Comparative And Evolutionary Analysis Of Abiotic Stress Related Gene Families AEE,β-amylases And Heat Stress Transcription Factors In Grasses

Grasses are one kind of the most economic valuable seed plants. They are the main source of human food and animal stock feed and important raw material of all sectors of society. In recent years, the development of genomic research has provided the basis for molecular evolutionary and functional study of gramineous genomes. The results of sequencing showed synteny among the sequenced gramineous genomes. However, there are large differences among them. It was supposed that chromosomes of the extant grasses were formed through gene duplication, chromosomal fusion and other evolutionary events. It was established that an increasing number of plant genes could belong to either large or small gene families. And they showed to be some species-specific with gene duplication and/or loss. Moreover, the duplicated genes may experience adaptive evolution and evolved new functions.High temperature, drought, salt stress and low temperature are the major factors which influence the whole growth of plants, especially place limits on crops’productivity and quality. In this research, a systematic molecular evolution analysis of abiotic stress related gene families AEE, beta-amylase and Hsf in five sequenced grasses (Oryza sativa, Zea mays, Sorghum bicolor, Setaria italica and Brachypodium distachyon) was performed with the methods of bioinformation and molecular biology. All these results provided a theoretical foundation not only for further functional study of these genes, but also for improving stress resistance of crops genetically. The main findings were as follows:(1) The L-Ala-D/L-Glu epimerases (AEEs), a subgroup of the enolase superfamily, catalyze the epimerization of L-Ala-D/L-Glu and other dipeptides in bacteria and contribute to the metabolism of the murein peptide of peptidoglycan. Although lacking in peptidoglycan, land plants possess AEE genes that show high similarity to those in bacteria. Similarity searches revealed that the AEE gene is ubiquitous in land plants, from bryophytas to angiosperms. However, other eukaryotes, including green and red algae, do not contain genes encoding proteins with an L-Ala-D/L-Glu_epimerase domain. Homologs of land plant AEE genes were found to only be present in prokaryotes, especially in bacteria. Phylogenetic analysis revealed that the land plant AEE genes formed a monophyletic group with some bacterial homologs. In addition, land plant AEE proteins showed the highest similarity with these bacterial homologs and shared motifs only conserved in land plant and these bacteria AEEs. Integrated information on the taxonomic distribution, phylogenetic relationships and sequence similarity of the AEE proteins revealed that the land plant AEE genes were acquired from bacteria through an ancient horizontal gene transfer (HGT) event. Morever, the transferred gene was acquired by plants in the initial stage of transmission from water to land, and may be related to the adaption to the new hostile environments. Further evidence revealed that land plant AEE genes had undergone positive selection so that fixed and inherited vertically in the land plants. The results of this study clearly demonstrated that the ancestor of land plants acquired an AEE gene from bacteria via an ancient HGT event. Other findings illustrated that adaptive evolution through positive selection has contributed to the functional adaptation and fixation of this gene in land plants. Expression analysis illustrated that transcription of AEE genes may be regulated by various abiotic stresses, hormones and light signal.(2) Beta-amylase (BAM) was a crucial amylase in the complete degradation of starch of plants, especially in the germination or malting of cereal grains. It was found to be involved in the abiotic stress responses of crops. In this research, the phylogeny classified the gramineous BAM genes into10clusters of orthologous genes (COGs), and the genes in the same COG shared the syntenic region. Functional divergence analysis provided statistical evidence that both the shift in the evolutionary rate pattern and cluster-specific alterations of amino acid physiochemical properties contributed to COG-specific functional evolution of BAM genes in grasses. In addition,3COGs were found to be influenced by positive selection through maximum likelihood analysis. Further investigation revealed that a total of18gramineous BAM genes subjected by positive selection, when we used the genes in the same COG as background. We also investigated the expression patterns of rice BAM genes, and the results revealed that some OsBAM genes exhibited abundant and tissue-specific expression patterns. Moreover, at least5OsBAM genes were found to be differentially expressed under the treatments of abiotic stresses. These observations may provide useful references for further functional detection of BAM genes in grasses.(3) Heat stress transcription factors (Hsfs) regulate gene expression in response to heat and many other environmental stresses in plants. Understanding the adaptive evolution of Hsf genes in the grass family will provide potentially useful information for the genetic improvement of modern crops to handle increasing global temperatures. In this work, we performed a genome-wide survey of Hsf genes in5grass species, including rice, maize, sorghum, Setaria, and Brachypodium, by describing their phylogenetic relationships, adaptive evolution, and expression patterns under abiotic stresses. The Hsf genes in grasses were divided into24clusters of orthologous genes (COGs) based on phylogeneitc relationship and synteny, suggesting that24Hsf genes were present in the ancestral grass genome. However,9duplication and5gene-loss events were identified in the tested genomes. A maximum-likelihood analysis revealed the effects of positive selection in the evolution of11COGs and suggested that COGs with duplicated or lost genes were more readily influenced by positive selection than other COGs. Further investigation revealed that positive selection acted on only one of the duplicated genes in8of9paralogous pairs, suggesting that neofunctionalization contributed to the evolution of these duplicated pairs. We also investigated the expression patterns of rice and maize Hsf genes under heat, salt, drought, and cold stresses. The results revealed divergent expression patterns between the duplicated genes.All those results of AEE, BAM and Hsf genes molecular evolution analysis in5grasses could provide a theoretical foundation for the further researching in the adaptive evolution and functions of these genes.