Gene Duplication And Evolution In The "Candidatus Liberibacter Asiaticus" Genome

Citrus Huanglangbing is a highly destructive disease in most worldwide citrusgrowing areas. Recently the finish of genome sequencing of the pathogen gives an opportunity for discerning some critical issues occurred in this organism such as molecular evolution of its genes and genome. Gene duplication is one of the paramount processes and one of primary driving forces during the evolution of genes and genomes. It supplies plentiful materials for genetic novelties in organism, e.g. creation of new genes. This study is an identification and evolution investigation of the duplicated genes in the "Candidatus Liberibacter asiaticus" genome.There are1109protein sequences in the "Candidatus Liberibacter asiaticus" genome.Using a local all-against-all BLAST search, we obtained208duplication genes which cover about18.8%of the total proteins in "Ca. L. asiaticus". We found the organization of very recent duplication genes in genome can be differentiated into dispersed, tandem, segmental, and mixed forms, and these duplication genes produced partly through unequal-crossing over. Based on the sequence alignments and analysis of their expression patterns of recent duplication genes, we found there were different genes suffering subfunctionalization, keeping conservation of original gene function, or experiencing neofunctionalization. The gene function description of duplicated genes and functional class were assigned through the functional annotation of COG, Pfam and GO database. Our analysis indicated that the gene duplication in "Ca. L. asiaticus" genome were associated with metabolism, information storage and processing, and cellular processes. Measuring the synonymous substitution rate (ds) and nonsynonymous substitution rate (dN), we found many of the duplicated genes in "Ca. L. asiaticus" were under the pressure of purifying selection.ABC transporters constitute one of the largest superfamilies in the "Ca.L.asiaticus" genome.17ABC transporter genes with one or two conserved ABC domain were obtained. These ABC transporter genes were categorized into three clusters based on their structure and the number of the ABC domains. The first cluster contained11genes, with only one ABC domain in their polypeptide chains. The second cluster had4genes, in which the N-terminal IM and the C-terminal ABC domains are fused as a single polypeptide chain (IM-ABC). No IM domain partners had been identified for ABC proteins falling into the third cluster, and these two proteins consist of two ABCs fused together (ABC2). ABC domain was characterized by six short sequence motifs, and these motifs were conserved in composition, number, position and the form of the amino acid. The major finding of the phylogenetic tree study was that ABC cassettes diverged into three main subdivisions or classes that matched well with the three structure divisions of ABC systems, but there were no obvious branch division between the ABC in the first cluster and the third cluster. Using the method of Nei and Gojobori implemented in MEGA, purifying selection were tested much more important than others."Ca. L. asiaticus" holds appreciably less duplication genes as compared to other bacteria. We supposed it may be due to the internal obligation of "Ca. L. asiaticus" in host which is not a free-living bacterium. Our analysis indicated that the gene duplication in "Ca. L. asiaticus" genome appeared mainly to be conserved in gene function. These functions are required to live for bacterial organisms. The three ABC transporter clusters based on the structure and number of the ABC domains may acted as importers, exporters, and some functions not involved in transport separately. The conservative gene and motifs maintained common functions of these duplicated ABC genes. We speculated that purifying selection enable the "Ca. L. asiaticus" to sustain the stability of genome and was benefit for its multiplicity.This study discerned gene duplication and evolution in the "Candidatus Liberibacter asiaticus" genome, and can provide beneficial references for further studies on the evolution of gene and genomic in this bacterium.