Evolution of NLR Resistance Genes in Magnoliids: Dramatic Expansions of CNLs and Multiple Losses of TNLs

Magnoliids are the third-largest group of angiosperms and occupy a critical position in angiosperm evolution. In the past years, due to the lack of sequenced genomes, the disease resistance gene (R gene) profile of magnoliids remains poorly understood. By the genome-wide identification of 1,832 NLR genes from seven magnoliid genomes, we built a framework for the evolution of magnoliid R genes. TNL genes were completely absent from five magnoliids, presumably due to immune pathway deficiencies. A total of 74 ancestral R genes (70 CNLs, 3 TNLs, and 1 RNL) were recovered in a common ancestor of magnoliids, from which all current NLR gene repertoires were derived. Tandem duplication served as the major drive for NLR genes expansion in seven magnoliid genomes, as most surveyed angiosperms. Due to recent rapid expansions, most magnoliids exhibited “a first expansion followed by a slight contraction and a further stronger expansion” evolutionary pattern, while both Litsea cubeba and Persea americana showed a two-times-repeated pattern of “expansion followed by contraction.” The transcriptome analysis of seven different tissues of Saururus chinensis revealed a low expression of most NLR genes, with some R genes displaying a relatively higher expression in roots and fruits. Overall, our study sheds light on the evolution of NLR genes in magnoliids, compensates for insufficiency in major angiosperm lineages, and provides an important reference for a better understanding of angiosperm NLR genes.

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Epithelial and stromal-specific immune pathway activation in the murine endometrium post-coitum

Reproduction ◽

10.1530/rep-15-0087 ◽

2015 ◽

Vol 150 (2) ◽

pp. 127-138 ◽

Cited By ~ 6

Author(s):

S L Field ◽

M Cummings ◽

N M Orsi

Keyword(s):

Genome Wide ◽

Pathway Activation ◽

Cd1 Mice ◽

Cytokine Networks ◽

Immune Pathway ◽

Expression Microarrays ◽

Trigger Mechanisms ◽

Laser Capture

The endometrium is a dynamic tissue, demonstrating cyclical growth/remodelling in preparation for implantation. In mice, seminal constituents trigger mechanisms to prepare the endometrium, a process dubbed ‘seminal priming’ that modifies immune system components and mediates endometrial remodelling in preparation for pregnancy. An array of cytokines has been reported to mediate this interaction, although much of the literature relates toin vitrostudies on isolated endometrial epithelial cells. This study measured changes in immune-related gene expression in endometrial epithelial and stromal cellsin vivofollowing natural mating. CD1 mice were naturally mated and sacrificed over the first 4 dayspost-coitum(n=3 each day). Endometrial epithelial and stromal compartments were isolated by laser capture microdissection. Labelled cRNA was generated and hybridised to genome-wide expression microarrays. Pathway analysis identified several immune-related pathways active within epithelial and stromal compartments, in particular relating to cytokine networks, matrix metalloproteinases and prostaglandin synthesis. Cluster analysis demonstrated that the expression of factors involved in immunomodulation/endometrial remodelling differed between the epithelial and stromal compartments in a temporal fashion. This study is the first to examine the disparate responses of the endometrial epithelial and stromal compartments to seminal plasmain vivoin mice, and demonstrates the complexity of the interactions between these two compartments needed to create a permissive environment for implantation.

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Natural selection and repeated patterns of molecular evolution following allopatric divergence

eLife ◽

10.7554/elife.45199 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 6

Author(s):

Yibo Dong ◽

Shichao Chen ◽

Shifeng Cheng ◽

Wenbin Zhou ◽

Qing Ma ◽

...

Keyword(s):

Positive Selection ◽

Divergence Time ◽

Purifying Selection ◽

Single Copy ◽

Orthologous Genes ◽

Allopatric Species ◽

Genome Wide ◽

Allopatric Divergence ◽

Selective Forces ◽

Repeated Pattern

Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10–15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.

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Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains

Legume Genomics - Methods in Molecular Biology ◽

10.1007/978-1-0716-0235-5_20 ◽

2020 ◽

pp. 365-375

Author(s):

Soodeh Tirnaz ◽

Yueqi Zhang ◽

Jacqueline Batley

Keyword(s):

Disease Resistance ◽

Resistance Gene ◽

Disease Resistance Gene ◽

Resistance Gene Analogs ◽

Conserved Domains ◽

Genome Wide

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Genome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghum

Scientific Reports ◽

10.1038/s41598-020-77684-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Rozalynne Samira ◽

Jennifer A. Kimball ◽

Luis Fernando Samayoa ◽

James B. Holland ◽

Tiffany M. Jamann ◽

...

Keyword(s):

Disease Resistance ◽

Leaf Spot ◽

Mapping Population ◽

Strong Association ◽

Disease Resistance Gene ◽

Oxygen Species ◽

Molecular Features ◽

Genome Wide ◽

Molecular Patterns ◽

Association Mapping Population

AbstractPlants have the capacity to respond to conserved molecular features known as microbe-associated molecular patterns (MAMPs). The goal of this work was to assess variation in the MAMP response in sorghum, to map loci associated with this variation, and to investigate possible connections with variation in quantitative disease resistance. Using an assay that measures the production of reactive oxygen species, we assessed variation in the MAMP response in a sorghum association mapping population known as the sorghum conversion population (SCP). We identified consistent variation for the response to chitin and flg22—an epitope of flagellin. We identified two SNP loci associated with variation in the flg22 response and one with the chitin response. We also assessed resistance to Target Leaf Spot (TLS) disease caused by the necrotrophic fungus Bipolaris cookei in the SCP. We identified one strong association on chromosome 5 near a previously characterized disease resistance gene. A moderately significant correlation was observed between stronger flg22 response and lower TLS resistance. Possible reasons for this are discussed.

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Evolution of the Cholesterol Biosynthesis Pathway in Animals

Molecular Biology and Evolution ◽

10.1093/molbev/msz167 ◽

2019 ◽

Vol 36 (11) ◽

pp. 2548-2556 ◽

Cited By ~ 3

Author(s):

Tingting Zhang ◽

Dongwei Yuan ◽

Jun Xie ◽

Yongxing Lei ◽

Jianguo Li ◽

...

Keyword(s):

Cholesterol Biosynthesis ◽

Biosynthesis Pathway ◽

Animal Kingdom ◽

Evolutionary Pattern ◽

Animal Development ◽

Genome Wide ◽

Last Common Eukaryotic Ancestor ◽

Evolutionarily Conserved ◽

Complete Set ◽

Cholesterol Biosynthesis Pathway

Abstract Cholesterol plays essential roles in animal development and disease progression. Here, we characterize the evolutionary pattern of the canonical cholesterol biosynthesis pathway (CBP) in the animal kingdom using both genome-wide analyses and functional experiments. CBP genes in the basal metazoans were inherited from their last common eukaryotic ancestor and evolutionarily conserved for cholesterol biosynthesis. The genomes of both the basal metazoans and deuterostomes retain almost the full set of CBP genes, while Cnidaria and many protostomes have independently experienced multiple massive losses of CBP genes that might be due to the geologic events during the Ediacaran period, such as the appearance of an exogenous sterol supply and the frequent perturbation of ocean oxygenation. Meanwhile, the indispensable utilization processes of cholesterol potentially strengthened the maintenance of the complete set of CBP genes in vertebrates. These results strengthen both biotic and abiotic roles in the macroevolution of a biosynthesis pathway in animals.

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An angiosperm NLR atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion

10.1101/2021.02.10.430603 ◽

2021 ◽

Author(s):

Yang Liu ◽

Zhen Zeng ◽

Qian Li ◽

Xing-Mei Jiang ◽

Zhen Jiang ◽

...

Keyword(s):

Signal Transduction ◽

Plant Disease Resistance ◽

Ecological Specialization ◽

Closely Related Species ◽

Evolutionary Pattern ◽

Copy Numbers ◽

Immune Pathway ◽

Plant Disease Resistance Genes ◽

Colonization Of Land

AbstractNucleotide-binding site-leucine-rich repeat receptor (NLR) genes comprise the largest family of plant disease resistance genes. NLR genes are phylogenetically divided into the TNL, CNL, and RNL subclasses. NLR copy numbers and subclass composition vary tremendously across angiosperm genomes. However, the evolutionary associations between genomic NLR content and plant lifestyle, or between NLR content and signal transduction components, are poorly characterized due to limited genome availability. Here, we established an angiosperm NLRatlas (ANNA, http://compbio.nju.edu.cn/app/ANNA/), which includes NLR genes from over 300 angiosperm genomes. Using ANNA, we revealed that NLR copy numbers differ up to 66-fold among closely related species due to rapid gene loss and gain. Interestingly, NLR contraction was associated with adaptations to aquatic, parasitic, and carnivorous lifestyles. The convergent NLR reduction in aquatic plants resembles the long-term evolutionary silence of NLR genes in green algae before the colonization of land. A co-evolutionary pattern between NLR subclasses and plant immune-pathway components was also identified, suggesting that immune pathway deficiencies may drive TNL loss. Finally, we recovered a conserved TNL lineage that may function independently of the RNL pathway. Our findings provide new insights into the evolution of NLR genes in the context of plant lifestyles and genome content variation.

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Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

International Journal of Molecular Sciences ◽

10.3390/ijms23020642 ◽

2022 ◽

Vol 23 (2) ◽

pp. 642

Author(s):

Tiantian Yang ◽

Pengyu Zhang ◽

Jiahui Pan ◽

Sikandar Amanullah ◽

Feishi Luan ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Pattern Analysis ◽

Bioinformatics Analysis ◽

Class Iii ◽

Functional Sites ◽

Lignin Synthesis ◽

Genome Wide ◽

Repeated Pattern ◽

Lignin Accumulation

Watermelon (Citrullus lanatus) is an important horticultural crop worldwide, but peel cracking caused by peel hardness severely decreases its quality. Lignification is one of the important functions of class III peroxidase (PRX), and its accumulation in the plant cell wall leads to cell thickening and wood hardening. For in-depth physiological and genetical understanding, we studied the relationship between peel hardness and lignin accumulation and the role of PRXs affecting peel lignin biosynthesis using genome-wide bioinformatics analysis. The obtained results showed that lignin accumulation gradually increased to form the peel stone cell structure, and tissue lignification led to peel hardness. A total of 79 ClPRXs (class III) were identified using bioinformatics analysis, which were widely distributed on 11 chromosomes. The constructed phylogenetics indicated that ClPRXs were divided into seven groups and eleven subclasses, and gene members of each group had highly conserved intron structures. Repeated pattern analysis showed that deletion and replication events occurred during the process of ClPRX amplification. However, in the whole-protein sequence alignment analysis, high homology was not observed, although all contained four conserved functional sites. Repeated pattern analysis showed that deletion and replication events occurred during ClPRXs’ amplification process. The prediction of the promoter cis-acting element and qRT-PCR analysis in four tissues (leaf, petiole, stem, and peel) showed different expression patterns for tissue specificity, abiotic stress, and hormone response by providing a genetic basis of the ClPRX gene family involved in a variety of physiological processes in plants. To our knowledge, we for the first time report the key roles of two ClPRXs in watermelon peel lignin synthesis. In conclusion, the extensive data collected in this study can be used for additional functional analysis of ClPRXs in watermelon growth and development and hormone and abiotic stress response.

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Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution

Communications Biology ◽

10.1038/s42003-020-01643-4 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Feng Wu ◽

Kangkang Niu ◽

Yong Cui ◽

Cencen Li ◽

Mo Lyu ◽

...

Keyword(s):

Evolutionary History ◽

Regulatory Mechanism ◽

Evolutionary Pattern ◽

Genome Wide Analysis ◽

Short Loop ◽

Genome Wide ◽

Representative Species ◽

Transcriptional Regulatory Mechanism ◽

Transcriptional Regulatory ◽

G Quadruplex

AbstractG-quadruplex (G4) structures have been predicted in the genomes of many organisms and proven to play regulatory roles in diverse cellular activities. However, there is little information on the evolutionary history and distribution characteristics of G4s. Here, whole-genome characteristics of potential G4s were studied in 37 evolutionarily representative species. During evolution, the number, length, and density of G4s generally increased. Immunofluorescence in seven species confirmed G4s’ presence and evolutionary pattern. G4s tended to cluster in chromosomes and were enriched in genetic regions. Short-loop G4s were conserved in most species, while loop-length diversity also existed, especially in mammals. The proportion of G4-bearing genes and orthologue genes, which appeared to be increasingly enriched in transcription factors, gradually increased. The antagonistic relationship between G4s and DNA methylation sites was detected. These findings imply that organisms may have evolutionarily developed G4 into a novel reversible and elaborate transcriptional regulatory mechanism benefiting multiple physiological activities of higher organisms.

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