Genome-scale examination of NBS-encoding genes in blueberry

Abstract

Blueberry is an important crop worldwide. It is, however, susceptible to a variety of diseases, which can lead to losses in yield and fruit quality. Although screening studies have identified resistant germplasm for some important diseases, still little is known about the molecular basis underlying that resistance. The most predominant type of resistance (R) genes contains nucleotide binding site and leucine rich repeat (NBS-LRR) domains. The identification and characterization of such a gene family in blueberry would enhance the foundation of knowledge needed for its genetic improvement. In this study, we searched for and found a total of 106 NBS-encoding genes (including 97 NBS-LRR) in the current blueberry genome. The NBS genes were grouped into eleven distinct classes based on their domain architecture. More than 22% of the NBS genes are present in clusters. Ten genes were mapped onto seven linkage groups. Phylogenetic analysis grouped these genes into two major clusters based on their structural variation, the first cluster having toll and interleukin-1 like receptor (TIR) domains and most of the second cluster containing a coiled-coil domain. Our study provides new insight into the NBS gene family in blueberry and is an important resource for the identification of functional R-genes.

Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.)

“…HanXRQChr05g0136351 and HanXRQChr06g0184071 possessed both TIR and coiled coil domain in the N-terminal of NBS proteins of sunflower and named CTN and CTNL, respectively. Such subgroups have been previously reported in many legumes and blueberries [ 16 , 19 ].…”

“…The CNL type constituted approximately 92% of the genes belonging to CNL subgroup, 67% of the genes belonging to TNL subgroup in the TNL type, 76% of the genes belonging to RNL subgroup in RNL type and 77% of the NL types genes are comprised of NL subgroup genes. The subgroups CN, CNNL, N, NN, and TTNL were also observed in M. truncatula , A. thaliana , and B. rapa [ 5 , 19 , 27 ]. HanXRQChr03g0067681 and HanXRQChr03g0073241 constituted both RPW8 and coiled-coil domains in the N-terminal and named RCNL, which were also reported in A. thaliana and B. rapa [ 5 ].…”

“…With the increasing availability of plant genome sequences, R gene proteins have been identified in many plant species, such as A. thaliana [ 5 , 14 ]; Vaccinium spp. [ 19 ]; Amborella trichopoda , Musa acuminata , Phyllostachys heterocycla , Capsicum annuum , and Sesamum indicum by Shao et al 2016 [ 13 ]; Cicer arietinum [ 20 ]; Glycine max [ 21 , 22 , 23 , 24 ]; Oryza sativa [ 25 , 26 ]; Medicago truncatula [ 27 ]; Vitis vinifera and Populus trichocarpa by Yang et al 2008 [ 28 ]; Solanum tuberosum [ 29 ]; Brassica rapa and Brassica oleracea by Zhang et al 2016 [ 30 ]; Hordeum vulgare [ 31 ]; Setaria italica [ 32 ]; Theobroma cacao [ 5 ]; Populus trichocarpa [ 5 ]; V. vinifera [ 5 ]; Cucumis sativus [ 33 ]; Phaseolus vulgaris [ 16 , 24 ], Lotus japonicas , Cajanus cajan , Glycine soja by Zheng et al 2016 [ 16 ], Gossypium arboretum [ 34 ], etc. A recent study by Li et al 2016 [ 35 ] has identified NBS-encoding genes as well as receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), collectively called as Resistance Gene Analogs (RGAs), for 50 plant genomes using a RGAugury pipeline.…”

Identification and expression profiling analysis of NBS–LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage

“…Similar to other species, the distribution of cabbage NBS-LRR genes is uneven and they mainly exist in clusters, as a result of rapid gene evolution (Leister 2004;Friedman and Baker 2007;Wan et al 2013;Lv et al 2015;Lozano et al 2015;Die et al 2018). However, only 51% of the cabbage NBS-LRR genes are present in 27 clusters (Yang et al 2008), whereas over 70% of the NBS-LRR genes in rice are present in 104 clusters.…”

Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome

“…The RAV1AAT elements regulate the expressions of multiple defense-related genes through the binding of RAV1 transcription factor proteins [60]. The abundance of the RAV1AAT element commonly found in the promoters of NBS genes indicates that this element is important for the regulation of defense-related responses [61,62]. Overall, the class of the most abundant motifs found in the asparagus NBS promoters indicates the significant cross-talk between abscisic acid-responsive signal transduction, abiotic stress responses, and disease tolerance-related signaling pathways [63,64,65].…”