1
|
Mallawaarachchi V, Wickramarachchi A, Xue H, Papudeshi B, Grigson SR, Bouras G, Prahl RE, Kaphle A, Verich A, Talamantes-Becerra B, Dinsdale EA, Edwards RA. Solving genomic puzzles: computational methods for metagenomic binning. Brief Bioinform 2024; 25:bbae372. [PMID: 39082646 PMCID: PMC11289683 DOI: 10.1093/bib/bbae372] [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: 04/18/2024] [Revised: 06/05/2024] [Accepted: 07/15/2024] [Indexed: 08/03/2024] Open
Abstract
Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research.
Collapse
Affiliation(s)
- Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Anuradha Wickramarachchi
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, NSW 2145, Australia
| | - Hansheng Xue
- School of Computing, National University of Singapore, Singapore 119077, Singapore
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Susanna R Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- The Department of Surgery—Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA 5011, Australia
| | - Rosa E Prahl
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, NSW 2145, Australia
| | - Anubhav Kaphle
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, NSW 2145, Australia
| | - Andrey Verich
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, NSW 2145, Australia
- The Kirby Institute, The University of New South Wales, Randwick, Sydney, NSW 2052, Australia
| | - Berenice Talamantes-Becerra
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, NSW 2145, Australia
| | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| |
Collapse
|
2
|
Blackman C, Subramaniam R. A Bioinformatic Guide to Identify Protein Effectors from Phytopathogens. Methods Mol Biol 2023; 2659:95-101. [PMID: 37249888 DOI: 10.1007/978-1-0716-3159-1_8] [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: 05/31/2023]
Abstract
Phytopathogenic fungi are a diverse and widespread group that has a significant detrimental impact on crops with an estimated annual average loss of 15% worldwide. Understanding the interaction between host plants and pathogenic fungi is critical to delineate underlying mechanisms of plant defense to mitigate agricultural losses. Fungal pathogens utilize suites of secreted molecules, called effectors, to modulate plant metabolism and immune response to overcome host defenses and promote colonization. Effectors come in many flavors including proteinaceous products, small RNAs, and metabolites such as mycotoxins. This review will focus on methods for identifying protein effectors from fungi. Excellent reviews have been published to identify secondary metabolites and small RNAs from fungi and therefore will not be part of this review.
Collapse
Affiliation(s)
- Christopher Blackman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
| |
Collapse
|
3
|
Yadav IS, Bhardwaj SC, Kaur J, Singla D, Kaur S, Kaur H, Rawat N, Tiwari VK, Saunders D, Uauy C, Chhuneja P. Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India. PLoS One 2022; 17:e0261697. [PMID: 36327308 PMCID: PMC9632834 DOI: 10.1371/journal.pone.0261697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.
Collapse
Affiliation(s)
- Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - S. C. Bhardwaj
- Regional Station, Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, India
| | - Jaspal Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Harmandeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland College Park, College Park, Maryland, United States of America
| | - Vijay Kumar Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland College Park, College Park, Maryland, United States of America
| | - Diane Saunders
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- * E-mail:
| |
Collapse
|
4
|
Kim D, Gilchrist CLM, Chun J, Steinegger M. UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Res 2022; 51:D777-D784. [PMID: 36271795 PMCID: PMC9825530 DOI: 10.1093/nar/gkac894] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/13/2022] [Accepted: 10/04/2022] [Indexed: 01/30/2023] Open
Abstract
In phylogenomics the evolutionary relationship of organisms is studied by their genomic information. A common approach to phylogenomics is to extract related genes from each organism, build a multiple sequence alignment and then reconstruct evolution relations through a phylogenetic tree. Often a set of highly conserved genes occurring in single-copy, called core genes, are used for this analysis, as they allow efficient automation within a taxonomic clade. Here we introduce the Universal Fungal Core Genes (UFCG) database and pipeline for genome-wide phylogenetic analysis of fungi. The UFCG database consists of 61 curated fungal marker genes, including a novel set of 41 computationally derived core genes and 20 canonical genes derived from literature, as well as marker gene sequences extracted from publicly available fungal genomes. Furthermore, we provide an easy-to-use, fully automated and open-source pipeline for marker gene extraction, training and phylogenetic tree reconstruction. The UFCG pipeline can identify marker genes from genomic, proteomic and transcriptomic data, while producing phylogenies consistent with those previously reported, and is publicly available together with the UFCG database at https://ufcg.steineggerlab.com.
Collapse
Affiliation(s)
- Dongwook Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Cameron L M Gilchrist
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongsik Chun
- Correspondence may also be addressed to Jongsik Chun. Tel: +82 2 880 8153;
| | | |
Collapse
|
5
|
Espinoza JL, Dupont CL. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. BMC Bioinformatics 2022; 23:419. [PMID: 36224545 PMCID: PMC9554839 DOI: 10.1186/s12859-022-04973-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth's natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ, however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes. RESULTS In this study, we introduce the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge, VEBA is the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes. VEBA implements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone. VEBA includes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally, VEBA is the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments. VEBA's capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives. CONCLUSIONS The VEBA software suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways. VEBA fully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions of VEBA to the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks. VEBA allows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.
Collapse
Affiliation(s)
- Josh L. Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037 USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037 USA
| | - Chris L. Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037 USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037 USA
| |
Collapse
|
6
|
Jakhesara, Tulsani NJ, Hinsu AT, Jyotsana B, Dafale NA, Patil NV, Purohit HJ, Joshi CG. Genome analysis and CAZy repertoire of a novel fungus Aspergillus sydowii C6d with lignocellulolytic ability isolated from camel rumen. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
7
|
Industrially Important Genes from Trichoderma. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
8
|
Xingxing P, Khan RAA, Yan L, Yuhong Y, Bingyan X, Zhenchuan M, Jian L. Draft Genome Resource of Fusarium oxysporum f. sp. capsici, the Infectious Agent of Pepper Fusarium Wilt. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:715-717. [PMID: 33512247 DOI: 10.1094/mpmi-12-20-0355-a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fusarium oxysporum f. sp. capsici is the specific pathogen of pepper Fusarium wilt and causes a significant reduction in pepper yield. Its narrow host specificity has led to the concept of formae speciales. This interesting phenomenon has great potential and needs to be analyzed at the molecular level. In this study, we obtained the draft genome sequence of F. oxysporum f. sp. capsici, using the Oxford Nanopore sequencing technology. The long read-based assembly consisted of 34 contigs, with a total length of 54,516,562 bp. The contig N50 was 4,962,668 bp and the GC content was 47.6%. Our genome assembly of F. oxysporum f. sp. capsici provides a valuable resource for the study of pepper Fusarium wilt, and the comparative genomic study of F. oxysporum.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Ping Xingxing
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Raja Asad Ali Khan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Department of Plant Pathology, The University of Agriculture Peshawar, 25000, Pakistan
| | - Li Yan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Yuhong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xie Bingyan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mao Zhenchuan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
9
|
Tagirdzhanova G, Saary P, Tingley JP, Díaz-Escandón D, Abbott DW, Finn RD, Spribille T. Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes. Genome Biol Evol 2021; 13:6163286. [PMID: 33693712 PMCID: PMC8355462 DOI: 10.1093/gbe/evab047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Basidiomycete yeasts have recently been reported as stably associated secondary
fungal symbionts of many lichens, but their role in the symbiosis remains
unknown. Attempts to sequence their genomes have been hampered both by the
inability to culture them and their low abundance in the lichen thallus
alongside two dominant eukaryotes (an ascomycete fungus and chlorophyte alga).
Using the lichen Alectoria sarmentosa, we selectively dissolved
the cortex layer in which secondary fungal symbionts are embedded to enrich
yeast cell abundance and sequenced DNA from the resulting slurries as well as
bulk lichen thallus. In addition to yielding a near-complete genome of the
filamentous ascomycete using both methods, metagenomes from cortex slurries
yielded a 36- to 84-fold increase in coverage and near-complete genomes for two
basidiomycete species, members of the classes Cystobasidiomycetes and
Tremellomycetes. The ascomycete possesses the largest gene repertoire of the
three. It is enriched in proteases often associated with pathogenicity and
harbors the majority of predicted secondary metabolite clusters. The
basidiomycete genomes possess ∼35% fewer predicted genes than the
ascomycete and have reduced secretomes even compared with close relatives, while
exhibiting signs of nutrient limitation and scavenging. Furthermore, both
basidiomycetes are enriched in genes coding for enzymes producing secreted
acidic polysaccharides, representing a potential contribution to the shared
extracellular matrix. All three fungi retain genes involved in dimorphic
switching, despite the ascomycete not being known to possess a yeast stage. The
basidiomycete genomes are an important new resource for exploration of lifestyle
and function in fungal–fungal interactions in lichen symbioses.
Collapse
Affiliation(s)
- Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
| | - Paul Saary
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jeffrey P Tingley
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - David Díaz-Escandón
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
10
|
Cissé OH, Ma L, Dekker JP, Khil PP, Youn JH, Brenchley JM, Blair R, Pahar B, Chabé M, Van Rompay KKA, Keesler R, Sukura A, Hirsch V, Kutty G, Liu Y, Peng L, Chen J, Song J, Weissenbacher-Lang C, Xu J, Upham NS, Stajich JE, Cuomo CA, Cushion MT, Kovacs JA. Genomic insights into the host specific adaptation of the Pneumocystis genus. Commun Biol 2021; 4:305. [PMID: 33686174 PMCID: PMC7940399 DOI: 10.1038/s42003-021-01799-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 11/21/2022] Open
Abstract
Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans. Cissé, Ma et al. utilize genomic data from Pneumocystis species infecting macaques, rabbit, dogs and rats to investigate the molecular basis of host specificity in Pneumocystis. Their analyses provide insight to the specific adaptations enabling the infection of humans by P. jirovecii.
Collapse
Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Jung-Ho Youn
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Robert Blair
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Rebekah Keesler
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Antti Sukura
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Li Peng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nathan S Upham
- Arizona State University, School of Life Sciences, Tempe, ARI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside-California, Riverside, CA, USA
| | - Christina A Cuomo
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melanie T Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| |
Collapse
|
11
|
Genome Assembly and Analyses of the Macrofungus Macrocybe gigantea. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6656365. [PMID: 33542921 PMCID: PMC7841450 DOI: 10.1155/2021/6656365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/19/2020] [Accepted: 01/01/2021] [Indexed: 12/31/2022]
Abstract
Macrocybe gigantea (M. gigantea) is a macrofungus genus that contains a big number of fairly fleshy gilled mushrooms with white spores. This macrofungus produces diverse bioactive compounds, antioxidants, and water-soluble polysaccharides. However, the genomic resources of this species remain unknown. Here, we assembled the genome of M. gigantea (41.23 Mb) into 336 scaffolds with a N50 size of 374,455 bp and compared it with the genomes of eleven other macrofungi. Comparative genomics study confirmed that M. gigantea belonged to the Macrocybe genus, a stand-alone genus different from the Tricholoma genus. In addition, we found that glycosyl hydrolase family 28 (GH28) in M. gigantea shared conserved motifs that were significantly different from their counterparts in Tricholoma. The genomic resource uncovered by this study will enhance our understanding of fungi biology, especially the differences in their growth rates and energy metabolism.
Collapse
|
12
|
Kanja C, Hammond‐Kosack KE. Proteinaceous effector discovery and characterization in filamentous plant pathogens. MOLECULAR PLANT PATHOLOGY 2020; 21:1353-1376. [PMID: 32767620 PMCID: PMC7488470 DOI: 10.1111/mpp.12980] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/03/2020] [Accepted: 07/05/2020] [Indexed: 05/26/2023]
Abstract
The complicated interplay of plant-pathogen interactions occurs on multiple levels as pathogens evolve to constantly evade the immune responses of their hosts. Many economically important crops fall victim to filamentous pathogens that produce small proteins called effectors to manipulate the host and aid infection/colonization. Understanding the effector repertoires of pathogens is facilitating an increased understanding of the molecular mechanisms underlying virulence as well as guiding the development of disease control strategies. The purpose of this review is to give a chronological perspective on the evolution of the methodologies used in effector discovery from physical isolation and in silico predictions, to functional characterization of the effectors of filamentous plant pathogens and identification of their host targets.
Collapse
Affiliation(s)
- Claire Kanja
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
- School of BiosciencesUniversity of NottinghamNottinghamUK
| | | |
Collapse
|
13
|
Saary P, Mitchell AL, Finn RD. Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. Genome Biol 2020; 21:244. [PMID: 32912302 PMCID: PMC7488429 DOI: 10.1186/s13059-020-02155-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022] Open
Abstract
Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.
Collapse
Affiliation(s)
- Paul Saary
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Alex L Mitchell
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| |
Collapse
|
14
|
Kemena C, Dohmen E, Bornberg-Bauer E. DOGMA: a web server for proteome and transcriptome quality assessment. Nucleic Acids Res 2020; 47:W507-W510. [PMID: 31076763 PMCID: PMC6602495 DOI: 10.1093/nar/gkz366] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 11/16/2022] Open
Abstract
Even in the era of next generation sequencing, in which bioinformatics tools abound, annotating transcriptomes and proteomes remains a challenge. This can have major implications for the reliability of studies based on these datasets. Therefore, quality assessment represents a crucial step prior to downstream analyses on novel transcriptomes and proteomes. DOGMA allows such a quality assessment to be carried out. The data of interest are evaluated based on a comparison with a core set of conserved protein domains and domain arrangements. Depending on the studied species, DOGMA offers precomputed core sets for different phylogenetic clades. We now developed a web server for the DOGMA software, offering a user-friendly, simple to use interface. Additionally, the server provides a graphical representation of the analysis results and their placement in comparison to publicly available data. The server is freely available under https://domainworld-services.uni-muenster.de/dogma/. Additionally, for large scale analyses the software can be downloaded free of charge from https://domainworld.uni-muenster.de.
Collapse
Affiliation(s)
- Carsten Kemena
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität Münster, Hüfferstrasse 1, NRW, 48149 Münster, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität Münster, Hüfferstrasse 1, NRW, 48149 Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität Münster, Hüfferstrasse 1, NRW, 48149 Münster, Germany
| |
Collapse
|
15
|
Abstract
The oomycetes are a class of ubiquitous, filamentous microorganisms that include some of the biggest threats to global food security and natural ecosystems. Within the oomycete class are highly diverse species that infect a broad range of animals and plants. Some of the most destructive plant pathogens are oomycetes, such as Phytophthora infestans, the agent of potato late blight and the cause of the Irish famine. Recent years have seen a dramatic increase in the number of sequenced oomycete genomes. Here we review the latest developments in oomycete genomics and some of the important insights that have been gained. Coupled with proteomic and transcriptomic analyses, oomycete genome sequences have revealed tremendous insights into oomycete biology, evolution, genome organization, mechanisms of infection, and metabolism. We also present an updated phylogeny of the oomycete class using a phylogenomic approach based on the 65 oomycete genomes that are currently available.
Collapse
Affiliation(s)
- Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland.
| |
Collapse
|
16
|
Greshake Tzovaras B, Segers FHID, Bicker A, Dal Grande F, Otte J, Anvar SY, Hankeln T, Schmitt I, Ebersberger I. What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen. Genome Biol Evol 2020; 12:309-324. [PMID: 32163141 PMCID: PMC7186782 DOI: 10.1093/gbe/evaa049] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/29/2022] Open
Abstract
Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.
Collapse
Affiliation(s)
- Bastian Greshake Tzovaras
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- Lawrence Berkeley National Laboratory, Berkeley, California
- Center for Research & Interdisciplinarity, Université de Paris, France
| | - Francisca H I D Segers
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
| | - Anne Bicker
- Institute for Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Germany
| | - Francesco Dal Grande
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Seyed Yahya Anvar
- Department of Human Genetics, Leiden University Medical Center, The Netherlands
| | - Thomas Hankeln
- Institute for Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Germany
| | - Imke Schmitt
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- Molecular Evolutionary Biology Group, Institute of Ecology, Diversity, and Evolution, Goethe University Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| |
Collapse
|
17
|
Rodrigues KA, Rocha RT, Mulinari FF, Guedes AV, Teixeira MDM, Motta DDO, Fernandes L, Magalhães BS, Felipe MSS, Pappas GJ, Parachin NS. Exploring the Brazilian diversity of Aspergillus sp. strains for lovastatin and itaconic acid production. Fungal Genet Biol 2020; 138:103367. [PMID: 32198121 DOI: 10.1016/j.fgb.2020.103367] [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: 10/31/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 11/17/2022]
Abstract
Filamentous fungi are well known for producing secondary metabolites applied in various industrial segments. Among these, lovastatin and itaconic acid, produced by Aspergillus terreus, have applications in the pharmaceutical and chemical industries. Lovastatin is primarily used for the control of hypercholesterolemia, while itaconic acid is a building block for the production of synthetic fibers, coating adhesives, among others. In this study, for the first time, 35 strains of Aspergillus sp. from four Brazilian culture collections were evaluated for lovastatin and itaconic acid production and compared to a reference strain, ATCC 20542. From an initial screening, the strains ATCC 20542, URM 224, URM1876, URM 5061, URM 5254, URM 5256, URM 5650, and URM 5961 were selected for genomic comparison. Among tested strains, the locus corresponding to the lovastatin genomic cluster was assembled, showing that all genes essential for lovastatin biosynthesis were present in producing URM 5961 and URM 5650 strains, with 100% and 98.5% similarity to ATCC 20542, respectively. However, in the no producing URM 1876, URM 224, URM 5254, URM 5061, and URM 5256 strains, this cluster was either fragmented or missing. Among the 35 strains evaluated for itaconic acid production in this study, only three strains had titers above 0.5 g/L, 16 strains had production below 0.5 g/L, and the remaining 18 strains had no production, with the highest production of itaconic acid observed in the URM 5254 strain with 2.2 g/L. The essential genes for itaconic acid production, mttA, cadA msfA were also mapped, where all three genes linked to itaconic acid production were found in a single contig in the assembly of each strain. In contrast to lovastatin loci, there is no correlation between the level of itaconic acid production and genetic polymorphisms in the genes associated with its biosynthesis.
Collapse
Affiliation(s)
- Kelly Assis Rodrigues
- Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil
| | - Rodrigo Theodoro Rocha
- Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Computational Genomics Group, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, CEP 70790-900, Brazil
| | - Flávia Furtado Mulinari
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Adevilton Viana Guedes
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Marcus de Melo Teixeira
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil; Faculdade de Medicina, Universidade de Medicina, Brasília, DF CEP 70910-900, Brazil
| | - Dielle de Oliveira Motta
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Larissa Fernandes
- Laboratório de Imunologia Aplicada, Instituto de Biologia, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Beatriz Simas Magalhães
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Maria Sueli Soares Felipe
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil
| | - Georgios Joannis Pappas
- Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Computational Genomics Group, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, CEP 70790-900, Brazil
| | - Nádia Skorupa Parachin
- Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF CEP 70790-160, Brazil.
| |
Collapse
|