Perspectives of genomic diversification and molecular recombination towards R-gene evolution in plants

Joshi, Raj Kumar; Nayak, Sanghamitra

doi:10.1007/s12298-012-0138-2

Cited by 49 publications

(42 citation statements)

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“…This finding was an indicative of sequence exchange between gene duplications which might occur in the evolutionary process of A diploids or even earlier. Similar phenomenon was also reported in other studies (Joshi and Nayak 2013;Leister 2004). It is evident that sequence exchange between divergent sequences are rare while exchange between similar genes appear frequently (Baumgarten et al 2003;Meyers et al 2003).…”

Section: Resultssupporting

confidence: 84%

Characterization of genomic sequence of a drought-resistant gene TaSnRK2.7 in wheat species

Zhang

Mao

et al. 2015

J Genet

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Section: Resultssupporting

confidence: 84%

Characterization of genomic sequence of a drought-resistant gene TaSnRK2.7 in wheat species

Zhang

Mao

et al. 2015

J Genet

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“…The Fusion/Histocompatibility (FuHC) locus in the colonial tunicate, Botryllus schlosseri , controls allogeneic fusion and rejection reactions among these sessile animals and shows sequence diversity, gene clustering, partial gene duplications and an extraordinary number of polymorphic alleles in the population for a subset of the genes (reviewed in [51]). Finally, excellent examples of repeat driven diversity are the anti-pathogen R gene families in higher plants, of which many are present in clusters of duplicated similar genes [15, 52]. R gene diversity results from unequal crossing over, gene conversion, duplications and deletions, all of which may lead to hybrid R genes or new genes with advantageous anti-pathogen functions [53].…”

Section: Discussionmentioning

confidence: 99%

Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family

et al. 2016

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BackgroundGenomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. A highly diverse immune gene family of the sea urchin (Strongylocentrotus purpuratus), called Sp185/333, is composed of clustered genes with similar sequence as well as several types of repeats ranging in size from short tandem repeats (STRs) to large segmental duplications. This repetitive structure may have been the basis for the incorrect assembly of this gene family in the sea urchin genome sequence. Consequently, we have resolved the structure of the family and profiled the members by sequencing selected BAC clones using Illumina and PacBio approaches.ResultsBAC insert assemblies identified 15 predicted genes that are organized into three clusters. Two of the gene clusters have almost identical flanking regions, suggesting that they may be non-matching allelic clusters residing at the same genomic locus. GA STRs surround all genes and appear in large stretches at locations of putatively deleted genes. GAT STRs are positioned at the edges of segmental duplications that include a subset of the genes. The unique locations of the STRs suggest their involvement in gene deletions and segmental duplications. Genomic profiling of the Sp185/333 gene diversity in 10 sea urchins shows that no gene repertoires are shared among individuals indicating a very high gene diversification rate for this family.ConclusionsThe repetitive genomic structure of the Sp185/333 family that includes STRs in strategic locations may serve as platform for a controlled mechanism which regulates the processes of gene recombination, gene conversion, duplication and deletion. The outcome is genomic instability and allelic mismatches, which may further drive the swift diversification of the Sp185/333 gene family that may improve the immune fitness of the species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3241-x) contains supplementary material, which is available to authorized users.

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“…Plant NLRs are modular proteins characterized by a common NB-ARC domain similar to the NACHT domain in mammalian immune receptor proteins [1]. On the population level, NLRs provide plants with sufficient diversity to maintain immunity to rapidly evolving pathogens [3,4]. Recent findings show that novel pathogen recognition specificities can also be acquired through the fusion of non-canonical domains to NLRs [5][6][7] and that such fusions are widespread across flowering plants [8,9].…”

Section: Introductionmentioning

confidence: 99%

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Bailey

Schudoma

Jackson

et al. 2017

Preprint

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Understanding evolution of plant immunity is necessary to inform rational approaches (Hall et al., 2009;Joshi et al., 2013).With over 50 fully sequenced plant genomes today, it is . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/100834 doi: bioRxiv preprint first posted online Jan. 20, 2017; Hotspots in Plant Immunity Gene Fusions 2 timely to apply comparative genomics approaches to investigate common trends in NLR evolution across the plant kingdom, including key crop species.In contrast to the highly conserved NB-ARC domains, the Leucine Rich Repeats (LRRs) of NLRs show high variability (Noel et al., 1999;Jacob, Vernaldi and Maekawa, 2013). The functional consequence of high LRR variation is thought to be the generation of novel recognition specificities (Bakker et al., 2006;Sukarta, Slootweg and Goverse, 2016). In addition, recent findings show that novel pathogen recognition specificities can also be acquired through the fusion of non-canonical domains to NLRs (Le Roux et al., 2015;Kroj et al., 2016). These exogenous domains can serve as 'baits' mimicking host targets of pathogen-derived effector molecules and therefore act in concert with LRR variation to broaden the spectra of recognised pathogenderived effectors (Cesari, Bernet al., 2014a; Cesari et al., 2014b;Le Roux et al., 2015).NLRs plant immune receptors were discovered over 20 years ago through cloning of plant disease resistance genes in Arabidopsis (Mindrinos et al., 1994; Bent et al., 1994) It is also clear that NLR(-ID) protein duplication has proliferated most strongly in these species for this hotspot clade ( Figure 1E). However, the relative ratio of NLRs with and without extra domains in this clade has remained relatively constant at around 59% suggesting that the rate of domain recycling has been constant across these species ( Figure 1B Expansion of the NLR-ID hotspot 1 clade is linked to diversification through new gene fusionsThe NLR-ID proteins from evolutionary hotspot 1 were examined further to test the hypothesis that the increase in the number of NLRs with integrated domains was due to the creation of novel gene fusions rather than the duplication of existing ID fusions. A clear expansion of the ID domain repertoire was found for this group of proteins, particularly for the Triticeae species (Table 1). It is possible that differences in the observed repertoires can be explained partly by incomplete annotation of genomes or fragmented assembly of NLRs; such proteins were omitted from the phylogenetic analysis if they were < 70 % complete across the NB-ARC domain.However, the overall trend across the genomes strongly suggests that differences cannot be explained solely by differences in genome assemblies. Moreover, genomes such as B. distachyon, Z. mays and O. sativa are assembled to much higher quality than those of the Triticeae species, yet they contain fewer NLR-IDs and have lower ID di...

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Perspectives of genomic diversification and molecular recombination towards R-gene evolution in plants

Cited by 49 publications

References 59 publications

Characterization of genomic sequence of a drought-resistant gene TaSnRK2.7 in wheat species

Characterization of genomic sequence of a drought-resistant gene TaSnRK2.7 in wheat species

Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

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