Dynamic Genomes - Mechanisms and consequences of genomic diversity impacting plant-fungal interactions

Physiological and Molecular Plant Pathology - Tập 125 - Trang 102006 - 2023
Jun Huang1, Sanzhen Liu1, David E. Cook1
1Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA

Tài liệu tham khảo

Eichler, 2019, Genetic variation, comparative genomics, and the diagnosis of disease, N. Engl. J. Med., 381, 64, 10.1056/NEJMra1809315 Preston, 2010, DNA replication fidelity and cancer, Semin. Cancer Biol., 20, 281, 10.1016/j.semcancer.2010.10.009 Nabel, 2012, The curious chemical biology of cytosine: deamination, Methylation,and oxidation as modulators of genomic potential, ACS Chem. Biol., 7, 20, 10.1021/cb2002895 Aramayo, 2013, Neurospora crassa, a model system for epigenetics research, Cold Spring Harbor Perspect. Biol., 5, a017921, 10.1101/cshperspect.a017921 Cheng, 1992, 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions, J. Biol. Chem., 267, 166, 10.1016/S0021-9258(18)48474-8 Floyd, 1989, Increased 8-hydroxyguanine content of chloroplast DNA from ozone-treated plants, Plant Physiol., 91, 644, 10.1104/pp.91.2.644 Møller, 2007, Oxidative modifications to cellular components in plants, Annu. Rev. Plant Biol., 58, 459, 10.1146/annurev.arplant.58.032806.103946 Kumar, 2020, The involvement of nucleotide excision repair proteins in the removal of oxidative DNA damage, Nucleic Acids Res., 48, 11227, 10.1093/nar/gkaa777 Lee, 2019, DNA oxidation and excision repair pathways, IJMS, 20, 6092, 10.3390/ijms20236092 Li, 2008, Mechanisms and functions of DNA mismatch repair, Cell Res., 18, 85, 10.1038/cr.2007.115 Chalissery, 2017, Repair of oxidative DNA damage in Saccharomyces cerevisiae, DNA Repair, 51, 2, 10.1016/j.dnarep.2016.12.010 Ene, 2018, Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen, Proc. Natl. Acad. Sci. U.S.A., 115, 10.1073/pnas.1806002115 Edwards, 2021, Accounting for the biological complexity of pathogenic fungi in phylogenetic dating, JoF, 7, 661, 10.3390/jof7080661 Wang, 2020, Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life, Genome Biol., 21, 142, 10.1186/s13059-020-02060-w Wang, 2022, Evasion of plant immunity by microbial pathogens, Nat. Rev. Microbiol., 20, 449, 10.1038/s41579-022-00710-3 Rovenich, 2014, Filamentous pathogen effector functions: of pathogens, hosts and microbiomes, Curr. Opin. Plant Biol., 20, 96, 10.1016/j.pbi.2014.05.001 Hatsugai, 2017, A plant effector-triggered immunity signaling sector is inhibited by pattern-triggered immunity, EMBO J., 36, 2758, 10.15252/embj.201796529 Ngou, 2021, Mutual potentiation of plant immunity by cell-surface and intracellular receptors, Nature, 592, 110, 10.1038/s41586-021-03315-7 Yuan, 2021, Pattern-recognition receptors are required for NLR-mediated plant immunity, Nature, 592, 105, 10.1038/s41586-021-03316-6 Cook, 2015, Understanding plant immunity as a surveillance system to detect invasion, Annu. Rev. Phytopathol., 53, 541, 10.1146/annurev-phyto-080614-120114 Jones, 2006, The plant immune system, Nature, 444, 323, 10.1038/nature05286 Li, 2009, The Magnaporthe oryzae avirulence gene AvrPiz-t encodes a predicted secreted protein that triggers the immunity in rice mediated by the blast resistance gene piz-t, MPMI (Mol. Plant-Microbe Interact.), 22, 411, 10.1094/MPMI-22-4-0411 Lin, 2022, Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii, Nat. Commun., 13, 3044, 10.1038/s41467-022-30784-9 Zhou, 2018, Loss of function of a rice TPR-domain RNA-binding protein confers broad-spectrum disease resistance, Proc. Natl. Acad. Sci. U.S.A., 115, 3174, 10.1073/pnas.1705927115 Priest, 2022, Uncontrolled transposition following RNAi loss causes hypermutation and antifungal drug resistance in clinical isolates of Cryptococcus neoformans, Nat. Microbiol., 7, 1239, 10.1038/s41564-022-01183-z Li, 2017, A natural allele of a transcription factor in rice confers broad-spectrum blast resistance, Cell, 170, 114, 10.1016/j.cell.2017.06.008 Mills, 2006, An initial map of insertion and deletion (INDEL) variation in the human genome, Genome Res., 16, 1182, 10.1101/gr.4565806 Alonge, 2020, Major impacts of widespread structural variation on gene expression and crop improvement in tomato, Cell, 182, 145, 10.1016/j.cell.2020.05.021 Ho, 2020, Structural variation in the sequencing era, Nat. Rev. Genet., 21, 171, 10.1038/s41576-019-0180-9 Aparicio, 2014, DNA double-strand break repair pathway choice and cancer, DNA Repair, 19, 169, 10.1016/j.dnarep.2014.03.014 Huang, 2022, The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens, FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Rev., 46 Shrivastav, 2008, Regulation of DNA double-strand break repair pathway choice, Cell Res., 18, 134, 10.1038/cr.2007.111 Chang, 2017, Non-homologous DNA end joining and alternative pathways to double-strand break repair, Nat. Rev. Mol. Cell Biol., 18, 495, 10.1038/nrm.2017.48 Bennett, 2020, INDEL detection, the ‘Achilles heel’ of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels, Nucleic Acids Res., 48, 10.1093/nar/gkaa975 Waterworth, 2007, NBS1 is involved in DNA repair and plays a synergistic role with ATM in mediating meiotic homologous recombination in plants: roles of NBS1 in meiosis and DNA repair, Plant J., 52, 41, 10.1111/j.1365-313X.2007.03220.x Koole, 2014, A Polymerase Theta-dependent repair pathway suppresses extensive genomic instability at endogenous G4 DNA sites, Nat. Commun., 5, 3216, 10.1038/ncomms4216 McVey, 2008, MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings, Trends Genet., 24, 529, 10.1016/j.tig.2008.08.007 Guyon-Debast, 2019, The XPF-ERCC1 complex is essential for genome stability and is involved in the mechanism of gene targeting in physcomitrella patens, Front. Plant Sci., 10, 588, 10.3389/fpls.2019.00588 Sfeir, 2015, Microhomology-mediated end joining: a back-up survival mechanism or dedicated pathway?, Trends Biochem. Sci., 40, 701, 10.1016/j.tibs.2015.08.006 Zhang, 2015, Function and evolution of Magnaporthe oryzae avirulence gene AvrPib responding to the rice blast resistance gene Pib, Sci. Rep., 5 Wang, 2014, Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew, Nat. Biotechnol., 32, 947, 10.1038/nbt.2969 Lu, 2020, A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew, Nat. Commun., 11, 680, 10.1038/s41467-020-14294-0 Kosugi, 2019, Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing, Genome Biol., 20, 117, 10.1186/s13059-019-1720-5 Kuzmin, 2022, Retention of duplicated genes in evolution, Trends Genet., 38, 59, 10.1016/j.tig.2021.06.016 Carvalho, 2016, Mechanisms underlying structural variant formation in genomic disorders, Nat. Rev. Genet., 17, 224, 10.1038/nrg.2015.25 Hoang, 2010, Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination, PLoS Genet., 6, 10.1371/journal.pgen.1001228 Hastings, 2009, Mechanisms of change in gene copy number, Nat. Rev. Genet., 10, 551, 10.1038/nrg2593 Kondrashov, 2002, Selection in the evolution of gene duplications, Genome Biol., 3, 10.1186/gb-2002-3-2-research0008 Ohno, 1970 Kuang, 2004, Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce[W], Plant Cell, 16, 2870, 10.1105/tpc.104.025502 Man, 2020, Structural evolution drives diversification of the large LRR-RLK gene family, New Phytol., 226, 1492, 10.1111/nph.16455 Steinbrenner, 2020, The evolving landscape of cell surface pattern recognition across plant immune networks, Curr. Opin. Plant Biol., 56, 135, 10.1016/j.pbi.2020.05.001 Prigozhin, 2021, Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites, Plant Cell, 33, 998, 10.1093/plcell/koab013 Wu, 2017, NLR network mediates immunity to diverse plant pathogens, Proc. Natl. Acad. Sci. U.S.A., 114, 8113, 10.1073/pnas.1702041114 van Wersch, 2019, Stronger when together: clustering of plant NLR disease resistance genes, Trends Plant Sci., 24, 688, 10.1016/j.tplants.2019.05.005 Liang, 2018, Receptor-like cytoplasmic kinases: central players in plant receptor kinase–mediated signaling, Annu. Rev. Plant Biol., 69, 267, 10.1146/annurev-arplant-042817-040540 Marchal, 2022, Show me your ID: NLR immune receptors with integrated domains in plants, Essays Biochem., 66, 527, 10.1042/EBC20210084 Sarris, 2015, A plant immune receptor detects pathogen effectors that target WRKY transcription factors, Cell, 161, 1089, 10.1016/j.cell.2015.04.024 Le Roux, 2015, A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity, Cell, 161, 1074, 10.1016/j.cell.2015.04.025 Barragan, 2021, Plant NLR diversity: the known unknowns of pan-NLRomes, Plant Cell, 33, 814, 10.1093/plcell/koaa002 Cesari, 2013, The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-pia and AVR1-CO39 by direct binding, Plant Cell, 25, 1463, 10.1105/tpc.112.107201 Krasileva, 2019, The role of transposable elements and DNA damage repair mechanisms in gene duplications and gene fusions in plant genomes, Curr. Opin. Plant Biol., 48, 18, 10.1016/j.pbi.2019.01.004 Cook, 2012, Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean, Science, 338, 1206, 10.1126/science.1228746 Cook, 2014, Distinct copy number, coding sequence, and locus methylation patterns underlie Rhg1 -mediated soybean resistance to soybean cyst nematode, Plant Physiol., 165, 630, 10.1104/pp.114.235952 Hu, 2018, Analysis of extreme phenotype bulk copy number variation (XP-CNV) identified the association of rp1 with resistance to Goss's wilt of maize, Front. Plant Sci., 9, 10.3389/fpls.2018.00110 Bradeen, 2009, Higher copy numbers of the potato RB transgene correspond to enhanced transcript and late blight resistance levels, MPMI (Mol. Plant-Microbe Interact.), 22, 437, 10.1094/MPMI-22-4-0437 Seidl, 2017, Transposable elements direct the coevolution between plants and microbes, Trends Genet., 33, 842, 10.1016/j.tig.2017.07.003 Möller, 2017, Evolution and genome architecture in fungal plant pathogens, Nat. Rev. Microbiol., 15, 756, 10.1038/nrmicro.2017.76 Elmore, 2015, Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages, Genome Biol. Evol., 7, 789, 10.1093/gbe/evv025 Upadhyaya, 2021, Genomics accelerated isolation of a new stem rust avirulence gene–wheat resistance gene pair, Native Plants, 7, 1220, 10.1038/s41477-021-00971-5 Zhong, 2020, Emergence of a hybrid PKS‐NRPS secondary metabolite cluster in a clonal population of the rice blast fungus Magnaporthe oryzae, Environ. Microbiol., 22, 2709, 10.1111/1462-2920.14994 Qutob, 2009, Copy number variation and transcriptional polymorphisms of Phytophthora sojae RXLR effector genes Avr1a and Avr3a, PLoS One, 4, 10.1371/annotation/2a2adcf8-afbc-4d46-92c6-d543d6b29182 Wapinski, 2007, Natural history and evolutionary principles of gene duplication in fungi, Nature, 449, 54, 10.1038/nature06107 Todd, 2020, Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs, Elife, 9, 10.7554/eLife.58349 Huang, 2022, CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae, Nat. Commun., 13, 7168, 10.1038/s41467-022-34736-1 Sánchez-Vallet, 2018, The genome biology of effector gene evolution in filamentous plant pathogens, Annu. Rev. Phytopathol., 56, 21, 10.1146/annurev-phyto-080516-035303 Inoue, 2017, Evolution of the wheat blast fungus through functional losses in a host specificity determinant, Science, 357, 80, 10.1126/science.aam9654 Sharma, 2014, Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the smut fungus Melanopsichium pennsylvanicum, Genome Biol. Evol., 6, 10.1093/gbe/evu148 Su, 2019, A deletion mutation in TaHRC confers Fhb1 resistance to Fusarium head blight in wheat, Nat. Genet., 51, 1099, 10.1038/s41588-019-0425-8 Weckselblatt, 2015, Human structural variation: mechanisms of chromosome rearrangements, Trends Genet., 31, 587, 10.1016/j.tig.2015.05.010 Faino, 2016, Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen, Genome Res., 26, 1091, 10.1101/gr.204974.116 Bao, 2017, PacBio sequencing reveals transposable elements as a key contributor to genomic plasticity and virulence variation in Magnaporthe oryzae, Mol. Plant, 10, 1465, 10.1016/j.molp.2017.08.008 Tsushima, 2019, Genomic plasticity mediated by transposable elements in the plant pathogenic fungus Colletotrichum higginsianum, Genome Biol. Evol., 11, 1487, 10.1093/gbe/evz087 Hartmann, 2017, A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements, ISME J., 11, 1189, 10.1038/ismej.2016.196 Sugihara, 2023, Disentangling the complex gene interaction networks between rice and the blast fungus identifies a new pathogen effector, PLoS Biol., 21, 10.1371/journal.pbio.3001945 Ma, 2010, Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium, Nature, 464, 367, 10.1038/nature08850 Habig, 2017, Forward genetics approach reveals host genotype-dependent importance of accessory chromosomes in the fungal wheat pathogen Zymoseptoria tritici, mBio, 8, 10.1128/mBio.01919-17 Orbach, 1996, Electrophoretic karyotypes of Magnaporthe grisea pathogens of diverse grasses, MPMI (Mol. Plant-Microbe Interact.), 9, 261, 10.1094/MPMI-9-0261 Peng, 2019, Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus, PLoS Genet., 15, 10.1371/journal.pgen.1008272 Langner, 2021, Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus, PLoS Genet., 17, 10.1371/journal.pgen.1009386 Chuma, 2011, Multiple translocation of the AVR-pita effector gene among chromosomes of the rice blast fungus Magnaporthe oryzae and related species, PLoS Pathog., 7, 10.1371/journal.ppat.1002147 Liu, 2022, Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia, bioRxiv, 2022 2000, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, 408, 796, 10.1038/35048692 Dean, 2005, The genome sequence of the rice blast fungus Magnaporthe grisea, Nature, 434, 980, 10.1038/nature03449 Zhong, 2018, Population genomic analysis of the rice blast fungus reveals specific events associated with expansion of three main clades, ISME J., 12, 1867, 10.1038/s41396-018-0100-6 Cao, 2011, Whole-genome sequencing of multiple Arabidopsis thaliana populations, Nat. Genet., 43, 956, 10.1038/ng.911 Chan, 2018, Structural variation detection and analysis using Bionano optical mapping, 193 Beló, 2010, Allelic genome structural variations in maize detected by array comparative genome hybridization, Theor. Appl. Genet., 120, 355, 10.1007/s00122-009-1128-9 Kozich, 2013, Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform, Appl. Environ. Microbiol., 79, 5112, 10.1128/AEM.01043-13 Li, 2023, HiSV: a control-free method for structural variation detection from Hi-C data, PLoS Comput. Biol., 19, 10.1371/journal.pcbi.1010760 Gilpatrick, 2020, Targeted nanopore sequencing with Cas9-guided adapter ligation, Nat. Biotechnol., 38, 433, 10.1038/s41587-020-0407-5 Gabrieli, 2018, Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH), Nucleic Acids Res., 46, 10.1093/nar/gky411 Madsen, 2020, Targeted sequencing of long DNA molecules from low input samples using droplet sorting, Hum. Mutat., 41, 1671, 10.1002/humu.24063 Geng, 2022, Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells, Genome Res., 10.1101/gr.276901.122 Evrony, 2021, Applications of single-cell DNA sequencing, Annu. Rev. Genom. Hum. Genet., 22, 171, 10.1146/annurev-genom-111320-090436 Abyzov, 2011, CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing, Genome Res., 21, 974, 10.1101/gr.114876.110 Lin, 2021, Chromosome-level genome assembly of a regenerable maize inbred line A188, Genome Biol., 22, 175, 10.1186/s13059-021-02396-x Chen, 2009, BreakDancer: an algorithm for high-resolution mapping of genomic structural variation, Nat. Methods, 6, 677, 10.1038/nmeth.1363 Rausch, 2012, DELLY: structural variant discovery by integrated paired-end and split-read analysis, Bioinformatics, 28, 10.1093/bioinformatics/bts378 Layer, 2014, LUMPY: a probabilistic framework for structural variant discovery, Genome Biol., 15, R84, 10.1186/gb-2014-15-6-r84 Kovaka, 2023, Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing, Nat. Methods, 20, 12, 10.1038/s41592-022-01716-8 English, 2014, Identifying genomic variants via long-read discordance and interrupted mapping, BMC Bioinf., 15, 180, 10.1186/1471-2105-15-180 Sedlazeck, 2018, Accurate detection of complex structural variations using single-molecule sequencing, Nat. Methods, 15, 461, 10.1038/s41592-018-0001-7 Heller, 2019, SVIM: structural variant identification using mapped long reads, Bioinformatics, 35, 2907, 10.1093/bioinformatics/btz041 Tham, 2020, NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing, Genome Biol., 21, 56, 10.1186/s13059-020-01968-7 Lin, 2022, SVision: a deep learning approach to resolve complex structural variants, Nat. Methods, 19, 1230, 10.1038/s41592-022-01609-w Thomma, 2016, Mind the gap; seven reasons to close fragmented genome assemblies, Fungal Genet. Biol., 90, 24, 10.1016/j.fgb.2015.08.010 Schwessinger, 2018, A near-complete haplotype-phased genome of the dikaryotic wheat stripe rust fungus Puccinia striiformis f. sp. tritici reveals high interhaplotype diversity, mBio, 9, 10.1128/mBio.02275-17 Walkowiak, 2020, Multiple wheat genomes reveal global variation in modern breeding, Nature, 588, 277, 10.1038/s41586-020-2961-x Marçais, 2018, MUMmer4: a fast and versatile genome alignment system, PLoS Comput. Biol., 14, 10.1371/journal.pcbi.1005944 Goel, 2019, SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies, Genome Biol., 20, 277, 10.1186/s13059-019-1911-0