Comparative Genomics and Gene Pool Analysis Reveal the Decrease of Genome Diversity and Gene Number in Rice Blast Fungi by Stable Adaption with Rice

Magnaporthe oryzae caused huge losses in rice and wheat production worldwide. Comparing to long-term co-evolution history with rice, wheat-infecting isolates were new-emerging. To reveal the genetic differences between rice and wheat blast on global genomic scale, 109 whole-genome sequences of M. oryzae from rice, wheat, and other hosts were reanalyzed in this study. We found that the rice lineage had gone through stronger selective sweep and fewer conserved genes than those of Triticum and Lolium lineages, which indicated that rice blast fungi adapted to rice by gene loss and rapid evolution of specific loci. Furthermore, 228 genes associated with host adaptation of M. oryzae were found by presence/absence variation (PAV) analyses. The functional annotation of these genes found that the fine turning of genes gain/loss involved with transport and transcription factor, thiol metabolism, and nucleotide metabolism respectively are major mechanisms for rice adaption. This result implies that genetic base of specific host plant may lead to gene gain/loss variation of pathogens, so as to enhance their adaptability to host. Further characterization of these specific loci and their roles in adaption and evaluation of the fungi may eventually lead to understanding of interaction mechanism and develop new strategies of the disease management.

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The Vertebrate TLR Supergene Family Evolved Dynamically by Gene Gain/Loss and Positive Selection Revealing a Host–Pathogen Arms Race in Birds

Diversity ◽

10.3390/d11080131 ◽

2019 ◽

Vol 11 (8) ◽

pp. 131 ◽

Cited By ~ 4

Author(s):

Imran Khan ◽

Emanuel Maldonado ◽

Liliana Silva ◽

Daniela Almeida ◽

Warren E. Johnson ◽

...

Keyword(s):

Positive Selection ◽

Rapid Evolution ◽

Immune Defense ◽

Arms Race ◽

Gene Gain ◽

Toll Like Receptor ◽

Viral Pathogens ◽

Host Pathogen ◽

Gain Loss ◽

Supergene Family

The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 reptiles, 1 amphibian, and 11 fishes) revealed differential gain/loss of 26 TLRs, including 6 (TLR3, TLR7, TLR8, TLR14, TLR21, and TLR22) that originated early in vertebrate evolution before the diversification of Agnatha and Gnathostomata. Subsequent dynamic gene gain/loss led to lineage-specific diversification with TLR repertoires ranging from 8 subfamilies in birds to 20 in fishes. Lineage-specific loss of TLR8-9 and TLR13 in birds and gains of TLR6 and TLR10-12 in mammals and TLR19-20 and TLR23-27 in fishes. Among avian species, 5–10% of the sites were under positive selection (PS) (omega 1.5–2.5) with radical amino-acid changes likely affecting TLR structure/functionality. In non-viral TLR4 the 20 PS sites (posterior probability PP > 0.99) likely increased ability to cope with diversified ligands (e.g., lipopolysaccharide and lipoteichoic). For viral TLR7, 23 PS sites (PP > 0.99) possibly improved recognition of highly variable viral ssRNAs. Rapid evolution of the TLR supergene family reflects the host–pathogen arms race and the coevolution of ligands/receptors, which follows the premise that birds have been important vectors of zoonotic pathogens and reservoirs for viruses.

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Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1810625115 ◽

2018 ◽

Vol 115 (48) ◽

pp. 12277-12282 ◽

Cited By ~ 18

Author(s):

Batbileg Bor ◽

Jeffrey S. McLean ◽

Kevin R. Foster ◽

Lujia Cen ◽

Thao T. To ◽

...

Keyword(s):

Host Cell ◽

Rapid Evolution ◽

Host Population ◽

Host Cells ◽

Host Susceptibility ◽

Bacterial Host ◽

Narrow Host Range ◽

Stable Relationship ◽

Candidate Phyla Radiation

Around one-quarter of bacterial diversity comprises a single radiation with reduced genomes, known collectively as the Candidate Phyla Radiation. Recently, we coisolated TM7x, an ultrasmall strain of the Candidate Phyla Radiation phylum Saccharibacteria, with its bacterial host Actinomyces odontolyticus strain XH001 from human oral cavity and stably maintained as a coculture. Our current work demonstrates that within the coculture, TM7x cells establish a long-term parasitic association with host cells by infecting only a subset of the population, which stay viable yet exhibit severely inhibited cell division. In contrast, exposure of a naïve A. odontolyticus isolate, XH001n, to TM7x cells leads to high numbers of TM7x cells binding to each host cell, massive host cell death, and a host population crash. However, further passaging reveals that XH001n becomes less susceptible to TM7x over time and enters a long-term stable relationship similar to that of XH001. We show that this reduced susceptibility is driven by rapid host evolution that, in contrast to many forms of phage resistance, offers only partial protection. The result is a stalemate where infected hosts cannot shed their parasites; nevertheless, parasite load is sufficiently low that the host population persists. Finally, we show that TM7x can infect and form stable long-term relationships with other species in a single clade of Actinomyces, displaying a narrow host range. This system serves as a model to understand how parasitic bacteria with reduced genomes such as those of the Candidate Phyla Radiation have persisted with their hosts and ultimately expanded in their diversity.

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Host defense mechanisms induce genome instability leading to rapid evolution in an opportunistic fungal pathogen

Infection and Immunity ◽

10.1128/iai.00328-21 ◽

2021 ◽

Author(s):

Amanda Smith ◽

Levi Morran ◽

Meleah A. Hickman

Keyword(s):

Fungal Pathogen ◽

Defense Mechanisms ◽

Large Scale ◽

Genome Instability ◽

Rapid Evolution ◽

Genomic Changes ◽

Opportunistic Fungal Pathogen ◽

Immunocompromised Hosts ◽

Stressful Environments

The ability to generate genetic variation facilitates rapid adaptation in stressful environments. The opportunistic fungal pathogen Candida albicans frequently undergoes large-scale genomic changes, including aneuploidy and loss-of heterozygosity (LOH), following exposure to host environments. However, the specific host factors inducing C. albicans genome instability remain largely unknown. Here, we leveraged the genetic tractability of nematode hosts to investigate whether innate immune components, including antimicrobial peptides (AMPs) and reactive oxygen species (ROS), induced host-associated C. albicans genome instability. C. albicans associated with immunocompetent hosts carried multiple large-scale genomic changes including LOH, whole chromosome, and segmental aneuploidies. In contrast, C. albicans associated with immunocompromised hosts deficient in AMPs or ROS production had reduced LOH frequencies and fewer, if any, additional genomic changes. To evaluate if extensive host-induced genomic changes had long-term consequences for C. albicans adaptation, we experimentally evolved C. albicans in either immunocompetent or immunocompromised hosts and selected for increased virulence. C. albicans evolved in immunocompetent hosts rapidly increased virulence, but not in immunocompromised hosts. Taken together, this work suggests that host-produced ROS and AMPs induces genotypic plasticity in C. albicans which facilitates rapid evolution.

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Rapid Evolution by Positive Selection and Gene Gain and Loss: PLA2 Venom Genes in Closely Related Sistrurus Rattlesnakes with Divergent Diets

Journal of Molecular Evolution ◽

10.1007/s00239-008-9067-7 ◽

2008 ◽

Vol 66 (2) ◽

pp. 151-166 ◽

Cited By ~ 74

Author(s):

H. Lisle Gibbs ◽

Wayne Rossiter

Keyword(s):

Positive Selection ◽

Rapid Evolution ◽

Gene Gain ◽

Gain And Loss

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Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae

BMC Genetics ◽

10.1186/1471-2156-15-45 ◽

2014 ◽

Vol 15 (1) ◽

pp. 45 ◽

Cited By ~ 59

Author(s):

Ju Huang ◽

Weina Si ◽

Qiming Deng ◽

Ping Li ◽

Sihai Yang

Keyword(s):

Magnaporthe Oryzae ◽

Rice Blast ◽

Rapid Evolution ◽

Rice Blast Fungus ◽

Avirulence Genes ◽

Blast Fungus

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Life and Death of Selfish Genes: Comparative Genomics Reveals the Dynamic Evolution of Cytoplasmic Incompatibility

Molecular Biology and Evolution ◽

10.1093/molbev/msaa209 ◽

2020 ◽

Vol 38 (1) ◽

pp. 2-15 ◽

Cited By ~ 3

Author(s):

Julien Martinez ◽

Lisa Klasson ◽

John J Welch ◽

Francis M Jiggins

Keyword(s):

Cytoplasmic Incompatibility ◽

Gene Gain ◽

Evolutionary Models ◽

Loss Of Function ◽

Genome Sequences ◽

Life And Death ◽

Selfish Genes ◽

Wolbachia Genome ◽

The Cross ◽

Gain Loss

Abstract Cytoplasmic incompatibility is a selfish reproductive manipulation induced by the endosymbiont Wolbachia in arthropods. In males Wolbachia modifies sperm, leading to embryonic mortality in crosses with Wolbachia-free females. In females, Wolbachia rescues the cross and allows development to proceed normally. This provides a reproductive advantage to infected females, allowing the maternally transmitted symbiont to spread rapidly through host populations. We identified homologs of the genes underlying this phenotype, cifA and cifB, in 52 of 71 new and published Wolbachia genome sequences. They are strongly associated with cytoplasmic incompatibility. There are up to seven copies of the genes in each genome, and phylogenetic analysis shows that Wolbachia frequently acquires new copies due to pervasive horizontal transfer between strains. In many cases, the genes have subsequently acquired loss-of-function mutations to become pseudogenes. As predicted by theory, this tends to occur first in cifB, whose sole function is to modify sperm, and then in cifA, which is required to rescue the cross in females. Although cif genes recombine, recombination is largely restricted to closely related homologs. This is predicted under a model of coevolution between sperm modification and embryonic rescue, where recombination between distantly related pairs of genes would create a self-incompatible strain. Together, these patterns of gene gain, loss, and recombination support evolutionary models of cytoplasmic incompatibility.

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A Genomic Survey of Signalling in the Myxococcaceae

Microorganisms ◽

10.3390/microorganisms8111739 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1739

Author(s):

David E. Whitworth ◽

Allison Zwarycz

Keyword(s):

Core Genome ◽

Gene Gain ◽

Fruiting Body Formation ◽

Two Component System ◽

Genome Sequences ◽

The Core ◽

Accessory Genes ◽

Two Component ◽

Gain Loss ◽

Core Genes

As prokaryotes diverge by evolution, essential ‘core’ genes required for conserved phenotypes are preferentially retained, while inessential ‘accessory’ genes are lost or diversify. We used the recently expanded number of myxobacterial genome sequences to investigate the conservation of their signalling proteins, focusing on two sister genera (Myxococcus and Corallococcus), and on a species within each genus (Myxococcus xanthus and Corallococcus exiguus). Four new C. exiguus genome sequences are also described here. Despite accessory genes accounting for substantial proportions of each myxobacterial genome, signalling proteins were found to be enriched in the core genome, with two-component system genes almost exclusively so. We also investigated the conservation of signalling proteins in three myxobacterial behaviours. The linear carotenogenesis pathway was entirely conserved, with no gene gain/loss observed. However, the modular fruiting body formation network was found to be evolutionarily plastic, with dispensable components in all modules (including components required for fruiting in the model myxobacterium M. xanthus DK1622). Quorum signalling (QS) is thought to be absent from most myxobacteria, however, they generally appear to be able to produce CAI-I (cholerae autoinducer-1), to sense other QS molecules, and to disrupt the QS of other organisms, potentially important abilities during predation of other prokaryotes.

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Metabolic depression and the evolution of hypoxia tolerance in threespine stickleback, Gasterosteus aculeatus

Biology Letters ◽

10.1098/rsbl.2017.0392 ◽

2017 ◽

Vol 13 (11) ◽

pp. 20170392 ◽

Cited By ~ 13

Author(s):

Matthew D. Regan ◽

Ivan S. Gill ◽

Jeffrey G. Richards

Keyword(s):

British Columbia ◽

Metabolic Rate ◽

Gasterosteus Aculeatus ◽

Rapid Evolution ◽

Agricultural Runoff ◽

Threespine Stickleback ◽

Hypoxia Tolerance ◽

Trout Lake ◽

Two Populations

Anthropogenic increases in global temperature and agricultural runoff are increasing the prevalence of aquatic hypoxia throughout the world. We investigated the potential for a relatively rapid evolution of hypoxia tolerance using two isolated (for less than 11 000 years) populations of threespine stickleback: one from a lake that experiences long-term hypoxia (Alta Lake, British Columbia) and one from a lake that does not (Trout Lake, British Columbia). Loss-of-equilibrium (LOE) experiments revealed that the Alta Lake stickleback were significantly more tolerant of hypoxia than the Trout Lake stickleback, and calorimetry experiments revealed that the enhanced tolerance of Alta Lake stickleback may be associated with their ability to depress metabolic rate (as indicated by metabolic heat production) by 33% in hypoxia. The two populations showed little variation in their capacities for O 2 extraction and anaerobic metabolism. These results reveal that intraspecific variation in hypoxia tolerance can develop over relatively short geological timescales, as can metabolic rate depression, a complex biochemical response that may be favoured in long-term hypoxic environments.

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