De novo genes are species-specific (orphan) genes that derive from DNA sequences that previously lacked coding potential
[6][51]. De novo genes are a subgroup of new genes that can code for proteins or serve as RNA genes
[115][159]. De novo genes have different features than other genes in the genome. For example, de novo genes are shorter in size, have a lower expression rate, and contain more extensively varied sequences
[116][160]. De novo gene birth is how new genes emerge from previously non-genic DNA sequences. De novo gene birth is essential for the divergence and adaptation of an organism
[117][161]. The
BSC4 gene in
Saccharomyces cerevisiae is an example of de novo gene birth
[118][162]. The origins of de novo genes in plants have been widely studied
[119][120][121][122][163,164,165,166]. Based on similarities to non-genic regions of
Arabidopsis lyrata, almost half of the orphan genes in
A. thaliana appear to have originated de novo
[120][164]. Plant responses to the environment seem to be influenced by orphan genes
[123][167]. For example, more than 80% of knockout mutants of unknown function genes in
A. thaliana showed an altered phenotype when stressed, conferring either protection against, or serving as suppressors of, different abiotic stressors, notably oxidative and osmotic stresses
[124][168]. A group of orphan genes was found in fungal pathogens limited to a single species or narrow clade. Pathogenic fungi may develop unique orphan genes to help infection or increase virulence. Because orphan genes lack homologs in closely related species, fungal effectors are ideal for orphan genes that developed for plant infection. Hundreds of orphan genes are encoded in the
Fusarium graminearum genome
[125][169]. The role of de novo or orphan genes in the pathogenic interactions and coevolution of pathogens with their host plants, however, remains unknown.
12. Epigenetic Modification of Gene Expression
Epigenetic modifications (e.g., DNA methylation, histone post-translational modifications, microRNAs, and the positioning of nucleosomes) are heritable alterations in gene expression patterns that occur without affecting the underlying DNA sequence and impacting the outcome of a locus or chromosome
[126][170]. Epigenetic changes can affect only a particular gene (RNA interference (RNAi)-based silencing), or they can affect whole chromosomal regions (for example, epigenetic silencing of sub-telomeric regions due to histone modifications)
[6][51]. Plant genomes are altered by various epigenetic pathways that regulate plant growth, development, and reproduction. Recent studies discovered many epigenetic factors participate in biotic and abiotic stress responses and adaptations in plants
[127][128][171,172].
DNA methylation refers to adding a methyl (CH
3) group to DNA and is an epigenetic mechanism that controls gene expression. As part of the plant’s defensive system, DNA methylation due to pathogen infection was reported in many plant species such as
Oryza sativa, A. thaliana, Nicotiana tabacum, Brassica rapa, Glycine max, Citrullus lanatus, and
Aegilops tauschii [129][130][131][132][133][134][135][136][137][138][173,174,175,176,177,178,179,180,181,182]. It was reported that pathogen detection provokes active changes in plant DNA methylation. For example, in
Arabidopsis, infection with
P. syringae pv.
tomato DC3000 led to DNA hypomethylation in several genomic regions, such as peri/centromeric repeats and
Athila retrotransposon
[139][183]. Additionally, RNA-directed DNA methylation (RdDM) controls plant responses to pathogen attack.
Arabidopsis ago4 (ARGONAUTE 4, a vital component of the RdDM pathway) mutants feature reduced DNA methylation rates at different genomic locations and showed increased susceptibility to virulent
P. syringae pv.
tomato DC3000
[140][184]. Moreover, DNA demethylation in transposon-containing promoters enhances plant disease resistance. For instance, the
Arabidopsis ros1 (REPRESSOR OF SILENCING 1, a DNA demethylase) mutant presented greater susceptibility to
P. syringae pv.
tomato DC3000, which corresponded with substantially elevated cytosine methylation in a TE (
AtREP11) present in the promoter of an
R gene (
RMG1 or
At4g11170) and consequently decreased gene expression
[130][174].
As other epigenetic mechanisms, histone methylation and histone acetylation are active and reversible processes controlled by histone methyltransferases and histone demethylases and histone acetyltransferases and histone deacetylases, respectively
[141][185]. Histone methylation and demethylation turn the genes in DNA “off” and “on”, respectively. Histone acetylation, on the other hand, is exclusively associated with gene activation
[142][186]. In plant–biotic interactions, histone (de)methylation regulates plant defense. For example, the methyltransferases SDG8 and SDG25 were implicated in PTI, ETI, and systemic acquired resistance against bacterial and fungal pathogens. Moreover,
sdg8 and
sdg25 single and
sdg8 sdg25 double mutants displayed increased susceptibility to
B. cinerea and
Pst [143][144][187,188]. The role of histone (de)acetylation in plant–pathogen interactions on
Arabidopsis has been examined in many studies
[145][146][147][189,190,191]. In addition, the control of plant–pathogen interactions via histone (de)acetylation was investigated in the wheat histone acetyltransferase complex TaGCN5–TaADA2, which triggers wheat wax biosynthesis, thereby delivering wax signals for germinating conidia in fungal pathogen
Bgt [148][192]. Additionally, rice HDAC OsHDT701 cooperates with the rice RNase P subunit Rpp30, and negatively controls rice defense responses to
M. oryzae and Xoo by facilitating histone deacetylation at PRR and defense genes
[149][193].
The transfer of ubiquitin to histone core proteins is known as histone ubiquitination. Histone ubiquitination, whether monoubiquitination or polyubiquitination, controls a series of cellular processes in plants. In
Arabidopsis, histone H2B monoubiquitination (H2Bub) is carried out via HISTONE MONOUBIQUITINATION (HUB1) and HUB2
[150][194], which control
SNC1 and
RPP4 expression following
P. syringae pv.
tomato DC3000 attack
[151][195].
13. Horizontal Gene/Chromosome Transfer
The non-sexual transfer of genetic material, either a single gene or whole chromosomes between unicellular and/or multicellular organisms and acceptor organisms without a parent–offspring relationship is known as horizontal gene transfer (HGT).
Agrobacterium-mediated transformation is the best example of HGT. After transferring a segment of
Agrobacterium DNA into the host’s genome,
Agrobacterium induces neoplastic growth or unregulated cell division, leading to crown galls or growing roots
[152][196]. HGT plays an important role in the evolution of prokaryotic clones by providing new genes involved in pathogenicity and promoting adaptive traits
[153][197]. Studies on fungal genomes suggest that HGT significantly influenced the evolution of pathogenic traits in fungal pathogens
[154][155][198,199]. There is also evidence that some characteristics of fungal biology may allow for gene transfer. For example, the anastomosis of fungal conidia, germ tubes, and hyphae results in cytoplasmic cell–cell linkages between cells of different species
[156][200]. In a
previous
study, Qiu et al.
[157][201] analyzed genomic data from the fungal pathogen
Magnaporthiopsis incrustans. The
resea
rcheuthors discovered two instances of exclusive sharing of HGT-derived gene markers between Magnaporthales and another lineage of plant–pathogenic fungi in the genus
Colletotrichum. Yin et al.
[158][202] identified 32 HGT events in
Valsa mali, most of which were HGTs from bacteria, along with several others from eukaryotes.
HCT between two vegetative incompatible biotypes of
C. gloeosporioides [159][203] and the transfer of supernumerary chromosomes (extra chromosomes composed primarily of DNA not found in all representatives of the species) into nonpathogenic strains of
A. alternata [160][204] are examples of HCT between fungi. Moreover, the horizontal transfer of chromosome 14 from
F. oxysporum f.sp.
lycopersici to nonpathogenic
F. oxysporum strains confers the pathogenicity of these strains towards tomato
[19][64].
14. Hybridization
The process of interbreeding individuals of different varieties or species to produce a hybrid is called hybridization. Breeding programs have yielded extensive hybridization between individuals of the same or different plant species. The introgression of genes for disease resistance between species has been widely studied in
Brassica species. For example, chromosome B4 from
Brassica nigra was introgressed into the rapeseed variety “Darmor” as a source of resistance against
L. maculans (causal agent of blackleg) and led to high resistance
[161][205]. Similarly, a B genome chromosome was introgressed from
B. carinata to
B. napus indicating high resistance against
L. maculans [162][206].
Other cases of resistance transfer through hybridization include hybridization between
B. carinata (donor) and
B. oleracea to enhance resistance against
Erysiphe polygoni (which can cause powdery mildew disease)
[163][207], the transfer of black rot resistance from
B. carinata to
B. oleracea [164][208], the transfer of brassica leaf blight resistance (caused by
Alternaria brassicae) from
B. hirta to
B. juncea [165][209], and the production of powdery mildew resistance from
B. carinata to
B. oleracea through embryo rescue followed by backcrossing to
B. oleracea [163][207]. From the pathogen side, Bertier et al.
[166][210] showed that hybridization increased
Phytophthora clade 8b pathogenicity.
15. Polyploidization
Polyploidization, or whole-genome duplication, refers to the acquisition of extra sets of chromosomes in a cell or organism and frequently occurs in vascular plants. Polyploidization is an essential aspect of plant evolution and can significantly modify a plant’s genetic make-up, physiology, morphology, and ecology within one or more generations
[167][211]. Polyploidization can affect biotic interactions and resistance to pathogens, with polyploids generally having enhanced pathogen resistance. Differences between diploids and polyploids in
R genes reflects altered pathogen resistance
[168][212]. For example, polyploidy can increase resistance within the gene-for-gene interactions that underlie many host–pathogen interactions and where genotype × genotype interactions are important
[169][213]. Quantitative resistance against
P. infestans and
Tecia solanivora in 4x potato was, moreover, observed using QTL analysis
[170][214]. In a
previous study, neopolyploids of a monogenic resistant apple cultivar showed increased resistance to
V. inaequalis compared to diploid cultivars
[171][215]. Another study found that synthetic tetraploids of Livingstone potato (
Plectranthus esculentus) were more resistant to root-knot nematodes than diploids
[172][216]. Pathogens can also change ploidy during infections; th
eis phenomenon occurred with
P. infestans, which caused the Great Irish Potato Famine
[173][217]. From the evidence available, polyploidy can induce changes in pathogen interactions and increase disease resistance by regulating genome expression, resulting in alterations in physiological characteristics, hormone biosynthesis, and improved antioxidant systems
[174][218], which make polyploids better competitors than diploids. For example, polyploidy was investigated in
Bremia lactucae by Fletcher et al.
[175][219] who reported a high incidence of heterokaryosis in
B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence.