Database Construction And Evolutionary Analysis Of Intronless Genes In Maize And Related Species

Introns are the parts of eukaryotic genes that do not contain coding information. However, prokaryotic genes lack introns. Intronless genes in eukaryotes, because of their prokaryotic architecture, provide interesting datasets for comparative genomics and evolutionary studies. Studying these genes can help to understand the evolutionary patterns of related genes and genomes. However, former evolutionary researches on intronless genes during the recent years have usually been limited to 1 to 2 species. In our study, genome-wide analysis of identification for intronless genes in maize and related species were performed. In addition, a comprehensive analysis, including chromosomal distribution, domain and functional prediction, subcellular location prediction, paralogues of intronless genes, conservation in different taxonomic groups and expression patterns, was provided. Based on the data, the orphan intronless genes in maize were further analyzed in terms of gene characteristics and single nucleotide polymorphism. Studying these genes will help us understand the functional role of maize-specific genes, and the mechanism of adaptive mutation in the process of domestication. It will provide basic information on the research of unknown functional genes. The following are the main results:1. A total of 54,336 intronless genes from five sequenced Poaceae species, including Sorghum bicolor, Zea mays, Setaria italica, Panicum virgatum and Brachypodium distachyon were identified. Meanwhile, detailed annotation and comparative analysis were performed, such as the number and percentage of intronless genes in genomes, the characteristics of gene sequences, functional categories, the distribution of intronless genes in different taxonomic groups. After integrating all of data, the Poaceae Intronless Genes Database (PIGD) was constructed in the form of website. The web interface of the PIGD was designed to comprise the some components, like BLAST, Browse (for the database), Comparison. The PIGD is the only existing intronless genes database in terms of plants.2.14,623 intronless genes in maize were identified. Chromosomal distribution analysis indicated that the ratio of intronless genes to genes was constant along chromosome (roughly 37%).The results showed that the number of intronless genes on each chromosome have a significant linear correlation with the number of total genes (including intronless genes and intron-containg genes) on the chromosome and the length of the chromosomes in maize. In addition, a trend that intronless genes enrich both ends of all 10 chromosomes was founded.3. Intronless genes may play a crucial role in translation and energy metabolism in maize. Subcellular localization of protein indicated that a number of intronless genes were expressed in nucleus and chloroplast. The expression profiles revealed that most of intronless genes have broad expression patterns. In addition, the intronless genes were expressed generally higher before pollination.4. About 26% of the maize intronless genes have at least one intronless gene paralog. It was suggested that more than a quarter of intronless genes in maize may have been derived from other intronless maize genes by gene duplication. Taxonomic distribution showed that the majority of intronless genes that have homologues only in eukaryotes, suggesting that most intronless genes emerged after the eukaryotes diverged from prokaryotes. Evolutionary analysis revealed that 2,601 intronless genes conserved among the three domains of life (ABE group) and 2,323 intronless genes that had no homology with genes of other species (ORFans).5. Compared with the ABE group, the intronless genes in ORFans shared many of the characteristics:1) ORFans were distributed unevenly on the maize chromosomes. And the number of ORFans in the region of centromere on each chromosome was significantly higher than that of ABE group.2) ORFans have shorter length, lower GC content, lower molecular weight (Mw) and higher isoelectric point (PI). Functional prediction showed that the significant enrichment of stress response proteins in ORFans annotated by gene ontology (GO). The temporal and spatial expression profile of ORFans revealed that they are specifically enriched in silk and anther. In addtion, single nucleotide polymorphism (SNP) analysis showed an elevated ratio of non-synonymous to synonymous SNPs within ORFans (1.83) relative to the ABE set (0.87), mainly caused by an elevated number of nonsynonymous SNPs, indicating that they are fast-evolving at the protein sequence level.In conclusion, intronless genes in maize and related species were identified and analyzed using bioinformatics, further suggesting the rule of function and evolution of intronless genes. Meanwhile, studing on functional of specific genes could provide crucial clues to understand the differentiation, phenotype, and morphology of the species in their evolutionary process. Specifically, the analysis will help us to select important functional genes.