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Field in science
Ancient pathogen genomics is a scientific field related to the study of pathogen genomes recovered from ancient human, plant or animal remains. Ancient
Ancient_pathogen_genomics
Method of archaeological study
Mark G. Thomas Eske Willerslev Carles Lalueza-Fox Turi King Ancient pathogen genomics Ancient protein Archaeogenetics Environmental DNA (eDNA) List of DNA
Ancient_DNA
Study of the past through preserved genetic material
Ancestral reconstruction Ancestral sequence reconstruction Ancient DNA Ancient pathogen genomics Archaeogenetics Molecular clock Paleobiochemistry Paleogenomics
Paleogenetics
Study of ancient DNA
provides clues about early human culture. Alu sequence Ancient DNA Ancient pathogen genomics DNA extraction DNA sequencing Genealogical DNA test Genetic
Archaeogenetics
Genus of fungi
and Genomics. Caister Academic Press. ISBN 978-1-904455-53-0. Geiser DM (2009). "Sexual structures in Aspergillus: morphology, importance and genomics".
Aspergillus
Reconstruction of genomes of extinct species
of Ancient DNA and Population and Evolutionary Genomic Inferences. In: Population Genomics, Springer, Cham. pp 1-38. Pääbo, S. (1989-03-01). "Ancient DNA:
Paleogenomics
previously extinct and deadly pathogens in order to better understand virulence. During the earlier times when genomics was being studied, scientists
Pathogenomics
Species of flowering plant
Pseudoperonospora cubensis, a plant pathogen that causes cucurbit downy mildew. It is also susceptible to infection by another plant pathogen, Podosphaera xanthii,
Melothria_scabra
Species of flowering plant with edible seeds
breeding cold-resistant varieties, is always linked with pathogen-resistance breeding as pathogens such as Ascochyta rabiei and F. o. f.sp. ciceris flourish
Chickpea
Species of single-celled organism
Solanaceae family, such as the potato (Solanum tuberosum) and the tomato. The pathogen favors moist, cool environments: sporulation is optimal at 12–18 °C (54–64 °F)
Phytophthora_infestans
16th century epidemics in New Spain
Om P., eds. (2019). Paleogenomics: Genome-Scale Analysis of Ancient DNA. Population Genomics. Springer International Publishing. ISBN 978-3-030-04752-8
Cocoliztli_epidemics
Family of viruses in the order Mononegavirales
LM, Garry RF (3 December 2018). "Bas-Congo virus - not an established pathogen". Archived from the original on 30 January 2020. Retrieved 30 January 2020
Rhabdoviridae
Species of fungus
strain CBS 554.65 reveals the MAT1-2 locus of Aspergillus niger". BMC Genomics. 22 (1) 679. doi:10.1186/s12864-021-07990-8. PMC 8454179. PMID 34548025
Aspergillus_niger
Danish evolutionary geneticist
team has been the first to conduct large scale genome sequencing of ancient pathogens. In 2015 they showed that plague was a likely driver of Bronze Age
Eske_Willerslev
Abnormal development of floral parts into leafy structures
A.; Šeruga Musić, M. (2010). "Phytoplasma Genomics, from Sequencing to Comparative and Functional Genomics – What Have We Learnt?". In Weintraub, P.G
Phyllody
Fungus that can act as a parasite of insects
evolved into highly specific pathogens of insects. The term entomopathogenic comes from the combination of the Ancient Greek word ἔντομον (éntomon) and
Entomopathogenic_fungus
Genus of bacteria
the mouth, skin, intestine, and upper respiratory tract. Some exist as pathogens and cause infections collectively known as streptococcosis, such as streptococcal
Streptococcus
Occurs when a reservoir population causes an epidemic in a novel host population
Spillover infection, also known as pathogen spillover and spillover event, occurs when a reservoir population with a high pathogen prevalence comes into contact
Spillover_infection
Species of fungus
of their phylogenetic positions and their specific interest as human pathogens, or as industrially or environmentally important yeasts. This work, which
Kluyveromyces_lactis
Canadian physical anthropologist
million people in 14th century Europe. The team also determined that the ancient pathogen is the predecessor of all modern variants of plague and the medieval
Kirsten_Bos
South Asia Genome Genome map Genome project Genome screen Genomic library Genomic sequence Genomics Genophore Genotype Germ cell Germ line Germ-line theory
Index_of_genetics_articles
All genetic material of an organism
chloroplasts with a chloroplast genome. The study of the genome is called genomics. The genomes of many organisms have been sequenced and various regions
Genome
necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus". BMC Genomics. 13 646. doi:10.1186/1471-2164-13-646. PMC 3532085. PMID 23171342
List of sequenced fungi genomes
List_of_sequenced_fungi_genomes
Species of bacterium
a P1+ pathogen by first identifying as a saprophyte, then as a P2-like pathogen, next into a P-1-like pathogen, then finally as a P1+ pathogen. P1+ pathogens
Leptospira_interrogans
Viruses can become part of the DNA of those they infect
"Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus". BMC Genomics. 18
Endogenization
Disease bacteria of tomato family, others
of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence". BMC Genomics. 11 (1): 379. doi:10
Ralstonia_solanacearum
Invasion of an organism's body by pathogenic agents
An infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they
Infection
Genus of parasitic flagellate protist in the Kinetoplastea class
Robert J.; Thomson, James D. (2006-05-01). "Plight of the bumble bee: Pathogen spillover from commercial to wild populations". Biological Conservation
Crithidia
Species of fungus
Vries, Ronald P. de; Dyer, Paul S. (2011-08-18). "Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea".
Botrytis_cinerea
Rapid spread of disease affecting a large number of people in a short time
genetic change in the pathogen reservoir or the introduction of an emerging pathogen to a host population (by movement of pathogen or host). Generally,
Epidemic
differentiation. Mycoplasma genitalium, minimal organism and human STD pathogen. Aliivibrio fischeri, quorum sensing, bioluminescence and animal-bacterial
List_of_model_organisms
Africans relate to diet, physiology, and evolutionary pressures from pathogens. Throughout Sub-Saharan Africa, genetic adaptation (e.g., rs334 mutation
History_of_West_Africa
Process by which a genome changes in structure or size over time
of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics. Genome evolution is a constantly
Genome_evolution
Open-Source Workflow Management Platform
for various applications and analyses in the genomics field. One notable use case is its role in pathogen surveillance during the COVID-19 pandemic. Swift
Nextflow
Archaeogenetic name for an ancestral genetic component
Underhill PA, Sánchez-Quinto F, et al. (May 2014). "Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry
Western_hunter-gatherer
Species of bacterium
Rodrigue N, Kassen R (September 2012). "Genomics of adaptation during experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa". PLOS Genetics
Pseudomonas_aeruginosa
Method of removing pollutants
Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-17-2. Meyer A, Panke S (2008). "Genomics in Metabolic Engineering
Microbial_biodegradation
Prize of the Microbiology Society
in bacteria: ancient and modern 2018 Geoffrey L Smith FRS, Vaccinia virus: a portrait of a poxvirus 2019 Gordon Dougan, Putting Genomics into Action 2021
Marjory_Stephenson_Prize
Species of bacterium
such as Pseudomonas aeruginosa, for example, which is an opportunistic pathogen. Based on 16S rRNA analysis, P. putida was taxonomically confirmed to be
Pseudomonas_putida
Species of fungus
a wheat plant pathogen causing septoria leaf blotch that is difficult to control due to resistance to multiple fungicides. The pathogen today causes one
Zymoseptoria_tritici
Genus of bacteria
PMID 29673200. Ventura, M.; et al. (2007). "Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum". Microbiology and Molecular Biology
Corynebacterium
Genus of parasitic flagellate protist
macrophage will ingest a pathogen within an enclosed endosome and then fill this endosome with enzymes which digest the pathogen. However, in the case of
Leishmania
Genus of Gram-positive bacteria
Staphylococcus, from Ancient Greek σταφυλή (staphulḗ), meaning "bunch of grapes", and κόκκος (kókkos), meaning "kernel" or "Kermes", is a genus of Gram-positive
Staphylococcus
Biological system protecting an organism against disease
organism from diseases. It detects and responds to a wide variety of pathogens, such as viruses, bacteria, and parasites, as well as cancer cells and
Immune_system
The history of Central Africa has been divided into its prehistory, its ancient history, the major polities flourishing, the colonial period, and the post-colonial
History_of_Central_Africa
inherited, and how their transcription levels vary to defend against pathogens like viruses and bacteria. The resistome was first used to describe the
Resistome
Species of bacterium
indica (VI), and enterica (I). A number of its serovars are serious human pathogens; many of them are (more specifically) serovars of Salmonella enterica
Salmonella_enterica
Overview of human–microbe interactions
(2004). "Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics". J. Biochem. Mol. Biol. 37 (1): 93–106
Human interactions with microbes
Human_interactions_with_microbes
Jennifer A.; Kleiman, Norman J.; Breen, Matthew (2024-11-17). "Contrasting pathogen prevalence between tick and dog populations at Chornobyl". Parasites &
Dogs in the Chernobyl exclusion zone
Dogs_in_the_Chernobyl_exclusion_zone
Subsystem of the immune system
is composed of specialized cells, organs, and processes that eliminate pathogens specifically. The acquired immune system is one of the two main immunity
Adaptive_immune_system
Genus of fungi
forest pathogens in Phaeolus (Polyporales, Basidiomycota) on Chinese coniferous trees were confirmed by molecular phylogeny". Evolutionary and Genomic Microbiology
Phaeolus
Scientific endeavours to determine the complete genome sequence of an organism
Wayback Machine An Echinoderm genomic database, (previous SpBase, a sea urchin genome database) NRCPB. Global Invertebrate Genomics Alliance (GIGA) Archived
Genome_project
been revolutionized by recent genomic and phylogenetic research. Current evidence suggests that tuberculosis is an ancient human disease that co-evolved
History_of_tuberculosis
Family of viruses in the order Mononegavirales
(2024). "Genomic transfers help to decipher the ancient evolution of filoviruses and interactions with vertebrate hosts". PLOS Pathogens. 20 (9) e1011864
Filoviridae
British microbiologist (born 1960)
"Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients". Microbial Genomics. 5 (9). doi:10.1099/mgen.0.000293
Mark_Pallen
at the genome level provides new insights into the pathogenesis of the pathogen. In industrialized nations, water sanitation and food handling improvements
History_of_typhoid_fever
American academic
PMID 23175615. Flurry, Alan (2015-01-12). "$23.4M contract to bolster pathogen genomics database". UGA Today. Retrieved 2019-08-02. "New open-access data
Jessica_Kissinger
Genus of viruses
Sergentomyia, and contain the prominent species that transmit the viral pathogens. The third genus was found in the New World and is called Lutzomyia. Other
Phlebovirus
Selective breeding of plants and animals to serve humans
Greger; Orlando, Ludovic (2020). "Animal domestication in the era of ancient genomics". Nature Reviews Genetics. 21 (8): 449–460. doi:10.1038/s41576-020-0225-0
Domestication
Genus of bacteria
("anaerobically") when oxygen is not available. Salmonella species are intracellular pathogens, of which certain serotypes cause illness such as salmonellosis. Most
Salmonella
Spanish biologist and researcher
"Ancient DNA reveals clues about how tuberculosis shaped the human immune system". EurekAlert!. 4 March 2021. Retrieved 5 October 2021. "Pathogens, the
Lluís_Quintana-Murci
Species of plant
Bin (2022). "Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics". Molecular Plant. 15 (4). Cell Press:
Oryza_sativa
Africans relate to diet, physiology, and evolutionary pressures from pathogens. Neolithic agriculturalists, who may have resided in Northeast Africa
Genetic_history_of_Africa
nonpathogenic strain was experimentally converted into a pathogen and could have contributed to pathogen adaption in large genome portions. Fusarium graminearum
Plant–fungus horizontal gene transfer
Plant–fungus_horizontal_gene_transfer
Bacterium that causes tuberculosis
et al. (September 2005). "Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis". PLOS Pathogens. 1 (1) e5. doi:10.1371/journal
Mycobacterium_tuberculosis
disease load of the tropics and so were more able to cope with novel pathogens, and partly because the higher numbers of Homo sapiens meant that even
Neanderthal_extinction
Christina; Colombi, Elena; McCann, Honour C. (2021). "Population Genomics of Bacterial Plant Pathogens". Phytopathology. 111 (1): 23–31. Bibcode:2021PhPat.111
Agriculture_in_California
Widespread human mitochondrial DNA grouping indicating common ancestry
Pre-Ptolemaic/late New Kingdom and Ptolemaic periods. The Ancient Egyptian mummies bore Near eastern genomic component most closely related to modern near easterners
Haplogroup_L3
Type of white blood cell
D: Genomic and Proteomics. 1(3), 283-291. DOI: 10.1016/j.cbd.2006.05.002 Hickey MJ, Kubes P (May 2009). "Intravascular immunity: the host-pathogen encounter
Neutrophil
Treponema. Tannerella forsythia being the most prevalent human oral pathogen found in ancient dental calculus up to date. Tannerella forsythia is an anaerobic
Evolution of the human oral microbiome
Evolution_of_the_human_oral_microbiome
West African genetic history
with certainty. As of 2017, human ancient DNA has not been found in the region of West Africa. As of 2020, human ancient DNA has not been forthcoming in
Genetic history of West Africa
Genetic_history_of_West_Africa
Species of virus affecting humans and animals
Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes". PLOS Pathogens. 6 (7) e1001030. doi:10.1371/journal
Zaire_ebolavirus
Theory of early hominid migration
diversification, and admixture in Asia". Human Population Genetics and Genomics 0001: 1–32. doi:10.47248/hpgg2202010001. Genetics and material culture
Recent African origin of modern humans
Recent_African_origin_of_modern_humans
American academic
Malaria Box Compound Collection for Neglected Diseases and Beyond". PLOS Pathogens. 12 (7) e1005763. doi:10.1371/journal.ppat.1005763. PMC 4965013. PMID 27467575
S._Joshua_Swamidass
Unclassified/poorly understood genetics
non-coding RNA produced by known organisms. Much of the genomic dark matter is thought to originate from ancient transposable elements and from other low-complexity
Biological_dark_matter
Citrus fruit
vector-transmitted citrus greening disease, where the vector is a psyllid bug, and the pathogen is a bacterium, Liberibacter. The fruit fly Anastrepha suspensa, a serious
Grapefruit
Soil fungus that can cause disease
intracellular pathogen that can utilize host phagocytes to spread within the body. C. neoformans was the first intracellular pathogen for which the non-lytic
Cryptococcus_neoformans
Cereal grass and grain
M. S.; et al. (2022). "Breeding oat for resistance to the crown rust pathogen Puccinia coronata f. sp. avenae: achievements and prospects". Theoretical
Oat
Organization and management of preventive measures against pandemics
practical actions "better surveillance of pathogen spillover and development of global databases of virus genomics and serology, better management of wildlife
Pandemic_prevention
archaeological evidence for migrations in the ancient Mediterranean, and the genetics and historical impact of ancient pathogens. "Inauguration of the Max Planck-Harvard
Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
Max_Planck_Harvard_Research_Center_for_the_Archaeoscience_of_the_Ancient_Mediterranean
Africans relate to diet, physiology, and evolutionary pressures from pathogens. Throughout Sub-Saharan Africa, genetic adaptation (e.g., rs334 mutation
History_of_East_Africa
Species of bacterium
sequences of the order Fusobacteriales. Its genus name comes from the Ancient Greek word στρεπτός : streptós for "curved" or "twisted", and the Latin
Streptobacillus_moniliformis
The history of Southern Africa has been divided into its prehistory, its ancient history, the major polities flourishing, the colonial period, and the post-colonial
History_of_Southern_Africa
Species of fungus
diversity in Blumeria graminis of cereals and its implications for host-pathogen co-evolution". Molecular Plant Pathology. 4 (3): 187–198. doi:10.1046/j
Blumeria_graminis
Disease in dogs and other canines
living as a unicellular, asexually reproducing (but sexually transmitted) pathogen. Sequence analysis of the genome suggests it diverged over 6,000 years
Canine transmissible venereal tumor
Canine_transmissible_venereal_tumor
Species of mosquito
Aedes aegypti (/ˈiːdiːz eɪˈdʒɪpti/; US: /eɪdz -, ˈeɪdiːz -/; from Ancient Greek αηδής (aēdḗs) 'unpleasant' and Latin aegyptī 'Egyptian') – sometimes called
Aedes_aegypti
Family of flowering plants
parts of the world. Their importance lies in the fact that they can host pathogens or diseases of the cultivated plants, therefore their presence increases
Solanaceae
Phylum of bacteria
KF, van Sinderen D (September 2007). "Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum". Microbiology and Molecular Biology
Actinomycetota
Species of grain
that can reduce production. Sorghum is subject to a variety of plant pathogens. The fungus Colletotrichum sublineolum causes anthracnose. The toxic ergot
Sorghum
Genome resulting from the mating of closely related species
fungal individuals led to the recent emergence of a unique widespread pathogen species". Proceedings of the National Academy of Sciences of the United
Eukaryote_hybrid_genome
Theory that viruses predate cellular life
proposed in 2012 hypothesizes that ancient cells coexisted with ancient virocells and that modern-day viruses evolved by genomic reduction. Their phylogenomic
Virus_world_hypothesis
Inherited retrovirus encoded in an organism's genome
1236–1241. doi:10.1126/science.285.5431.1236. PMID 10455044. "Genomics England › Integrated Pathogens and Mobile Elements GeCIP Domain". Archived from the original
Endogenous_retrovirus
Condition where cells have more than two sets of chromosomes
Y (2003). "Investigating ancient duplication events in the Arabidopsis genome". Journal of Structural and Functional Genomics. 3 (1–4): 117–129. doi:10
Polyploidy
Disease caused by the bacteria Salmonella typhi
Salmonella typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types". Frontiers
Typhoid_fever
Eukaryotes other than animals, plants or fungi
et al. (2022). "Txikispora philomaios n. sp., n. g., a micro-eukaryotic pathogen of amphipods, reveals parasitism and hidden diversity in Class Filasterea"
Protist
541–549 AD in the Byzantine Empire, later northern Europe
from the 6th Century AD Reveals Insights into Justinianic Plague". PLOS Pathogens. 9 (5) e1003349. doi:10.1371/journal.ppat.1003349. PMC 3642051. PMID 23658525
Plague_of_Justinian
Applied science devoted to the study of food
Biology: From Genomics to Probiotics. Caister Academic Press. ISBN 978-1-904455-41-7. Mayo, B (2010). van Sinderen, D (ed.). Bifidobacteria: Genomics and Molecular
Food_science
David J. (June 2021). "Peopling of the Americas as inferred from ancient genomics". Nature. 594 (7863): 356–364. Bibcode:2021Natur.594..356W. doi:10
Indigenous peoples of the Americas
Indigenous_peoples_of_the_Americas
Family of cell surface receptors
germline-encoded host sensors, which detect molecules typical for the pathogens. They are proteins expressed mainly by cells of the innate immune system
Pattern_recognition_receptor
Study of fungi
majority of plant pathogens are fungi. A biologist specializing in mycology is called a mycologist. The word mycology comes from the Ancient Greek: μύκης (mukēs)
Mycology
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ANCIENT PATHOGEN-GENOMICS
ANCIENT PATHOGEN-GENOMICS
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ANCIENT PATHOGEN-GENOMICS
ANCIENT PATHOGEN-GENOMICS
ANCIENT PATHOGEN-GENOMICS
ANCIENT PATHOGEN-GENOMICS
ANCIENT PATHOGEN-GENOMICS
ANCIENT PATHOGEN-GENOMICS
ANCIENT PATHOGEN-GENOMICS
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