ArticleBMC genomics2015
Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 89 citations in OpenAlex.
- Diversity and Evolution ofBiology · 2024Article
- Evolutionary analysis of TIR- and non-TIR-NBS-LRR disease resistance genes in wild strawberries.Frontiers in plant science · 2024Article
- The mMolecular plant pathology · 2023Article
- The devastating oomycete phytopathogen Phytophthora cactorum: Insights into its biology and molecular features.Molecular plant pathology · 2023Review
- Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Horticulture research · 2023Article
- Evolution and functional analysis of the GRAS family genes in six Rosaceae species.BMC plant biology · 2022Article
- Chromosome-level genome assembly of Mentha longifolia L. reveals gene organization underlying disease resistance and essential oil traits.G3 (Bethesda, Md.) · 2022Article
- Different scales of gene duplications occurring at different times have jointly shaped the NBS-LRR genes in Prunus species.Molecular genetics and genomics : MGG · 2022Article
- Genome-wide analysis of NBS-LRR genes in Rosaceae species reveals distinct evolutionary patterns.Frontiers in genetics · 2022Article
- Adaptive evolution driving the young duplications in six Rosaceae species.BMC genomics · 2021Article
- Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears.BMC genomics · 2020Article
- Identification and Analysis of NBS-LRR Genes inPlants (Basel, Switzerland) · 2020Article
- Resistance Gene Analogs in the Brassicaceae: Identification, Characterization, Distribution, and Evolution.Plant physiology · 2020Article
- The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns.PloS one · 2020Article
- Quantitative trait loci controllingHorticulture research · 2019Article
- Article
- Sorbitol Modulates Resistance toThe Plant cell · 2018Article
- Genome-scale examination of NBS-encoding genes in blueberry.Scientific reports · 2018Article
- Lineage-specific duplications of NBS-LRR genes occurring before the divergence of six Fragaria species.BMC genomics · 2018Article
- Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution ofPeerJ · 2017Article
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Authors and funding
5 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDisease resistance (R) genes from different Rosaceae species have been identified by map-based cloning for resistance breeding. However, there are few reports describing the pattern of R-gene evolution in Rosaceae species because several Rosaceae genome sequences have only recently become available.
resultsSince most disease resistance genes encode NBS-LRR proteins, we performed a systematic genome-wide survey of NBS-LRR genes between five Rosaceae species, namely Fragaria vesca (strawberry), Malus × domestica (apple), Pyrus bretschneideri (pear), Prunus persica (peach) and Prunus mume (mei) which contained 144, 748, 469, 354 and 352 NBS-LRR genes, respectively. A high proportion of multi-genes and similar Ks peaks (Ks = 0.1- 0.2) of gene families in the four woody genomes were detected. A total of 385 species-specific duplicate clades were observed in the phylogenetic tree constructed using all 2067 NBS-LRR genes. High percentages of NBS-LRR genes derived from species-specific duplication were found among the five genomes (61.81% in strawberry, 66.04% in apple, 48.61% in pear, 37.01% in peach and 40.05% in mei). Furthermore, the Ks and Ka/Ks values of TIR-NBS-LRR genes (TNLs) were significantly greater than those of non-TIR-NBS-LRR genes (non-TNLs), and most of the NBS-LRRs had Ka/Ks ratios less than 1, suggesting that they were evolving under a subfunctionalization model driven by purifying selection.
conclusionsOur results indicate that recent duplications played an important role in the evolution of NBS-LRR genes in the four woody perennial Rosaceae species. Based on the phylogenetic tree produced, it could be inferred that species-specific duplication has mainly contributed to the expansion of NBS-LRR genes in the five Rosaceae species. In addition, the Ks and Ka/Ks ratios suggest that the rapidly evolved TNLs have different evolutionary patterns to adapt to different pathogens compared with non-TNL resistant genes.
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