Construction And Application Of Identification And Analysis Process Of Full-length LTR-Retrotransposons

Long terminal repeat retrotransposons(LTR-retrotransposons)are a ubiquitous component of plant genomes and are especially abundant in species with large genomes.However,little is known about the role of full-length LTR-retrotransposons(FL-LTR-retrotransposons)in the evolution of plant genomes.A large number of plant genome has been sequenced,providing a data source for the study of LTR-retrotransposons.This study is to establish a process for analyzing LTR-retrotransposons.Firstly,the identification process of LTR-retrotransposons is constructed by understanding of the algorithms of each identification software,combining the advantages and disadvantages of Smith-Waterman and greedy algorithm.And identifying the LTR-retrotransposons internal functional domain.Secondly,we construct the LTR-retrotransposons analysis process.We construct the analysis process of LTR-retrotransposons from three aspects.Insertion age,Subfamilies of the LTR-retrotransposons and the regulation of LTR-retrotransposons captured genes.Finally,we selected four monocotyledonous plants and four dicotyledonous plants for analysis.The LTR-retrotransposons were analyzed by the process we built.Estimation of LTR-retrotransposon insertion age suggested that most were inserted into the host genome much more recently than plant speciation.Analysis of the lineages indicated that the monocotyledon genomes carried more of the Gypsy-type Tat subfamily and Copia-type Maxiums subfamily,while the dicotyledon genomes carried more Gypsy-type Athila subfamily and Copia-type Ale subfamily.We identified the genes located within the LTR-retrotransposons,also known as an LTR-retrotransposon-captured gene(LTRCG).The variance of expression patterns were observed in most of the LTRCGs from the analysis of RNA-Seq data.Consequently,insertion of the FL-LTR-retrotransposons is important to evolution of plant genomes.