Comparative And Evolutionary Analysis Of F-box And LBD Gene Families In Grasses

Poaceae, also known as Gramineae or the grass family, defines a type of most widely distributed monocotyledons across the world, which is of significant economic value. They are the main source of human food and animal stock feed, and are also important raw materials of starch processing, sugar engineering, brewing industry, papermaking, knitting, construction industry, etc. In recent years, with the rapid development of genomics research, whole-genome sequencing of more and more gramineous crops have been completed, such as Oryza sativa, Zea mays, Brachypodium distachyon, Sorghum bicolor and Setaria italic. The completion of whole-genome sequencing of the gramineous genomes establishes a foundation for further analyzing and mining valuable information stored inside and carrying out evolutionary and genetic researches. The comparative study of the gramineous genomes suggested synteny among them, however, large differences occurred as well. The genomes of extant grasses were supposed to form through gene duplication/loss, chromosomal fusion and other evolutionary events. Duplicated genes might experience subsequent adaptive evolution with the involvement of purifying or positive selection. Most of the genes in gramineous genomes could belong to gene families, and confer species-specific expansions or contractions with gene duplication or loss. In our research, a set of systematic bioinformatic approaches were employed to perform comparative and phylogenetic analyses for gramineous F-box and LBD family, which provided a theoretical foundation for a deeper exploration of plant molecular evolution. The main findings were concluded as follows:(1) F-box proteins (FBPs) occur extensively in eukaryotes and are characterized by an N-terminal F-box domain. FBPs play a crucial role in cell cycle progression, transcriptional regulation, apoptosis and cell signaling transduction via interacting with specific protein substrates in ubiquitin-proteasome pathway (UPP). In most plants, F-box family is one of the largest and most rapidly evolving families. To further illustrate the evolutionary pattern of F-box gene family in grasses, our research selected the genomes of five representative gramineous crops, including Brachypodium distachyon, Zea mays, Oryza sativa, Sorghum bicolor and Setaria italic, to perform a comparative and evolutionary analysis on F-box gene family. The numbers of F-box genes showed a significant difference among the five gramineous genomes, and 641,322,742,576 and 753 F-box genes were identified in B. distachyon, Z. mays, O. sativa, S. bicolor and S. italic, respectively. Also, it was manifest that the distribution of F-box genes among the five species was not proportional to that of whole genes, indicating that the gramineous species have undergone large-scale gene duplication and/or loss events. A further exploration presented that, frequent gene duplication events occurred in the genomes of O. sativa and S. italic, while frequent loss events in the genome of Z. mays. Through an adaptive evolution analysis for clusters of orthologous genes (COGs), purifying selection was recognized as the dominant force for the evolution of F-box family. However, an unneglectable amount of F-box COGs experienced positive selection. Notably, paralogous F-box genes in Z. mays genome seemed to be less readily influenced by positive selection signatures, which was predicted to be the direct consequence of purifying selection resulted from less gene duplication events. Additionally, in our study, research methods of coevolution were expanded to a more widely scope, where Kendall rank correlation coefficient was introduced into the detection of coevolution among amino acid sites. The results indicated that, except for the FBA-containing and Herpes_UL92-containing subfamilies, the other nine subfamilies were all detected of coevolving site-site pairs.(2) LBD genes define a class of plant-specific genes characterized by a conserved N-terminal LOB domain. LBD gene family plays a central role in the initiation of lateral organs primordium, formation of lateral organs and establishment of boundaries between lateral organs and SAM (shoot apical meristem) and so on. In our research, on the ground of the phylogenetic analyses performed on the 189 LBD genes in the genomes of five representative gramineous plants, including Brachypodium distachyon, Zea mays, Oryza sativa, Sorghum bicolor and Setaria italic, the LBD family could be clustered into 33 clusters of orthlogous genes (COGs). Therefore, it was induced that at least 33 LBD genes existed in the genome of gramineous plant ancestor. In combination with the phylogeny of gramineous LBD genes, we estimated gene duplication and loss events in each genome, and found that frequent gene duplication events occurred in the genomes of rice and maize. A further investigation of paralogous LBD genes suggested that tandem duplication was responsible for most rice and maize LBD gene duplication events. An adaptive evolution analysis for COGs suggested that purifying selection was the principal driving force for the evolution of LBD genes, however, a significant number of LBD COGs underwent positive selection. Finally, a deep exploration of expression patterns under abiotic stresses of rice LBD genes was made, and one pair of paralogous rice LBD genes were discovered to exhibit divergent expression patterns under heat shock condition, indicating functional divergence between them.