Researches Of The Angiosperm Genome Evolution

Gene order and location in chromosomes of species are non-random.During the evolution process,there is a certain regularity in the change of gene location.For example,some genes are adjacent to each other and later separated,some genes are not adjacent to each other,after evolution to other species,they become neighboring genes.Some studies have shown that the Whole Genome Duplication events(WGDs)have been recognized as an important evolutionary force.But after evolution,if there is a potential relationship between the separation of neighboring genes and WGDs and the relationship between them can be explained by a model needs to be investigated.In addition,it is unknown that whether there is intra-chromosomal colocalization between the separation of neighboring gene pairs,and is there some similarity between them like co-expression,co-modifications and conservation across species.In evolution,the proximity of genes can be divided into three types: linear proximity,spatial proximity,and evolutionary proximity.However,the contribution of linear proximity,spatial proximity,and evolutionary proximity to these similarities remain unclear,and it is unknown that together with whether the presence of several types of proximity can strengthens the similarities.Due to technical limitations,we can only study the relationship between gene pairs from a two-dimensional perspective.With the development of technology,we can now study the spatial relationship of gene pairs from a three-dimensional perspective.Chromatin three-dimensional conformation capture technology represented by Hi-C acquires three-dimensional conformation of chromatin by generating high-throughput sequencing data.In order to study the three-dimensional relationship between these genes in evolution,we need to analyze the data of these large amounts of biological information.First of all,this paper introduces the separation of neighboring gene pairs is closely related to whole genome duplication events.Furthermore,there is a double linear relationship between separated neighboring genes,total genes,and WGDs.The process of separation of neighboring genes caused by WGDs is also not random but abides by the double linear model.Next,this paper predicts the recent whole genome duplication events of angiosperms by using the previously constructed binary linear model.Comparing the predicted results with the known reports,it is found that the predicted results are in good agreement,which indicates that the construction of binary linear model is relatively successful.Then,by analyzing the three-dimensional spatial data of Arabidopsis thaliana chromatin,some linear but spatial interaction gene pairs in Arabidopsis thaliana chromatin were obtained.Then we find homologous gene pairs of these genes in other species and make evolutionary analysis of these linearly non-adjacent but spatially interactive genes find that separated neighboring gene pairs tend to show intra-chromosomal colocalization.By analyzing the species number and histone modification data of these spatially interacting evolutionary isolation gene pairs,it was found that the conservativism of separated neighboring genes and histone modification facilitate the intra-chromosomal colocalization of neighboring genes after their separation.Next,this paper introduces three kinds of colocalized gene pairs: intra-chromosomal colocalized gene pairs,always-neighboring gene pairs,and evolutionary neighboring gene pairs.This paper find that(1)Different types of colocalized genes differentially contribute to co-expression,co-modifications and conservation across species;(2)Intrachromosomal colocalization can strengthen co-expression and co-modification of neighboring gene pairs and their conservation across species;(3)The combination of the three kinds of colocalization can lead to the strongest co-modification and is most strongly conserved across species through data analysis.