Gene Evolution And Expression Of The NBS-LRR Families In Saccharum Spontaneum

As an important sugar-yielding crops,sugarcane also suffered the plant disease which caused by the virus,bacteria,fungi and nematodes as well.Besides artificial control,plant has its defense mechanisms to resistant the pathogens.Plant disease resistance genes(R genes)encoding resistance proteins which has function for preventing the invasion of exogenous pathogen.The genes encoding nucleotide binding site and leucine-rich repeat proteins(NBS-LRR genes)comprise the largest class and account for more than half of R genes in plant,and were revealed to play a critical role in defending plants from a multitude of pathogens and pests.Modern sugarcane were derived from the crosses between S.officinarum and S.sponteaneum.High sugar content trait of hybrid cultivars was suggested to be contributed by S.officinarum,while the stress tolerance was attributed by S.spontaneum.In this study,combined comparative genomics and whole genome sequences resources of S.spontaneum,the whole set of NBS-type genes were identified and characterized from S.spontaneum.Phylogenic and gene structure analysis were used to study the evolutional relationship of NBS-LRR gene families in S.spontaneum and angiosperm.Moreover,the gene expression profiles of NBS-LRR gene families were investigated for evaluating the gene functions in S.spontaneum.The main results are as follows:(1)Based on HMM and Pfam database,a total of 506 genes were identified to be the NBS class of genes in S.spontaneum species.The functional domain analysis revealed that the NBS family can be divided into four types with different domain organizations,including 242 Coiled-coil NBS-LRR genes,120 NBS-LRR genes,113 Coiled-coil-NBS and 31 NBS genes.(2)With the MEME analysis,eight conserved motifs(P-LOOP,GLPL,Kinase,RNBS-A,RNBS-B,RNBS-C,RNBS-D,MHDV)of plant NBS type genes were also found from the four types of NBS-encoding genes.Among the eight motifs,GLPL,MHDV,P-LOOP and Kinase-2 are the top four conserved motifs of NBS domain in different subfamily of sugarcane.Noteworthy,in sugarcane,instread of MHDV,VHDM or MHDL were presented in NBS-LRR of sugarcane.In addition,RNBS-A,RNBS-B and RNBS-C are usual presented in NBS domain,while,RNBS-C was absent both NBS-LRR subfamily and NBS subfamily in sugarcane.(3)Similar to previous study in monocotyledons,TIR domain was absent in NBS families in sugarcane.Based on the gene number comparisons among the examinated plant species,there were no correlation between the monoploidy genome size and the numbers of NBS-LRR genes in plant.(4)Comparative analysis of gene structures and phylogenetic evolution were performed among arabidopsis,pinapple,rice,maize,sorghum and sugarcane.Phylogenetic analysis showed that the four type of NBS-LRR genes were not group together,suggesting that the four subfamilies were originated before the last common ancestor of NBS-LRR families.The phylogenetic distribution of sugarcane NBS resistance genes was consistent to that of sorghum,demonstrating that there were no gene gain/loss event after the divergence of sorghum and sugarcane.(5)To investigate the expressional level of NBS-LRR genes in S.spontaneum,we performed comparative transcriptome profiling at different tissue under four hormone treatments(ABA,Et,GA,IAA).Noteworthy,a CC-NBS-LRR gene AP850660980 presented in opposite directions for the gene expression profiles between IAA treatment and the other three kinds of hormones.The gene has the highest expresional epxression under the treatment of IAA at 96 hours in stem,while,showed no variation under the other three hormone treatments;in contrast,the gene presented no variation under the treatment of IAA at 24 hours in stem,while,reached the highest under the other three kinds of hormone.Thus,it is speculated that there is a complementary relationship between IAA and the other three hormones for regulating the expression of the gene.In addition,NBS-LRR gene AP851288080 was also deserved to be paid attention.This gene have consistent expressional profiles under the treatment of GA and IAA,indicating that the genes has the similar cross-talk mechanism under these two kinds of hormone.Our study is the first report for the whole gene families of NBS-LRR in S.spontaneum,providing an important basis for further investigating the molecular mechanism of the disease-resistant and assistant the molecular breeding in plants.