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022]
Abstract
The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Ching-Ho Chang
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Danielle E Khost
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
- FAS Informatics and Scientific Applications, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jeffrey R Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | | | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
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47
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Liao Y, Zhang X, Chakraborty M, Emerson JJ. Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. Genome Res 2021; 31:397-410. [PMID: 33563719 PMCID: PMC7919452 DOI: 10.1101/gr.266130.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022]
Abstract
Topologically associating domains (TADs) were recently identified as fundamental units of three-dimensional eukaryotic genomic organization, although our knowledge of the influence of TADs on genome evolution remains preliminary. To study the molecular evolution of TADs in Drosophila species, we constructed a new reference-grade genome assembly and accompanying high-resolution TAD map for D. pseudoobscura Comparison of D. pseudoobscura and D. melanogaster, which are separated by ∼49 million years of divergence, showed that ∼30%-40% of their genomes retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower expression divergence than those located in nonconserved TADs. Furthermore, we found that a substantial proportion of long genes (>50 kbp) in D. melanogaster (42%) and D. pseudoobscura (26%) constitute their own TADs, implying transcript structure may be one of the deterministic factors for TAD formation. By using structural variants (SVs) identified from 14 D. melanogaster strains, its three closest sibling species from the D. simulans species complex, and two obscura clade species, we uncovered evidence of selection acting on SVs at TAD boundaries, but with the nature of selection differing between SV types. Deletions are depleted at TAD boundaries in both divergent and polymorphic SVs, suggesting purifying selection, whereas divergent tandem duplications are enriched at TAD boundaries relative to polymorphism, suggesting they are adaptive. Our findings highlight how important TADs are in shaping the acquisition and retention of structural mutations that fundamentally alter genome organization.
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Affiliation(s)
- Yi Liao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Xinwen Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.,Center for Complex Biological Systems, University of California, Irvine, California 92697, USA
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48
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Dainat J, Pontarotti P. Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach. Methods Mol Biol 2021; 2324:21-34. [PMID: 34165706 DOI: 10.1007/978-1-0716-1503-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The discovery that pseudogenes are involved in important biological processes has excited enthusiasm and increased the research interest on them. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow for studying pseudogene history are described.
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Affiliation(s)
- Jacques Dainat
- Department of Medical Biochemistry Microbiology and Genomics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Pierre Pontarotti
- Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Marseille, France
- SNC5039 CNRS, Marseille, France
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Kim JB, Yang HR, Lee SH, Park TH. The complete chloroplast genome sequence of the Alstroemeria hybrid variety 'Hanhera'. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3808-3809. [PMID: 33426285 PMCID: PMC7759260 DOI: 10.1080/23802359.2020.1840936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Alstroemeria, a member of the Alstroemeriaceae family, is a species from South America. The chloroplast genome of Alstroemeria spp. was completed by de novo assembly using a small amount of whole genome sequencing data. The chloroplast genome of Alstroemeria spp. was 155,672 bp in length consisting of 84,379 bp of large single copy, 17,815 bp of small single copy, and 26,739 bp of a pair of inverted repeat regions. A total of 157 genes were annotated including 103 protein-coding genes (PCGs), 46 tRNA genes, and eight rRNA genes. Maximum likelihood phylogenetic analysis with seven species belonging to the Alstroemeriaceae or Liliaceae family revealed that Alstroemeria spp. is grouped with the species in the Alstroemeriaceae family.
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Affiliation(s)
- Jong-Bo Kim
- Department of Biotechnology, Research Institute for Biomedical & Health Sciences, College of Biomedical & Health Sciences, Glocal Campus, Konkuk University, Chungju, South Korea
| | - Hwan-Rae Yang
- Department of Biotechnology, Research Institute for Biomedical & Health Sciences, College of Biomedical & Health Sciences, Glocal Campus, Konkuk University, Chungju, South Korea
| | - Sang-Hee Lee
- Department of Biotechnology, Research Institute for Biomedical & Health Sciences, College of Biomedical & Health Sciences, Glocal Campus, Konkuk University, Chungju, South Korea
| | - Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
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50
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Vakhrusheva OA, Mnatsakanova EA, Galimov YR, Neretina TV, Gerasimov ES, Naumenko SA, Ozerova SG, Zalevsky AO, Yushenova IA, Rodriguez F, Arkhipova IR, Penin AA, Logacheva MD, Bazykin GA, Kondrashov AS. Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nat Commun 2020; 11:6421. [PMID: 33339818 PMCID: PMC7749112 DOI: 10.1038/s41467-020-19614-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/23/2020] [Indexed: 01/08/2023] Open
Abstract
Sexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridization between divergent lineages. Analysis of triallelic sites independently corroborates these findings. Our results provide evidence for interindividual genetic exchange and recombination in A. vaga, a species previously thought to be anciently asexual.
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Affiliation(s)
- Olga A Vakhrusheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation.
| | - Elena A Mnatsakanova
- Department of General Ecology and Hydrobiology, Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Yan R Galimov
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
| | - Tatiana V Neretina
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, 119435, Russian Federation
| | - Sergey A Naumenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, 02115, USA
| | - Svetlana G Ozerova
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
- Medkvadrat, Moscow, 115409, Russian Federation
| | - Arthur O Zalevsky
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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