BIOMAT Database Logo BIOMAT Database Logo

Extreme expansion of NBS-encoding genes in Rosaceae. 2015

YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China. xiaohuizhang@nju.edu.cn.

BACKGROUND Nucleotide binding site leucine-rich repeats (NBS-LRR) genes encode a large class of disease resistance (R) proteins in plants. Extensive studies have been carried out to identify and investigate NBS-encoding gene families in many important plant species. However, no comprehensive research into NBS-encoding genes in the Rosaceae has been performed. RESULTS In this study, five whole-genome sequenced Rosaceae species, including apple, pear, peach, mei, and strawberry, were analyzed to investigate the evolutionary pattern of NBS-encoding genes and to compare them to those of three Cucurbitaceae species, cucumber, melon, and watermelon. Considerable differences in the copy number of NBS-encoding genes were observed between Cucurbitaceae and Rosaceae species. In Rosaceae species, a large number and a high proportion of NBS-encoding genes were observed in peach (437, 1.52%), mei (475, 1.51%), strawberry (346, 1.05%) and pear (617, 1.44%), and apple contained a whopping 1303 (2.05%) NBS-encoding genes, which might be the highest number of R-genes in all of these reported diploid plant. However, no more than 100 NBS-encoding genes were identified in Cucurbitaceae. Many more species-specific gene families were classified and detected with the signature of positive selection in Rosaceae species, especially in the apple genome. CONCLUSIONS Taken together, our findings indicate that NBS-encoding genes in Rosaceae, especially in apple, have undergone extreme expansion and rapid adaptive evolution. Useful information was provided for further research on the evolutionary mode of disease resistance genes in Rosaceae crops.

UI MeSH Term Description Entries
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D005810 Multigene Family A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed) Gene Clusters,Genes, Reiterated,Cluster, Gene,Clusters, Gene,Families, Multigene,Family, Multigene,Gene Cluster,Gene, Reiterated,Multigene Families,Reiterated Gene,Reiterated Genes
D017343 Genes, Plant The functional hereditary units of PLANTS. Plant Genes,Gene, Plant,Plant Gene
D054884 Host-Pathogen Interactions The interactions between a host and a pathogen, usually resulting in disease. Host Pathogen Interaction,Host-Pathogen Relations,Pathogen-Host Interaction,Pathogen-Host Interactions,Host Pathogen Interactions,Host Pathogen Relations,Host-Pathogen Interaction,Host-Pathogen Relation,Interaction, Host Pathogen,Interaction, Host-Pathogen,Interaction, Pathogen-Host,Interactions, Host Pathogen,Interactions, Host-Pathogen,Interactions, Pathogen-Host,Pathogen Host Interaction,Pathogen Host Interactions,Pathogen Interaction, Host,Pathogen Interactions, Host,Relation, Host-Pathogen,Relations, Host-Pathogen
D060467 Disease Resistance The capacity of an organism to defend itself against pathological processes or the agents of those processes. This most often involves innate immunity whereby the organism responds to pathogens in a generic way. The term disease resistance is used most frequently when referring to plants. Resistance, Disease,Disease Resistances,Resistances, Disease
D018745 Genome, Plant The genetic complement of a plant (PLANTS) as represented in its DNA. Plant Genome,Genomes, Plant,Plant Genomes
D020440 Gene Duplication Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES. Duplication, Gene,Duplications, Gene,Gene Duplications
D023281 Genomics The systematic study of the complete DNA sequences (GENOME) of organisms. Included is construction of complete genetic, physical, and transcript maps, and the analysis of this structural genomic information on a global scale such as in GENOME WIDE ASSOCIATION STUDIES. Functional Genomics,Structural Genomics,Comparative Genomics,Genomics, Comparative,Genomics, Functional,Genomics, Structural
D027824 Rosaceae The rose plant family in the order ROSALES and class Magnoliopsida. They are generally woody plants. A number of the species of this family contain cyanogenic compounds. Amelanchier,Cercocarpus,Chaenomeles,Coleogyne,Cotoneaster,Cydonia,Mahogany, Mountain,Mountain Mahogany,Quince,Quince, Flowering,Serviceberry,Dryas Plant,Amelanchiers,Chaenomele,Coleogynes,Cotoneasters,Cydonias,Dryas Plants,Flowering Quince,Flowering Quinces,Mahoganies, Mountain,Mountain Mahoganies,Plant, Dryas,Plants, Dryas,Quinces,Quinces, Flowering,Serviceberries

Related Publications

YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae.
January 2014, PloS one,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Phylogenetic and evolutionary analysis of NBS-encoding genes in Rosaceae fruit crops.
July 2007, Molecular phylogenetics and evolution,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species.
February 2015, BMC genomics,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops.
February 2013, BMC genomics,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Evolution of plant NBS encoding disease resistance genes.
December 2014, Yi chuan = Hereditas,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Genome-scale examination of NBS-encoding genes in blueberry.
February 2018, Scientific reports,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Genome-wide analysis of NBS-LRR genes in Rosaceae species reveals distinct evolutionary patterns.
January 2022, Frontiers in genetics,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Recent duplications dominate NBS-encoding gene expansion in two woody species.
September 2008, Molecular genetics and genomics : MGG,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis.
April 2003, The Plant cell,
YanXiao Jia, and Yang Yuan, and Yanchun Zhang, and Sihai Yang, and Xiaohui Zhang
Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes.
May 2004, Molecular genetics and genomics : MGG,
Copied contents to your clipboard!