Phylogenetic and evolutionary analysis of NBS-encoding genes in Rutaceae fruit crops

Xu, Qiang; Biswas, Manosh Kumar; Hong, Liu; Zeng, Wenfang; Liu, Chaoyang; Xu, Jidi; Deng, Xiuxin

doi:10.1007/s00438-010-0593-9

Cited by 7 publications

(6 citation statements)

References 53 publications

(49 reference statements)

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“…In our study, the gene number discrepancy among the three Solanaceae species was also quite large, with 255, 447, and 306 in tomato, potato, and pepper, respectively. The numbers of NBS-encoding genes identified from tomato, potato, and pepper were generally consistent with previous studies (Andolfo et al 2013, 2014; Jupe et al 2012; Shao et al 2016; Xu et al 2011). However, we identified fewer genes compared with Wei et al (2016) because we excluded genes lacking the NBS domain, whereas Wei et al (2016) included these partial genes with only TIR or LRR domains present.…”

Section: Discussionsupporting

confidence: 89%

“…RNLs in Solanaceae were classified into CNLs in previous studies (Andolfo et al 2013, 2014; Jupe et al 2012; Lozano et al 2012; Xu et al 2011) due to the extremely small number of RNLs in Solanaceae compared with the two other subclasses. RNLs are limited among all angiosperms (Collier et al 2011; Shao et al 2014; Zhang et al 2016).…”

Section: Discussionmentioning

confidence: 99%

“…For example, Rpi-blb2 of potato provides P. infestans resistance (Vossen et al 2005), SW5 of tomato confers tomato spotted wilt virus resistance (Brommonschenkel et al 2000), and BS2 of pepper protects against X. campestris (Tai et al 1999). The evolutionary characteristics of certain NBS-encoding genes in the tomato and potato genomes have also been analyzed (Andolfo et al 2013, 2014; Jupe et al 2012; Lozano et al 2012; Xu et al 2011). A systematic evaluation of NBS-encoding genes at the genome level in more Solanaceae species is required to obtain a better understanding of the resistance to the diversity of pathogen invasions.…”

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confidence: 99%

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Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species

Qian

Zhou

Sun

et al. 2017

G3 Genes|Genomes|Genetics

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Plant resistance conferred by nucleotide binding site (NBS)-encoding resistance genes plays a key role in the defense against various pathogens throughout the entire plant life cycle. However, comparative analyses for the systematic evaluation and determination of the evolutionary modes of NBSencoding genes among Solanaceae species are rare. In this study, 447, 255, and 306 NBS-encoding genes were identified from the genomes of potato, tomato, and pepper, respectively. These genes usually clustered as tandem arrays on chromosomes; few existed as singletons. Phylogenetic analysis indicated that three subclasses [TNLs (TIR-NBS-LRR), CNLs (CC-NBS-LRR), and RNLs (RPW8-NBS-LRR)] each formed a monophyletic clade and were distinguished by unique exon/intron structures and amino acid motif sequences. By comparing phylogenetic and systematic relationships, we inferred that the NBS-encoding genes in the present genomes of potato, tomato, and pepper were derived from 150 CNL, 22 TNL, and 4 RNL ancestral genes, and underwent independent gene loss and duplication events after speciation.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species

Qian

Zhou

Sun

et al. 2017

G3 Genes|Genomes|Genetics

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“…In comparison to other plants that already have genome wide NBS-encoding resistance gene identification and analysis [3], [4], [7], [9]–[14], [16], [17], [24], [26], [49], the most distinct feature in G. raimondii is the high diversity domains at the N-termini of these NBS resistance genes.…”

Section: Discussionmentioning

confidence: 99%

Systematic Analysis and Comparison of Nucleotide-Binding Site Disease Resistance Genes in a Diploid Cotton Gossypium raimondii

Wei

Sun

et al. 2013

PLoS ONE

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Plant disease resistance genes are a key component of defending plants from a range of pathogens. The majority of these resistance genes belong to the super-family that harbors a Nucleotide-binding site (NBS). A number of studies have focused on NBS-encoding genes in disease resistant breeding programs for diverse plants. However, little information has been reported with an emphasis on systematic analysis and comparison of NBS-encoding genes in cotton. To fill this gap of knowledge, in this study, we identified and investigated the NBS-encoding resistance genes in cotton using the whole genome sequence information of Gossypium raimondii. Totally, 355 NBS-encoding resistance genes were identified. Analyses of the conserved motifs and structural diversity showed that the most two distinct features for these genes are the high proportion of non-regular NBS genes and the high diversity of N-termini domains. Analyses of the physical locations and duplications of NBS-encoding genes showed that gene duplication of disease resistance genes could play an important role in cotton by leading to an increase in the functional diversity of the cotton NBS-encoding genes. Analyses of phylogenetic comparisons indicated that, in cotton, the NBS-encoding genes with TIR domain not only have their own evolution pattern different from those of genes without TIR domain, but also have their own species-specific pattern that differs from those of TIR genes in other plants. Analyses of the correlation between disease resistance QTL and NBS-encoding resistance genes showed that there could be more than half of the disease resistance QTL associated to the NBS-encoding genes in cotton, which agrees with previous studies establishing that more than half of plant resistance genes are NBS-encoding genes.

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“…Phylogenetic analyses of partial NBS genes of Poncirus trifoliata (trifoliate orange), Citrus reticulata (tangerine) and their F1 progeny showed that NBS genes of Poncirus trifoliata (trifoliate orange), Citrus reticulata formed genus-specific clades. Additionally, NBS genes of their F1 progeny had sister relationships to only one of the parents [22]. This suggests that NBS genes in crossing hybrid citrus species are also different from those in original citrus species.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Comparative Analysis Reveals Possible Common Ancestors of NBS Domain Containing Genes in Hybrid Citrus sinensis Genome and Original Citrus clementina Genome

Wang

Zhou

et al. 2014

Preprint

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Background Recently available whole genome sequences of three citrus species: one Citrus clementina and two Citrus sinensis genomes have made it possible to understand the features of candidate disease resistance genes with nucleotide-binding sites (NBS) domain in Citrus and how NBS genes differ between hybrid and original Citrus species. Result We identified and re-annotated NBS genes from three citrus genomes and found similar numbers of NBS genes in those citrus genomes. Phylogenetic analysis of all citrus NBS genes across three genomes showed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR) domain and two different groups that contain the Coiled Coil (CC) domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three citrus genomes. This suggests that NBS genes in three citrus genomes may come from shared ancestral origins. We also mapped the re-sequenced reads of three pomelo and three Mandarin orange genomes onto the Citrus sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genome. The homologous NBS genes in pomelo and mandarin may explain why the NBS genes in their hybrid Citrus sinensis are similar to those in Citrus clementina in this study. Furthermore, sequence variation amongst citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different citrus genomes. Conclusion Our comparative analyses yield valuable insight into the understanding of the structure, evolution and organization of NBS genes in Citrus genomes. There are significantly more NBS genes in Citrus genomes compared to other plant species. NBS genes in hybrid C. sinensis genomes are very similar to those in progenitor C. clementina genome and they may be derived from possible common ancestral gene copies. Furthermore, our comprehensive analysis showed that there are three groups of plant NBS genes while CC-containing NBS genes can be divided into two groups.

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Phylogenetic and evolutionary analysis of NBS-encoding genes in Rutaceae fruit crops

Cited by 7 publications

References 53 publications

Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species

Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species

Systematic Analysis and Comparison of Nucleotide-Binding Site Disease Resistance Genes in a Diploid Cotton Gossypium raimondii

Genome-wide Comparative Analysis Reveals Possible Common Ancestors of NBS Domain Containing Genes in Hybrid Citrus sinensis Genome and Original Citrus clementina Genome

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