The Optimization Of Computational Technology In Forestry Phylogenetics

In recent years,with the rapid development of high-throughput sequencing technologies,the scale of storage and management of biological data has been continuously expanding,and various types of biological data have grown explosively,gradually forming a "sequence-chromosome-genome" difference.On the scale of genetic data,forestry is an important research object,and its genetic research has also entered the era of big data.In order to fully store,manage,and tap the biological information contained in these mass data,based on the analysis of the research status at home and abroad,this paper uses the methods of bioinformatics and big data to conduct in-depth excavation of forest tree genomic data.Work and innovation are as follows:1.Location based sequence alignment algorithm and its application in genetic function feature predictionOn the microscopic molecular level,sequence alignment technology is the basis of gene homology analysis.Based on the homology between genes,phylogenetic relationships among species can be obtained.In order to study the phylogenetic relationships of forest trees,an improved sequence alignment algorithm based on location features,LB-BLAST,was proposed for the first time.This algorithm was combined with the full annotation information of Arabidopsis thaliana plants to achieve homology matching.In principle,the corresponding genetic functions in the Tamarix genome are predicted for the first time.Compared with the traditional BLAST sequence alignment algorithm,LB-BLAST algorithm uses the position information of genes to constrain the results on the basis of accuracy,which significantly reduces the time complexity of the algorithm.In addition,the LB-BLAST was used successfully to analyze the chromosome breakage and fusion of poplar and willow in the evolution process,which provided an important reference for the future tree evolution analysis.2.Thegenome homology analysis algorithm and its application in tree system developmentAt the genomic level,a novel gene homology analysis mapping algorithm was proposed for the large differences in the genetic diversity of the forest tree genomes,and an online platform for gene homology analysis was constructed using LB-BLAST—VGSC.For the first time,the homologous species genes were compared in the form of online services,and the collinearity relationship of the forest tree genomes was quickly and efficiently converted into visualized graphs,including bitmaps,dual linear graphs,bar graphs,and circular graphs.The analytic graphing algorithm combines the characteristics of vector graphics in terms of orientation independence and size independence,providing a quick and accurate basis for analyzing the interspecific relationships of the forest tree genome and the intraspecific gene characteristics.Using this method,the WRKY gene family of Tamarix was analyzed by phylogenetic analysis.It was found that the WRKY gene family in willow was amplified in the chromosome by the pattern of fragment replication,and only a few genes were tandemly replicated,indicating that the WRKY gene was in the willow.Co-expressing or inhibiting events rarely occurs,but they are distributed on different chromosomes to play a regulatory role.At the same time,this provided evidence for the verification of two large-scale chromosome replication events in the evolution of higher plants.At the same time,due to the versatility and ease of editing of the data results of this method,it is particularly suitable for the analysis and mapping of high-throughput sequencing results.Therefore,many key researches at home and abroad such as buckwheat,willow and Qianhuigu have been published since their publication.It played an important supporting role.3.Phylogenetic tree generation method for tree organelle genomeOn the whole genome level,a new set of methods for extracting,cleaning and visualizing plant organelle genome data based on big data was designed using the advantages of a high degree of homology in the phylogeny of plant organelle genomes,combined with features of different organelles.A phylogenetic tree generation algorithm for different organelle genomes was designed and implemented.Among them,the 16 S and 23 S ribosomal RNA genes in the chloroplast genome are of relatively long sequence lengths,and there are obvious conserved and polymorphic regions.It is to construct a chloroplast phylogenetic tree.It is better to choose a rapid method to construct a phylogenetic tree based on the chloroplast 16 S or 23 S rRNA gene.The mitochondrial genome is present in most eukaryotes and can be used not only for phylogenetic structures between forest trees,but also for phylogenetic trees.Comparative genomics studies with other organisms have proposed mitochondrial ORF recognition algorithms and phylogenetic tree construction algorithms based on mitochondrial conserved genes.Finally,based on the above novel method,a set of phylogenetic analysis platforms for the tree organelle genome was constructed to study the evolutionary relationship between forest trees and forest trees and other species.In summary,this paper aims at the phylogenetic study of forestrytrees,and proposes a computational optimization scheme for the development of existing forest systems at three levels from microscopic to macroscopic.The LB-BLAST uses the restriction of the introduction sequence position for the first time.The conditions optimized the comparison of the microscopic sequences.VGSC optimized mapping methods for interspecific and intraspecific homology analysis of species.OGTree was the first to comprehensively use the big data technology to realize the computational system of forestry tree evolution analysis on the macroscopic level.These methods are applied to forest tree genome research.