Genome-wide Analysis Of LBD (LATERAL ORGAN BOUNDARIES Domain) Gene Family And Codon Usage Patterns In Zea Mays

Maize(Zea mays L.) is one of the oldest and most important world-wide crops that are relied upon for human food, animal feed and for starch ethanol production. The completion of maize genome project signaled the era of genomics. Maize research now enters the era of post-genomics and systems biology. The investigation of transcription factor (TF) families is a major focus of post-genomic research. The plant-specific ASL (ASYMMETRIC LEAVES2-Like)/LBD (LATERAL ORGAN BOUNDARIES Domain) proteins constitute a major zinc-finger-like domain transcription factor family, and are renowned for their roles in regulating diverse biological processes in the plants. In this study, a total of44LBD genes were identified in maize genome and were phylogenetically clustered into two groups (Ⅰ and Ⅱ), together with LBDs from Arabidopsis. The predicted maize LBDs were distributed across all the10chromosomes with different densities. In addition, the gene structures of maize LBD swere analysed. The expression profiles of the maize LBD genes under normal growth conditions were analysed by microarray data and qRT-PCR. The results indicated that LBDs might be involved in various aspects of physiological and developmental processes in maize. This is the first report of a genome wide analysis of the maize LBD gene family, which would provide valuable information for understanding the classification and putative functions of the gene family.We get the basic information of codon usage through the CDS sequences analysis of Zea mays. Taking the hot research points into consideration, we performed detailed codon usage patterns of Zea mays, by the methods of bioinformatics, multielement statistical analysis and correlation analysis. The results are of important reference value to guide gene-transformation and molecular modification of gene to increase the expression efficiency in Zea mays, to consummate gene prediction software and to improve accuracy of gene prediction and genome annotation, and meanwhile could provide theoretical basis for the further research on gene structure and function, molecular evolution and so on.The main results were summarized as follows:(1) According to the analysis, a total of44ASL/LBD genes from the entire maize genome were isolated. Two subfamilies (group Ⅰ and group Ⅱ) as being monophyletic were identified by phylogenetic relationships, and found11sister pairs of paralogous ASL/LBDs (marked by red shadow) with very strong bootstrap support (>90%). Class Ⅰ and Ⅱ could be further divided into five (la, Ib, Ic, Id and Ie) and two (Ⅱa and Ⅱb) subgroups, respectively.(2) In maize ASL/LBDs, the exons number ranged from1within fourteen genes to5in ZmASL/LBD44. Most ZmASL/LBD genes shared1or2exons including28genes with two exons and14genes with one exon. Only one gene (ZmASL/LBD18) had3exons and one gene (ZmASL/LBD44) had5exons. Most members within the same subgroup shared a similar intron/exon structure and gene length. The conserved intron/exon structure in each subgroup supported their close evolutionary relationships and the stated classification of subfamilies.(3) Chromosomal location analyses showed that44ZmASL/LBD genes presented on10chromosomes by the MapDraw tool, which dispersed throughout their respective genomes. Chromosome1contains the highest number of ZmASL/LBDs, with13out of44members (-30%), while only one ZmASL/LBD gene was found on each of chromosomes7and10, as well as2genes on chromosomes2and5. Otherwise,3or more were located on other chromosomes3,4,6,8and9. Interestingly, two pairs of ZmASL/LBDs (ZmASL/LBD4/ZmASL/LBD9and ZmASL/LBD24/ZmASL/LBD25) were located in the same chromosome and other nine sister pairs (linked by red line) located on different chromosomes. Therefore, it is suggested that segmental duplication and transposition events all have played roles in the evolution of AS2ILOB gene family in maize.(4) The ASL/LBD had a conserved the AS2/LOB domain in the N terminus of the proteins, and there were two conserved blocks in the AS2/LOB domain of the class I proteins, that is, the C block and GAS block. Multiple sequence alignments showed that all44predicted ZmASL/LBD protein sequences had a completely conserved CX2CX6CX3C zinc-finger-like domain while a LX6LX3LX6L leucine-zipper-like domain existed only in26of the class I ASL/LBD.(5) We analyzed the temporal and spatial expression patterns of the ZmASL/LBD genes under normal growth conditions in eighteen different tissues, including the pericarp, tassel, caryopsis, endosperm, style (silk), coleoptile, blade (lamina), embryo, ear, foliar leaf, adult leaf, juvenile leaf, seeding, culm (mainstem), internode, radicle, primary root and anther. Among the44predicted genes, the expression profiles of32gene models (including seven other alternatively spliced forms) were obtained, whereas those of the other12genes were not detectable in the Genevestigator analysis. One possible explanation lies in that the12genes either show too low transcript abundances to be detected or had special temporal and spatial expression patterns not examined. Next, we used real-time quantitative RT-PCR to validate the expression patterns in different tissues resulting from microarray database. Eleven genes were selected to confirm their expression in primary root, pericarp, internode, adult leaf, silk, culm, seedling, endosperm, embryo and tassel. From these results, it is speculated that some ASL/LBD genes with different expression levels in all the maize detected organs might play key roles in plant development and several ASL/LBD genes might have unique functions in the specific developmental stages.(6) The GC contentment of Zea mays genome was55.7%, and the G/C frequence of the third codon base was61.3%, indicating that Zea mays prefer to use G/C ending codons.(7) The codon pares started and ended with G had the highest proportion of10.10%,, followed by the codon pares started with C and ended with G, accounting for10.03%. The codon pares of AC had the lowest proportion of3.21%.(8) The analysis of relative degree between codon RSCU and tRNA copy numbers indicated that they are not entirely relevant.(9) There was some significant correlation betweenT3s, C3s, A3s, G3s, GC3s and CAI, CBI, Fop, Nc, indicating that the major factor effecting the codon usage of Zea mays is the codon base composition. The anlysis of Nc-plot showed that the codon usage of Zea mays is also affected by other factors such as natural selection in addition to the impact of codon base composition.