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Saffer A, Tateosian L, Saville AC, Yang YP, Ristaino JB. Reconstructing historic and modern potato late blight outbreaks using text analytics. Sci Rep 2024; 14:2523. [PMID: 38360880 PMCID: PMC10869797 DOI: 10.1038/s41598-024-52870-2] [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: 10/11/2023] [Accepted: 01/24/2024] [Indexed: 02/17/2024] Open
Abstract
In 1843, a hitherto unknown plant pathogen entered the US and spread to potato fields in the northeast. By 1845, the pathogen had reached Ireland leading to devastating famine. Questions arose immediately about the source of the outbreaks and how the disease should be managed. The pathogen, now known as Phytophthora infestans, still continues to threaten food security globally. A wealth of untapped knowledge exists in both archival and modern documents, but is not readily available because the details are hidden in descriptive text. In this work, we (1) used text analytics of unstructured historical reports (1843-1845) to map US late blight outbreaks; (2) characterized theories on the source of the pathogen and remedies for control; and (3) created modern late blight intensity maps using Twitter feeds. The disease spread from 5 to 17 states and provinces in the US and Canada between 1843 and 1845. Crop losses, Andean sources of the pathogen, possible causes and potential treatments were discussed. Modern disease discussion on Twitter included near-global coverage and local disease observations. Topic modeling revealed general disease information, published research, and outbreak locations. The tools described will help researchers explore and map unstructured text to track and visualize pandemics.
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Affiliation(s)
- Ariel Saffer
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, USA
| | - Laura Tateosian
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, USA
| | - Amanda C Saville
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Yi-Peng Yang
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, USA
| | - Jean B Ristaino
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.
- Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC, USA.
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2
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Burbano HA, Gutaker RM. Ancient DNA genomics and the renaissance of herbaria. Science 2023; 382:59-63. [PMID: 37797028 DOI: 10.1126/science.adi1180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/02/2023] [Indexed: 10/07/2023]
Abstract
Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.
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Affiliation(s)
- Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Rafal M Gutaker
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey TW9 3AE, UK
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3
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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4
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El-Ganainy SM, Iqbal Z, Awad HM, Sattar MN, Tohamy AM, Abbas AO, Squires J, Cooke DEL. Genotypic and Phenotypic Structure of the Population of Phytophthora infestans in Egypt Revealed the Presence of European Genotypes. J Fungi (Basel) 2022; 8:jof8050468. [PMID: 35628724 PMCID: PMC9147654 DOI: 10.3390/jof8050468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/10/2022] Open
Abstract
Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from potato and tomato plants during three growing seasons in 2010–2012. The characterization was achieved by mating-type assay, metalaxyl sensitivity assay, and virulence pattern. Additionally, genotyping of 85 Egyptian isolates and 15 reference UK isolates was performed using 12 highly informative microsatellite (SSR) markers David E. L. Cooke and five effector (RxLR) genes. Mating-type testing showed that 58% (118 of 205) of the isolates belonged to mating type A1, 35% (71 isolates) to mating type A2, and the rest 8% (16 isolates) were self-fertile. The phenotype of metalaxyl response was represented as 45% resistant, 43% sensitive, and 12% as intermediate. Structure analysis grouped the 85 identified genotypes into two main clonal lineages. The first clonal lineage comprised 21 isolates belonging to A2 mating type and 8 self-fertile isolates. This clonal lineage was identified as Blue_13 or EU_13_A2. The second main clonal lineage comprised 55 isolates and was identified as EU_23_A1. A single isolate with a novel SSR genotype that formed a distinct genetic grouping was also identified. The effector sequencing showed good correspondence with the virulence data and highlighted differences in the presence and absence of loci as well as nucleotide polymorphism that affect gene function. This study indicated a changing population of P. infestans in Egypt and discusses the findings in the context of late blight management.
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Affiliation(s)
- Sherif Mohamed El-Ganainy
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Vegetable Diseases Research Department, Plant Pathology Research Institute, ARC, Giza 12619, Egypt;
- Correspondence: (S.M.E.-G.); (D.E.L.C.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (Z.I.); (M.N.S.)
| | - Hossam Mohamed Awad
- Agriculture Botany Department, Menofia University, Shibin El-Kom 32415, Egypt;
| | - Muhammad Naeem Sattar
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (Z.I.); (M.N.S.)
| | - Abdel Mohsen Tohamy
- Vegetable Diseases Research Department, Plant Pathology Research Institute, ARC, Giza 12619, Egypt;
| | - Ahmed O. Abbas
- Department of Animal and Fish Production, College of Agricultural and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia;
| | | | - David E. L. Cooke
- The James Hutton Institute, Dundee DD2 5DA, UK;
- Correspondence: (S.M.E.-G.); (D.E.L.C.)
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5
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Fletcher K, Han R, Smilde D, Michelmore R. Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state. BMC Bioinformatics 2022; 23:150. [PMID: 35468720 PMCID: PMC9040317 DOI: 10.1186/s12859-022-04685-z] [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: 09/30/2021] [Accepted: 03/10/2022] [Indexed: 11/28/2022] Open
Abstract
Background Polyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to infer polyploidy and heterokaryosis in diverse organisms using read sets sequenced to greater than 50× whole-genome coverage. However, sequencing to adequate depth is costly if applied to multiple individuals or large genomes. Results We developed VCFvariance.pl to utilize the variance of allele balance to infer polyploidy and/or heterokaryosis at low sequence coverage. This analysis requires as little as 10× whole-genome coverage and reduces the allele balance profile down to a single value, which can be used to determine if an individual has two or more haplotypes. This approach was validated using simulated, synthetic, and authentic read sets from the oomycete species Bremia lactucae and Phytophthora infestans, the fungal species Saccharomyces cerevisiae, and the plant species Arabidopsis arenosa. This approach was deployed to determine that nine of 21 genotyped European race-type isolates of Bremia lactucae were inconsistent with diploidy and therefore likely heterokaryotic. Conclusions Variance of allele balance is a reliable metric to detect departures from a diploid state, including polyploidy, heterokaryosis, a mixed sample, or chromosomal copy number variation. Deploying this strategy is computationally inexpensive, can reduce the cost of sequencing by up to 80%, and used to test any organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04685-z.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, USA
| | - Rongkui Han
- The Genome Center, University of California, Davis, USA.,The Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
| | - Diederik Smilde
- Naktuinbouw, Postbus 40, Sotaweg 22, 2370 AA, Roelofarendsveen, The Netherlands
| | - Richard Michelmore
- The Genome Center, University of California, Davis, USA. .,Departments of Plant Sciences, Molecular and Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, USA.
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6
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Global historic pandemics caused by the FAM-1 genotype of Phytophthora infestans on six continents. Sci Rep 2021; 11:12335. [PMID: 34117299 PMCID: PMC8196071 DOI: 10.1038/s41598-021-90937-6] [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: 01/25/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022] Open
Abstract
The FAM-1 genotype of Phytophthora infestans caused late blight in the 1840s in the US and Europe and was responsible for the Irish famine. We sampled 140 herbarium specimens collected between 1845 and 1991 from six continents and used 12-plex microsatellite genotyping (SSR) to identify FAM-1 and the mtDNA lineage (Herb-1/Ia) present in historic samples. FAM-1 was detected in approximately 73% of the historic specimens and was found on six continents. The US-1 genotype was found later than FAM-1 on all continents except Australia/Oceania and in only 27% of the samples. FAM-1 was the first genotype detected in almost all the former British colonies from which samples were available. The data from historic outbreak samples suggest the FAM-1 genotype was widespread, diverse, and spread to Asia and Africa from European sources. The famine lineage spread to six continents over 144 years, remained widespread and likely spread during global colonization from Europe. In contrast, modern lineages of P. infestans are rapidly displaced and sexual recombination occurs in some regions.
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7
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Kahlon PS, Verin M, Hückelhoven R, Stam R. Quantitative resistance differences between and within natural populations of Solanum chilense against the oomycete pathogen Phytophthora infestans. Ecol Evol 2021; 11:7768-7778. [PMID: 34188850 PMCID: PMC8216925 DOI: 10.1002/ece3.7610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 01/01/2023] Open
Abstract
The wild tomato species Solanum chilense is divided into geographically and genetically distinct populations that show signs of defense gene selection and differential phenotypes when challenged with several phytopathogens, including the oomycete causal agent of late blight Phytophthora infestans. To better understand the phenotypic diversity of this disease resistance in S. chilense and to assess the effect of plant genotype versus pathogen isolate, respectively, we evaluated infection frequency in a systematic approach and with large sample sizes. We studied 85 genetically distinct individuals representing nine geographically separated populations of S. chilense. This showed that differences in quantitative resistance can be observed between but also within populations at the level of individual plants. Our data also did not reveal complete immunity in any of the genotypes. We further evaluated the resistance of a subset of the plants against P. infestans isolates with diverse virulence properties. This confirmed that the relative differences in resistance phenotypes between individuals were mainly determined by the plant genotype under consideration with modest effects of pathogen isolate used in the study. Thus, our report suggests that the observed quantitative resistance against P. infestans in natural populations of a wild tomato species S. chilense is the result of basal defense responses that depend on the host genotype and are pathogen isolate-unspecific.
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Affiliation(s)
| | - Melissa Verin
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Ralph Hückelhoven
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Remco Stam
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
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8
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Winkworth RC, Bellgard SE, McLenachan PA, Lockhart PJ. The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the "kauri killing" Phytophthora in New Zealand. PLoS One 2021; 16:e0250422. [PMID: 34019564 PMCID: PMC8139493 DOI: 10.1371/journal.pone.0250422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Phytophthora agathidicida is associated with a root rot that threatens the long-term survival of the iconic New Zealand kauri. Although it is widely assumed that this pathogen arrived in New Zealand post-1945, this hypothesis has yet to be formally tested. Here we describe evolutionary analyses aimed at evaluating this and two alternative hypotheses. As a basis for our analyses, we assembled complete mitochondrial genome sequences from 16 accessions representing the geographic range of P. agathidicida as well as those of five other members of Phytophthora clade 5. All 21 mitogenome sequences were very similar, differing little in size with all sharing the same gene content and arrangement. We first examined the temporal origins of genetic diversity using a pair of calibration schemes. Both resulted in similar age estimates; specifically, a mean age of 303.0-304.4 years and 95% HPDs of 206.9-414.6 years for the most recent common ancestor of the included isolates. We then used phylogenetic tree building and network analyses to investigate the geographic distribution of the genetic diversity. Four geographically distinct genetic groups were recognised within P. agathidicida. Taken together the inferred age and geographic distribution of the sampled mitogenome diversity suggests that this pathogen diversified following arrival in New Zealand several hundred to several thousand years ago. This conclusion is consistent with the emergence of kauri dieback disease being a consequence of recent changes in the relationship between the pathogen, host, and environment rather than a post-1945 introduction of the causal pathogen into New Zealand.
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Affiliation(s)
- Richard C. Winkworth
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Stanley E. Bellgard
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Peter J. Lockhart
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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9
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Duchêne S, Ho SYW, Carmichael AG, Holmes EC, Poinar H. The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Curr Biol 2020; 30:R1215-R1231. [PMID: 33022266 PMCID: PMC7534838 DOI: 10.1016/j.cub.2020.08.081] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest - pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) - and for three equally important endemic human disease agents - Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.
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Affiliation(s)
- Sebastián Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L9, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada.
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10
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Cai G, Scofield SR. Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes. PLoS One 2020; 15:e0231296. [PMID: 32407378 PMCID: PMC7224479 DOI: 10.1371/journal.pone.0231296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Phytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3' truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.
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Affiliation(s)
- Guohong Cai
- Crop Production and Pest Control Research Unit, Agricultural Research Service, USDA, and College of Agriculture, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
| | - Steven R. Scofield
- Crop Production and Pest Control Research Unit, Agricultural Research Service, USDA, and College of Agriculture, Purdue University, West Lafayette, Indiana, United States of America
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11
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Ristaino JB. The Importance of Mycological and Plant Herbaria in Tracking Plant Killers. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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12
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Saville A, Ristaino JB. Genetic Structure and Subclonal Variation of Extant and Recent U.S. Lineages of Phytophthora infestans. PHYTOPATHOLOGY 2019; 109:1614-1627. [PMID: 31066347 DOI: 10.1094/phyto-09-18-0357-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The oomycete Phytophthora infestans is an important plant pathogen on potato and tomato crops. We examined the genetic structure of extant 20th and 21st century U.S. lineages of P. infestans and compared them with populations from South America and Mexico to examine genetic relationships and potential sources of lineages. US-23, currently the most prevalent lineage detected in the United States, shared genetic similarity primarily with the BR-1 lineage identified in the 1990s from Bolivia and Brazil. Lineages US-8, US-14, and US-24, predominantly virulent on potato, formed a cluster distinct from other U.S. lineages. Many of the other U.S. lineages shared significant genetic similarity with Mexican populations. The US-1 lineage, dominant in the mid-20th century, clustered with US-1 lineages from Peru. A survey of the presence of RXLR effector PiAVR2 revealed that some lineages carried PiAVR2, its resistance-breaking variant PiAVR2-like, or both. Minimum spanning networks developed from simple sequence repeat genotype datasets from USABlight outbreaks clearly showed the expansion of US-23 over a 6-year time period and geographic substructuring of some lineages in the western United States. Many clonal lineages of P. infestans in the United States have come from introductions from Mexico, but the US-23 and US-1 lineages were most likely introduced from other sources.
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Affiliation(s)
- Amanda Saville
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Jean Beagle Ristaino
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
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13
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Martin FN, Zhang Y, Cooke DEL, Coffey MD, Grünwald NJ, Fry WE. Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs. PLoS One 2019; 14:e0208606. [PMID: 30601865 PMCID: PMC6314598 DOI: 10.1371/journal.pone.0208606] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 11/20/2018] [Indexed: 01/08/2023] Open
Abstract
In many parts of the world the damaging potato late blight pathogen, Phytophthora infestans, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 P. infestans isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of P. infestans.
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Affiliation(s)
- Frank N. Martin
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, California, United States of America
| | - Yonghong Zhang
- Plant Pathology and Microbiology Department, University of California, Riverside, California, United States of America
| | | | - Mike D. Coffey
- USDA-ARS, Horticultural Crops Research Laboratory, Corvallis, Oregon, United States of America
| | - Niklaus J. Grünwald
- USDA-ARS, Horticultural Crops Research Laboratory, Corvallis, Oregon, United States of America
| | - William E. Fry
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
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14
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Lang PLM, Willems FM, Scheepens JF, Burbano HA, Bossdorf O. Using herbaria to study global environmental change. THE NEW PHYTOLOGIST 2019; 221:110-122. [PMID: 30160314 PMCID: PMC6585664 DOI: 10.1111/nph.15401] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/19/2018] [Indexed: 05/14/2023]
Abstract
During the last centuries, humans have transformed global ecosystems. With their temporal dimension, herbaria provide the otherwise scarce long-term data crucial for tracking ecological and evolutionary changes over this period of intense global change. The sheer size of herbaria, together with their increasing digitization and the possibility of sequencing DNA from the preserved plant material, makes them invaluable resources for understanding ecological and evolutionary species' responses to global environmental change. Following the chronology of global change, we highlight how herbaria can inform about long-term effects on plants of at least four of the main drivers of global change: pollution, habitat change, climate change and invasive species. We summarize how herbarium specimens so far have been used in global change research, discuss future opportunities and challenges posed by the nature of these data, and advocate for an intensified use of these 'windows into the past' for global change research and beyond.
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Affiliation(s)
- Patricia L. M. Lang
- Research Group for Ancient Genomics and EvolutionMax Planck Institute for Developmental Biology72076TübingenGermany
| | - Franziska M. Willems
- Plant Evolutionary EcologyInstitute of Evolution and EcologyUniversity of Tübingen72076TübingenGermany
| | - J. F. Scheepens
- Plant Evolutionary EcologyInstitute of Evolution and EcologyUniversity of Tübingen72076TübingenGermany
| | - Hernán A. Burbano
- Research Group for Ancient Genomics and EvolutionMax Planck Institute for Developmental Biology72076TübingenGermany
| | - Oliver Bossdorf
- Plant Evolutionary EcologyInstitute of Evolution and EcologyUniversity of Tübingen72076TübingenGermany
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15
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Abstract
The population structure of the Phytophthora infestans populations that caused the recent 2013–14 late blight epidemic in eastern India (EI) and northeastern India (NEI) was examined. The data provide new baseline information for populations of P. infestans in India. A migrant European 13_A2 genotype was responsible for the 2013–14 epidemic, replacing the existing populations. Mutations have generated substantial sub-clonal variation with 24 multi-locus genotypes (MLGs) found, of which 19 were unique variants not yet reported elsewhere globally. Samples from West Bengal were the most diverse and grouped alongside MLGs found in Europe, the UK and from neighbouring Bangladesh but were not linked directly to most samples from south India. The pathogen population was broadly more aggressive on potato than on tomato and resistant to the fungicide metalaxyl. Pathogen population diversity was higher in regions around the international borders with Bangladesh and Nepal. Overall, the multiple shared MLGs suggested genetic contributions from UK and Europe in addition to a sub-structure based on the geographical location within India. Our data indicate the need for improved phytosanitary procedures and continuous surveillance to prevent the further introduction of aggressive lineages of P. infestans into the country.
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16
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MtDNA allows the sensitive detection and haplotyping of the crayfish plague disease agent Aphanomyces astaci showing clues about its origin and migration. Parasitology 2018; 145:1210-1218. [PMID: 29478421 DOI: 10.1017/s0031182018000227] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The oomycete Aphanomyces astaci, the causative agent of crayfish plague, is listed as one of the 100 worst invasive species in the world, destroying the native crayfish populations throughout Eurasia. The aim of this study was to examine the potential of selected mitochondrial (mt) genes to track the diversity of the crayfish plague pathogen A. astaci. Two sets of primers were developed to amplify the mtDNA of ribosomal rnnS and rnnL subunits. We confirmed two main lineages, with four different haplogroups and five haplotypes among 27 studied A. astaci strains. The haplogroups detected were (1) the A-haplogroup with the a-haplotype strains originating from Orconectes sp., Pacifastacus leniusculus and Astacus astacus; (2) the B-haplogroup with the b-haplotype strains originating from the P. leniusculus; (3) the D-haplogroup with the d1 and d2-haplotypes strains originating from Procambarus clarkii; and (4) the E-haplogroup with the e-haplotype strains originating from the Orconectes limosus. The described markers are stable and reliable and the results are easily repeatable in different laboratories. The present method has high applicability as it allows the detection and characterization of the A. astaci haplotype in acute disease outbreaks in the wild, directly from the infected crayfish tissue samples.
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17
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Gutaker RM, Burbano HA. Reinforcing plant evolutionary genomics using ancient DNA. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:38-45. [PMID: 28160617 DOI: 10.1016/j.pbi.2017.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/07/2016] [Accepted: 01/13/2017] [Indexed: 05/11/2023]
Abstract
Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place. Comparison of historical samples of barley (Hordeum vulgare) and maize (Zea mays ssp. mays) with their present-day counterparts enabled assessment of selection during different stages of domestication. These examples show how aDNA already improved our evolutionary inferences. Increasing quality and amount of sequencing data retrieved from historical plants will further advance our understanding of plant evolution.
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Affiliation(s)
- Rafal M Gutaker
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 37-39, Tuebingen 72076, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 37-39, Tuebingen 72076, Germany.
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18
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Wang J, Fernández‐Pavía SP, Larsen MM, Garay‐Serrano E, Gregorio‐Cipriano R, Rodríguez‐Alvarado G, Grünwald NJ, Goss EM. High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin. Mol Ecol 2017; 26:1091-1107. [DOI: 10.1111/mec.14000] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 12/11/2016] [Accepted: 12/21/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Jianan Wang
- Department of Plant Pathology and Emerging Pathogens Institute University of Florida Gainesville FL 32611 USA
| | - Sylvia P. Fernández‐Pavía
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | | | - Edith Garay‐Serrano
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | - Rosario Gregorio‐Cipriano
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | - Gerardo Rodríguez‐Alvarado
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | | | - Erica M. Goss
- Department of Plant Pathology and Emerging Pathogens Institute University of Florida Gainesville FL 32611 USA
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19
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Saville AC, Martin MD, Ristaino JB. Historic Late Blight Outbreaks Caused by a Widespread Dominant Lineage of Phytophthora infestans (Mont.) de Bary. PLoS One 2016; 11:e0168381. [PMID: 28030580 PMCID: PMC5193357 DOI: 10.1371/journal.pone.0168381] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/29/2016] [Indexed: 12/04/2022] Open
Abstract
Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, was responsible for the Irish potato famine of the 1840s. Initial disease outbreaks occurred in the US in 1843, two years prior to European outbreaks. We examined the evolutionary relationships and source of the 19th-century outbreaks using herbarium specimens of P. infestans from historic (1846-1970) and more recent isolates (1992-2014) of the pathogen. The same unique SSR multilocus genotype, named here as FAM-1, caused widespread outbreaks in both US and Europe. The FAM-1 lineage shared allelic diversity and grouped with the oldest specimens collected in Colombia and Central America. The FAM-1 lineage of P. infestans formed a genetic group that was distinct from more recent aggressive lineages found in the US. The US-1 lineage formed a second, mid-20th century group. Recent modern US lineages and the oldest Mexican lineages formed a genetic group with recent Mexican lineages, suggesting a Mexican origin of recent US lineages. A survey of mitochondrial haplotypes in a larger set of global herbarium specimens documented the more frequent occurrence of the HERB-1 (type Ia) mitochondrial haplotype in archival collections from 1866-75 and 1906-1915 and the rise of the Ib mitochondrial lineage (US-1) between 1946-1955. The FAM-1 SSR lineage survived for almost 100 years in the US, was geographically widespread, and was displaced first in the mid-20th century by the US-1 lineage and then by distinct new aggressive lineages that migrated from Mexico.
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Affiliation(s)
- Amanda C. Saville
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Formerly Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jean B. Ristaino
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
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20
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Makkonen J, Vesterbacka A, Martin F, Jussila J, Diéguez-Uribeondo J, Kortet R, Kokko H. Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans. Sci Rep 2016; 6:36089. [PMID: 27808238 PMCID: PMC5093560 DOI: 10.1038/srep36089] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/10/2016] [Indexed: 11/11/2022] Open
Abstract
The genus Aphanomyces (Saprolegniales, Oomycetes) includes species with a variety of ecologies from saprotrophs to plant and animal parasites. Two important species in this genus are A. astaci, the cause of crayfish plague and its close relative, A. invadans, which causes the epizootic ulcerative syndrome on fish. In this study, we have assembled and annotated the mitochondrial (mt) genomes of A. astaci and A. invadans from the whole genome shotgun sequence reads (PRJNA187372; PRJNA258292, respectively). The assembly was generated from A. astaci Pc-genotype strain APO3 and A. invadans strain NJM9701. The sizes of the mtDNAs were 49,489 bp and 49,061 bp for A. astaci and A. invadans, respectively. The species shared similar genetic content and organization encoding 35 proteins, two ribosomal RNAs, three putative open reading frames and 33 transfer RNAs of 19 amino acids for peptide synthesis. Both species also had a large inverted repeat region (LIR) of approximately 12 kb, the LIR contained large and small ribosomal RNAs and eight protein coding genes. These annotated mt genomes serve as a valuable genetic backbone for further development of diagnostic methods and phylogenetic and migration studies of the animal parasitic species of Aphanomyces.
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Affiliation(s)
- Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Arto Vesterbacka
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Frank Martin
- United States Department of Agriculture, ARS, 1636 E. Alisal St., CA-93905 Salinas, USA
| | - Japo Jussila
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | | | - Raine Kortet
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Department of Biology, Biological & Geological Sciences, University of Western Ontario, 1151 Richmond St N, London, Ontario N6A 5B7, Canada
| | - Harri Kokko
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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21
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Hansen ZR, Everts KL, Fry WE, Gevens AJ, Grünwald NJ, Gugino BK, Johnson DA, Johnson SB, Judelson HS, Knaus BJ, McGrath MT, Myers KL, Ristaino JB, Roberts PD, Secor GA, Smart CD. Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology. PLoS One 2016; 11:e0165690. [PMID: 27812174 PMCID: PMC5094694 DOI: 10.1371/journal.pone.0165690] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 10/17/2016] [Indexed: 01/24/2023] Open
Abstract
Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study were US-8 (n = 28), US-11 (n = 27), US-23 (n = 166), and US-24 (n = 36), with isolates originating from 23 of the United States and Ontario, Canada. The majority of isolates were collected between 2010 and 2014 (94%), with the remaining isolates collected from 1994 to 2009, and 2015. Between 3,774 and 5,070 single-nucleotide polymorphisms (SNPs) were identified within each lineage and were used to investigate relationships among individuals. K-means hierarchical clustering revealed three clusters within lineage US-23, with US-23 isolates clustering more by collection year than by geographic origin. K-means hierarchical clustering did not reveal significant clustering within the smaller US-8, US-11, and US-24 data sets. Neighbor-joining (NJ) trees were also constructed for each lineage. All four NJ trees revealed evidence for pathogen dispersal and overwintering within regions, as well as long-distance pathogen transport across regions. In the US-23 NJ tree, grouping by year was more prominent than grouping by region, which indicates the importance of long-distance pathogen transport as a source of initial late blight inoculum. Our results support previous studies that found significant genetic diversity within clonal lineages of P. infestans and show that GBS offers sufficiently high resolution to detect sub-structuring within clonal populations.
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Affiliation(s)
- Zachariah R. Hansen
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States of America
| | - Kathryne L. Everts
- Department of Plant Science and Landscape Architecture, University of Maryland, Salisbury, MD, United States of America
| | - William E. Fry
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America
| | - Amanda J. Gevens
- Department of Plant Pathology, University of Wisconsin, Madison, WI, United States of America
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture–Agricultural Research Service, Corvallis, OR, United States of America
| | - Beth K. Gugino
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States of America
| | - Dennis A. Johnson
- Department of Plant Pathology, Washington State University, Pullman, WA, United States of America
| | - Steven B. Johnson
- University of Maine Cooperative Extension, Presque Isle, ME, United States of America
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA, United States of America
| | - Brian J. Knaus
- Horticultural Crops Research Laboratory, United States Department of Agriculture–Agricultural Research Service, Corvallis, OR, United States of America
| | - Margaret T. McGrath
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Riverhead, NY, United States of America
| | - Kevin L. Myers
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America
| | - Jean B. Ristaino
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States of America
| | - Pamela D. Roberts
- Department of Plant Pathology, University of Florida, Immokalee, FL, United States of America
| | - Gary A. Secor
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States of America
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States of America
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22
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Knaus BJ, Tabima JF, Davis CE, Judelson HS, Grünwald NJ. Genomic Analyses of Dominant U.S. Clonal Lineages of Phytophthora infestans Reveals a Shared Common Ancestry for Clonal Lineages US11 and US18 and a Lack of Recently Shared Ancestry Among All Other U.S. Lineages. PHYTOPATHOLOGY 2016; 106:1393-1403. [PMID: 27348344 DOI: 10.1094/phyto-10-15-0279-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Populations of the potato and tomato late-blight pathogen Phytophthora infestans are well known for emerging as novel clonal lineages. These successions of dominant clones have historically been named US1 through US24, in order of appearance, since their first characterization using molecular markers. Hypothetically, these lineages can emerge through divergence from other U.S. lineages, recombination among lineages, or as novel, independent lineages originating outside the United States. We tested for the presence of phylogenetic relationships among U.S. lineages using a population of 31 whole-genome sequences, including dominant U.S. clonal lineages as well as available samples from global populations. We analyzed ancestry of the whole mitochondrial genome and samples of nuclear loci, including supercontigs 1.1 and 1.5 as well as several previously characterized coding regions. We found support for a shared ancestry among lineages US11 and US18 from the mitochondrial genome as well as from one nuclear haplotype on each supercontig analyzed. The other nuclear haplotype from each sample assorted independently, indicating an independent ancestry. We found no support for emergence of any other of the U.S. lineages from a common ancestor shared with the other U.S. lineages. Each of the U.S. clonal lineages fit a model where populations of new clonal lineages emerge via migration from a source population that is sexual in nature and potentially located in central Mexico or elsewhere. This work provides novel insights into patterns of emergence of clonal lineages in plant pathogen genomes.
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Affiliation(s)
- B J Knaus
- First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521
| | - J F Tabima
- First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521
| | - C E Davis
- First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521
| | - H S Judelson
- First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521
| | - N J Grünwald
- First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521
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23
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Grünwald NJ, McDonald BA, Milgroom MG. Population Genomics of Fungal and Oomycete Pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:323-46. [PMID: 27296138 DOI: 10.1146/annurev-phyto-080614-115913] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We are entering a new era in plant pathology in which whole-genome sequences of many individuals of a pathogen species are becoming readily available. Population genomics aims to discover genetic mechanisms underlying phenotypes associated with adaptive traits such as pathogenicity, virulence, fungicide resistance, and host specialization, as genome sequences or large numbers of single nucleotide polymorphisms become readily available from multiple individuals of the same species. This emerging field encompasses detailed genetic analyses of natural populations, comparative genomic analyses of closely related species, identification of genes under selection, and linkage analyses involving association studies in natural populations or segregating populations resulting from crosses. The era of pathogen population genomics will provide new opportunities and challenges, requiring new computational and analytical tools. This review focuses on conceptual and methodological issues as well as the approaches to answering questions in population genomics. The major steps start with defining relevant biological and evolutionary questions, followed by sampling, genotyping, and phenotyping, and ending in analytical methods and interpretations. We provide examples of recent applications of population genomics to fungal and oomycete plant pathogens.
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Affiliation(s)
- Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330;
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853;
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland;
| | - Michael G Milgroom
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853;
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24
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Martin MD, Vieira FG, Ho SYW, Wales N, Schubert M, Seguin-Orlando A, Ristaino JB, Gilbert MTP. Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans. Mol Biol Evol 2016; 33:478-91. [PMID: 26576850 PMCID: PMC4866541 DOI: 10.1093/molbev/msv241] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed, as does the New World center of origin of the species itself. Both Mexico and South America have been proposed, generating considerable controversy. Here, we readdress the pathogen's origins using a genomic data set encompassing 71 globally sourced modern and historical samples of P. infestans and the hybrid species P. andina, a close relative known only from the Andean highlands. Previous studies have suggested that the nuclear DNA lineage behind the initial outbreaks in Europe in 1845 is now extinct. Analysis of P. andina's phased haplotypes recovered eight haploid genome sequences, four of which represent a previously unknown basal lineage of P. infestans closely related to the famine-era lineage. Our analyses further reveal that clonal lineages of both P. andina and historical P. infestans diverged earlier than modern Mexican lineages, casting doubt on recent claims of a Mexican center of origin. Finally, we use haplotype phasing to demonstrate that basal branches of the clade comprising Mexican samples are occupied by clonal isolates collected from wild Solanum hosts, suggesting that modern Mexican P. infestans diversified on Solanum tuberosum after a host jump from a wild species and that the origins of P. infestans are more complex than was previously thought.
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Affiliation(s)
- Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Department of Integrative Biology, Center for Theoretical Evolutionary Genomics, University of California, Berkeley
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jean B Ristaino
- Department of Plant Pathology, North Carolina State University
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
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25
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Lassiter ES, Russ C, Nusbaum C, Zeng Q, Saville AC, Olarte RA, Carbone I, Hu CH, Seguin-Orlando A, Samaniego JA, Thorne JL, Ristaino JB. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species. Curr Genet 2015; 61:567-77. [PMID: 25754775 PMCID: PMC4659649 DOI: 10.1007/s00294-015-0480-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 01/24/2023]
Abstract
Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.
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Affiliation(s)
- Erica S Lassiter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | | | | | - Amanda C Saville
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Rodrigo A Olarte
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ignazio Carbone
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Chia-Hui Hu
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jose A Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jeffrey L Thorne
- Department of Biological Sciences and Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
| | - Jean B Ristaino
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
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26
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Abstract
Trade in plant and plant products has profoundly affected the global distribution and diversity of plant pathogens. Identification of migration pathways can be used to monitor or manage pathogen movement for proactive disease management or quarantine measures. Genomics-based genetic marker discovery is allowing unprecedented collection of population genetic data for plant pathogens. These data can be used for detailed analysis of the ancestry of population samples and therefore for analysis of migration. Reconstruction of migration histories has confirmed previous hypotheses based on observational data and led to unexpected new findings on the origins of pathogens and source populations for past and recent migration. The choice of software for analysis depends on the type of migration being studied and the reproductive mode of the pathogen. Biased sampling and complex population structures are potential challenges to accurate inference of migration pathways.
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Affiliation(s)
- Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611;
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27
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Kamoun S, Furzer O, Jones JDG, Judelson HS, Ali GS, Dalio RJD, Roy SG, Schena L, Zambounis A, Panabières F, Cahill D, Ruocco M, Figueiredo A, Chen XR, Hulvey J, Stam R, Lamour K, Gijzen M, Tyler BM, Grünwald NJ, Mukhtar MS, Tomé DFA, Tör M, Van Den Ackerveken G, McDowell J, Daayf F, Fry WE, Lindqvist-Kreuze H, Meijer HJG, Petre B, Ristaino J, Yoshida K, Birch PRJ, Govers F. The Top 10 oomycete pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2015; 16:413-34. [PMID: 25178392 PMCID: PMC6638381 DOI: 10.1111/mpp.12190] [Citation(s) in RCA: 464] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.
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Affiliation(s)
- Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L. Ancient genomics. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130387. [PMID: 25487338 PMCID: PMC4275894 DOI: 10.1098/rstb.2013.0387] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ross Barnett
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Fernández
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Yoshida K, Sasaki E, Kamoun S. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:771. [PMID: 26442080 PMCID: PMC4585160 DOI: 10.3389/fpls.2015.00771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/07/2015] [Indexed: 05/20/2023]
Abstract
The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.
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Affiliation(s)
- Kentaro Yoshida
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe UniversityKobe, Japan
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
- *Correspondence: Kentaro Yoshida, Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-Ku, Kobe, Japan,
| | - Eriko Sasaki
- Gregor Mendel Institute, Austrian Academy of Sciences, ViennaAustria
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
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Ho SYW. The changing face of the molecular evolutionary clock. Trends Ecol Evol 2014; 29:496-503. [PMID: 25086668 DOI: 10.1016/j.tree.2014.07.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/03/2014] [Accepted: 07/08/2014] [Indexed: 11/30/2022]
Abstract
The molecular clock has played an important role in biological research, both as a description of the evolutionary process and as a tool for inferring evolutionary timescales. Genomic data have provided valuable insights into the molecular clock, allowing the patterns and causes of evolutionary rate variation to be characterized in increasing detail. I explain how genome sequences offer exciting opportunities for estimating the timescale of the Tree of Life. I describe the different approaches that have been used to deal with the computational and statistical challenges encountered in molecular clock analyses of genomic data. Finally, I offer a perspective on the future of molecular clocks, highlighting some of the key limitations and the most promising research directions.
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Affiliation(s)
- Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.
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