Molecular Mechanisms Of SET Gene Family And Biotransferectomy Of Arabidopsis Thaliana Based On RNA-Seq Technique

Gene duplication is a fundamental source of new genes during evolution and can provide novel opportunities for evolutionary success. Whole-genome duplications (WGDs) can simultaneously generate a large number of duplicates and have been documented in animals, plants and fungi. Evidence for WGDs has been detected in all sequenced angiosperms, including at least five rounds of WGDs in Arabidopsis thaliana since its separation from the most recent common ancestor of seed plants. WGDs at important diverging points in eukaryotic evolution and the resulting gene amplifications might have contributed to the appearance of lineage-specific novelties.Plants and animals have very different developmental processes, yet share conserved epigenetic regulatory mechanisms, such as histone modifications. One of the most important forms of histone modification is methylation on lysine residues of the tails. Histone lysine methylation modifies chromatin structure and thereby regulates eukaryotic gene transcription and a variety of developmental and physiological processes. SET domain proteins are lysine methyltransferases containing the evolutionarily-conserved SET domain, which is known to be the catalytic domain. To broaden our understanding about the evolution of the histone methylation system, we investigated the evolutionary history of SET genes using comparative genomic analysis of the SET genes in sequenced genomes.The phylogenetic analyses of the SET genes in human and Arabidopsis, as representatives of animals and plants, respectively, support the grouping of SET genes into seven main subfamilies [Suv, Ash, Trx, E(z), PRDM, SMYD and SETD].The Suv, Ash, Trx and E(z) genes are highly conserved among animals and plants. Although with lower phylogenetic support, the SMYD and SETD genes have domain organizations that are conserved in animals and plants. Furthermore, domain organization differ between different subfamilies and between animal and plant SET genes in some subfamilies, suggesting that SET genes have evolved distinctive regulatory interactions. In animals and plants, most orthology groups have invertebrates and algae homologs in eachsubfamily, respectively, which suggests that these orthology groups originated and functionally conserved in early animals and plants. We observed that many gene duplication events occurred in the Suv, Ash, Trx and E(z) subfamilies, implying diversification of these highly conserved SET genes. The SET genes have expanded after the divergence of animals and plants, and again after the separation of vertebrate and invertebrate animals, also after the split of land plants and chlorophytes. The more recent set of duplications in both vertebrate animals and land plants are likely due to whole-genome or segmental duplications. The evolution of the SET gene family shows that gene duplications and segmental duplications likely contribute to the complexity of epigenetic regulation and provide insight into the evolution of chromatin structure regulation.Here we show that the plant gene ASHH4originated through a whole-genome duplication35to85million years ago andunderwent diversifying selection in the coding region after duplication, like the MEA. ASHH4continues to evolve rapidly in Arabidopsis thaliana but not in Arabidopsis lyrata. The paralogue of ASHH4, ASHH3, evolved under strong purifying selection because it probably retained the ancestral function of the common precursor gene.We have performed high-throughput sequencing of three normalized cDNA libraries, apical mutant reproductive meristems, floral stages1～9and stagel2floral buds, which resulted in a high coverage transcriptome map of Arabidopsis. We detected24542genes expressed in the three samples. Compared with the previous Affymetrix ATH1arrays using the same tissues, we detected about8,000genes not found in previous arrays. A large number of these genes are low expressed, that are enriched environment and stress-related gene family, which include transcription factors, such as the NAC, bHLH, AP2and MYB. Compared with seedling, we identified a large number of differentially expressed genes in flower development. These genes are enriched with the ATPase, chromatin modification and RNA synthesis-related gene family,such as theAAA, WD40, SET, Helicase_C and DEAD gene families. Transcription factors and epigenetic genes are highly expressed in early flower. Additionally, we found that some unknown function (DUF) gene families have tissue-specific gene expression, such as DUF577that was specifically expressed during meiosis and DUF1216specifically expressed in floral stages1-9.