Genome-Level Evolution of Resistance Genes in Arabidopsis thaliana

Genetics ◽  
2003 ◽  
Vol 165 (1) ◽  
pp. 309-319
Author(s):  
Andrew Baumgarten ◽  
Steven Cannon ◽  
Russ Spangler ◽  
Georgiana May
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Resistance Genes ◽  
Gene Diversity ◽  
Chromosome Region ◽  
Gene Families ◽  
Evolutionary Mechanisms ◽  
Chromosome Duplication ◽  
Gene Copies ◽  
Genome Level

Abstract Pathogen resistance genes represent some of the most abundant and diverse gene families found within plant genomes. However, evolutionary mechanisms generating resistance gene diversity at the genome level are not well understood. We used the complete Arabidopsis thaliana genome sequence to show that most duplication of individual NBS-LRR sequences occurs at close physical proximity to the parent sequence and generates clusters of closely related NBS-LRR sequences. Deploying the statistical strength of phylogeographic approaches and using chromosomal location as a proxy for spatial location, we show that apparent duplication of NBS-LRR genes to ectopic chromosomal locations is largely the consequence of segmental chromosome duplication and rearrangement, rather than the independent duplication of individual sequences. Although accounting for a smaller fraction of NBS-LRR gene duplications, segmental chromosome duplication and rearrangement events have a large impact on the evolution of this multi-gene family. Intergenic exchange is dramatically lower between NBS-LRR sequences located in different chromosome regions as compared to exchange between sequences within the same chromosome region. Consequently, once translocated to new chromosome locations, NBS-LRR gene copies have a greater likelihood of escaping intergenic exchange and adopting new functions than do gene copies located within the same chromosomal region. We propose an evolutionary model that relates processes of genome evolution to mechanisms of evolution for the large, diverse, NBS-LRR gene family.

scholarly journals Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family in Solanum pimpinellifolium and Arabidopsis thaliana

2020 ◽  
Vol 16 ◽  
pp. 117693432091105
Author(s):  
Huawei Wei ◽  
Jia Liu ◽  
Qinwei Guo ◽  
Luzhao Pan ◽  
Songlin Chai ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Phylogenetic Analysis ◽  
Gene Family ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Chromosome Mapping ◽  
Gene Families ◽  
Gene Clusters ◽  
Motif Analysis ◽  
Solanum Pimpinellifolium

NBS-LRR (nucleotide-binding site and leucine-rich repeat) is one of the largest resistance gene families in plants. The completion of the genome sequencing of wild tomato Solanum pimpinellifolium provided an opportunity to conduct a comprehensive analysis of the NBS-LRR gene superfamily at the genome-wide level. In this study, gene identification, chromosome mapping, and phylogenetic analysis of the NBS-LRR gene family were analyzed using the bioinformatics methods. The results revealed 245 NBS-LRRs in total, similar to that in the cultivated tomato. These genes are unevenly distributed on 12 chromosomes, and ~59.6% of them form gene clusters, most of which are tandem duplications. Phylogenetic analysis divided the NBS-LRRs into 2 subfamilies (CNL-coiled-coil NBS-LRR and TNL-TIR NBS-LRR), and the expansion of the CNL subfamily was more extensive than the TNL subfamily. Novel conserved structures were identified through conserved motif analysis between the CNL and TNL subfamilies. Compared with the NBS-LRR sequences from the model plant Arabidopsis thaliana, wide genetic variation occurred after the divergence of S. pimpinellifolium and A thaliana. Species-specific expansion was also found in the CNL subfamily in S. pimpinellifolium. The results of this study provide the basis for the deeper analysis of NBS-LRR resistance genes and contribute to mapping and isolation of candidate resistance genes in S. pimpinellifolium.

Intron Loss and Gain During Evolution of the Catalase Gene Family in Angiosperms

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 355-365
Author(s):  
Julia A Frugoli ◽  
Mark A McPeek ◽  
Terry L Thomas ◽  
C Robertson McClung
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Gene Families ◽  
Intron Loss ◽  
Flowering Plants ◽  
Chromosome 1 ◽  
Chromosome 4 ◽  
Splice Sites ◽  
Catalase Gene ◽  
Sequence Of Events

Abstract Angiosperms (flowering plants), including both monocots and dicots, contain small catalase gene families. In the dicot, Arabidopsis thaliana, two catalase (CAT) genes, CAT1 and CAT3, are tightly linked on chromosome 1 and a third, CAT2, which is more similar to CAT1 than to CAT3, is unlinked on chromosome 4. Comparison of positions and numbers of introns among 13 angiosperm catalase genomic sequences indicates that intron positions are conserved, and suggests that an ancestral catalase gene common to monocots and dicots contained seven introns. Arabidopsis CAT2 has seven introns; both CAT1 and CAT3 have six introns in positions conserved with CAT2, but each has lost a different intron. We suggest the following sequence of events during the evolution of the Arabidopsis catalase gene family. An initial duplication of an ancestral catalase gene gave rise to CAT3 and CAT1. CAT1 then served as the template for a second duplication, yielding CAT2. Intron losses from CAT1 and CAT3 followed these duplications. One subclade of monocot catalases has lost all but the 5′-most and 3′-most introns, which is consistent with a mechanism of intron loss by replacement of an ancestral intron-containing gene with a reverse-transcribed DNA copy of a fully spliced mRNA. Following this event of concerted intron loss, the Oryza sativa (rice, a monocot) CAT1 lineage acquired an intron in a novel position, consistent with a mechanism of intron gain at proto-splice sites.

scholarly journals NLR Diversity and Candidate Fusiform Rust Resistance Genes in Loblolly Pine

2021 ◽  
Author(s):  
Daniel Ence ◽  
Katherine E Smith ◽  
Shenghua Fan ◽  
Leandro Gomide Neves ◽  
Robin Paul ◽  
...  
Keyword(s):  
Gene Family ◽  
Resistance Gene ◽  
Loblolly Pine ◽  
Resistance Genes ◽  
Rust Resistance ◽  
De Novo ◽  
Gene Diversity ◽  
Gene Family Evolution ◽  
Fusiform Rust ◽  
Geographic Diversity

Abstract Resistance to fusiform rust disease in loblolly pine (Pinus taeda) is a classic gene-for-gene system. Early resistance gene mapping in the P. taeda family 10-5 identified RAPD markers for a major fusiform rust resistance gene, Fr1. More recently SNP markers associated with resistance were mapped to a full-length gene model in the loblolly pine genome encoding for an NLR protein. NLR genes are one of the most abundant gene families in plant genomes and are involved in effector-triggered immunity. Inter- and intraspecies studies of NLR gene diversity and expression have resulted in improved disease resistance. To characterize NLR gene diversity and discover potential resistance genes, we assembled de novo transcriptomes from 92 loblolly genotypes from across the natural range of the species. In these transcriptomes, we identified novel NLR transcripts that are not present in the loblolly pine reference genome and found significant geographic diversity of NLR genes providing evidence of gene family-evolution. We designed capture probes for these NLRs to identify and map SNPs that stably cosegregate with resistance to the SC20-21 isolate of Cronartium quercuum f.sp. fusiforme (Cqf) in half-sib progeny of the 10-5 family. We identified ten SNPs and two QTL associated with resistance to SC20-21 Cqf. The geographic diversity of NLR genes provides evidence of NLR gene family-evolution in loblolly pine. The SNPs associated with rust resistance provide a resource to enhance breeding and deployment of resistant pine seedlings.

scholarly journals Structure and Evolution of the Actin Gene Family in Arabidopsis thaliana

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 587-602 ◽  
Author(s):  
John M McDowell ◽  
Shurong Huang ◽  
Elizabeth C McKinney ◽  
Yong-Qiang An ◽  
Richard B Meagher
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Higher Plants ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Gene Families ◽  
Plant Evolution ◽  
Actin Gene ◽  
Specific Expression ◽  
Phylogenetic Structure

Abstract Higher plants contain families of actin-encoding genes that are divergent and differentially expressed. Progress in understanding the functions and evolution of plant actins has been hindered by the large size of the actin gene families. In this study, we characterized the structure and evolution of the actin gene family in Arabidopsis thaliana. DNA blot analyses with gene-specific probes suggested that all 10 of the Arabidopsis actin gene family members have been isolated and established that Arabidopsis has a much simpler actin gene family than other plants that have been examined. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least two ancient classes of genes that diverged early in land plant evolution and may have separated vegetative from reproductive actins. Subsequent divergence produced a total of six distinct subclasses of actin, and five showed a distinct pattern of tissue specific expression. The concordance of expression patterns with the phylogenetic structure is discussed. These subclasses appear to be evolving independently, as no evidence of gene conversion was found. The Arabidopsis actin proteins have an unusually large number of nonconservative amino acid substitutions, which mapped to the surface of the actin molecule, and should effect protein-protein interactions.

scholarly journals Evolutionary patterns of 64 vertebrate genomes (species) revealed by phylogenomics analysis of protein-coding gene families

2020 ◽  
Author(s):  
Jia Song ◽  
Xia Han ◽  
Kui Lin
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Species Tree ◽  
Whole Genome ◽  
Species Trees ◽  
High Concentration ◽  
Evolutionary Mechanisms ◽  
Study Results ◽  
Tree Inference ◽  
Species Tree Inference

AbstractBackgroundRecent studies have demonstrated that phylogenomics is an important basis for answering many fundamental evolutionary questions. With more high-quality whole genome sequences published, more efficient phylogenomics analysis workflows are required urgently.ResultsTo this end and in order to capture putative differences among evolutionary histories of gene families and species, we developed a phylogenomics workflow for gene family classification, gene family tree inference, species tree inference and duplication/loss events dating. Our analysis framework is on the basis of two guiding ideas: 1) gene trees tend to be different from species trees but they influence each other in evolution; 2) different gene families have undergone different evolutionary mechanisms. It has been applied to the genomic data from 64 vertebrates and 5 out-group species. And the results showed high accuracy on species tree inference and few false-positives in duplication events dating.ConclusionsBased on the inferred gene duplication and loss event, only 9∼16% gene families have duplication retention after a whole genome duplication (WGD) event. A large part of these families have ohnologs from two or three WGDs. Consistent with the previous study results, the gene function of these families are mainly involved in nervous system and signal transduction related biological processes. Specifically, we found that the gene families with ohnologs from the teleost-specific (TS) WGD are enriched in fat metabolism, this result implyng that the retention of such ohnologs might be associated with the environmental status of high concentration of oxygen during that period.

scholarly journals Conserved Molecular Function and Regulatory Subfunctionalization of the LORELEI Gene Family in Brassicaceae

2020 ◽  
Author(s):  
Jennifer A. Noble ◽  
Ming-Che James Liu ◽  
Thomas A. DeFalco ◽  
Martin Stegmann ◽  
Kara McNamara ◽  
...  
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Gene Families ◽  
Single Copy ◽  
Gene Family Evolution ◽  
Duplicated Genes ◽  
Evolutionary Mechanisms ◽  
Functional Conservation ◽  
Signaling Complex ◽  
And Function

AbstractA signaling complex comprising members of the LORELEI (LRE)-LIKE GPI-anchored protein (LLG) and Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) families perceive RAPID ALKALINIZATION FACTOR (RALF) peptides and regulate growth, development, reproduction, and immunity in Arabidopsis thaliana. Duplications in each component, which potentially could generate thousands of combinations of this signaling complex, are also evident in other angiosperms. Widespread duplication in angiosperms raises the question what evolutionary mechanisms underlie the expansion and retention of these gene families, as duplicated genes are typically rendered non-functional. As genetic and genomic resources make it a tractable model system, here we investigated this question using LLG gene family evolution and function in Brassicaceae. We first established that the LLG homologs in the Brassicaceae resulted from duplication events that pre-date the divergence of species in this family. Complementation of vegetative phenotypes in llg1 by LRE, LLG2, and LLG3 showed that the molecular functions of LLG homologs in A. thaliana are conserved. We next tested the possibility that differences in gene expression (regulatory subfunctionalization), rather than functional divergence, played a role in retention of these duplicated genes. For this, we examined the function and expression of LRE and LLG1 in A. thaliana and their single copy ortholog in Cleome violacea (Clevi LRE/LLG1), a representative species outside the Brassicaceae, but from the same order (Brassicales). We showed that expression of LLG1 and LRE did not overlap in A. thaliana and that Clevi-LRE/LLG1 expression in C. violacea encompassed all the expression domains of A. thaliana LRE + LLG1. Still, complementation experiments showed that LLG1 rescued reproductive phenotypes in lre and that Clevi LRE/LLG1 rescued both vegetative and reproductive phenotypes in llg1 and lre. Additionally, we found that expression of LLG2 and LLG3 in A. thaliana have also diverged from the expression of their corresponding single copy ortholog (Clevi LLG2/LLG3) in C. violacea. Our findings demonstrated how regulatory subfunctionalization, rather than functional divergence, underlies the retention of the LLG gene family in Brassicaceae. Our findings on the regulatory divergence and functional conservation provide an experimental framework to characterize the combinatorial assembly and function of this critical plant cell signaling complex.

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