Comparative Whole Chloroplast Genomics Of Castanea And Fagales Family

Castanea Mill is an important economic tree species belonging to Fagaceae.Chinese chestnut species occupy an important position in the world's chestnut plants because of their good disease resistance characteristics.At present,the research on chestnut plants mainly focuses on the genetic diversity research.The comparative study of the chloroplast genome sequence of the chestnut plants and the sequence of the Fagaceae is helpful to enhance the deeper understanding of the evolution and classification of the origin of the chestnut plants.The chloroplast genome is one of the traditional methods for studying the evolution of species and rebuilding the relationship between angiosperm systems,and the frequent use of chloroplast genomes in this type of analysis is based on a simple conservative structure of its one-parent inheritance: one-parent inheritance through the maternal line.Therefore,in this study,high-throughput second-generation sequencing technology was used to sequence and assemble the chloroplast genomes of Chinese chestnut plants(Castanea mollissima),Mao chestnut(C.seguinii),and chestnut(C.henryi),which are endemic to China.At the same time,the Chloroplast genome sequence data published at the beginning of the study was downloaded from the Gen Bank database.Finally,the comparatively rapid genomics analysis of the selected sequences is carried out using the rapidly developing bioinformatics method.Provide more valuable research basis for the world chestnut plants and the chloroplast genomes of Fagaceae.The main research contents and results of this study are as follows:1)Chloroplast comparative genome analysis of CastaneaThe four sequences assembled from the Castanea plant and the f Ive downloaded Chloroplast genome sequences including four chestnut species of Castanea pumila were compared and analyzed.Chloroplast genome length of Castanea plants range from 160805bp(C.mollissima2)to 161010bp(C.seguinii2).During the annotation process of the chloroplast genome of Castanea,each sequence of the annotated genes has 130 functional genes,including 37 t RNA genes(7 genes in the IR region)and 8 r RNA genes(all located in the IR In the region),the number of genes appearing as a single copy is 116.Among them,the pseudogene ndh D was also found in chestnut C.mollissima1 and C.mollissima2,and the pseudogene ndh K was found in C.henryi1.The ycf1 genes in Castanea sequences are all pseudogenes.Each sequence in the chloroplast genome of the Castanea plant contains108-120 simple repeats.The simple repeats obtained by statistics are compared and analyzed,and 17 pairs of common SSR primers for the chloroplast of Castanea are designed.A total of 335 repeats of intermittent repeats obtained from chestnut plants.The overall number of tandem repeats is relatively small,with a total of 73 repeat counts.The analysis of comparative genomics of Castanea using Chinese chestnut as a reference showed that: Castanea had no significant differences at the IR / SC border;polymorphisms such as single nucleotide polymorphism sites(SNP)and insertion deletion sites(Indel)The statistics of sex sites show that the variation in the SC region is significantly more than that in the IR region,and the mutation rate in the non-coding region is significantly higher than that in the coding region.The genes with large variation in the coding region are psbl,acc D,pet G,pet D,rpl2,ycf1,and ndh A.There are 25 regions in the non-coding region with large variation.The genes mat K,ndh D and rpo C2 are under strong positive selection pressure during evolution.Spider sliding window draws three coding regions rpo B,rpl2,acc D and two non-coding regions trn K-UUU-rps16 and pet A-psb J sequences as DNA candidate barcodes.A phylogenetic tree was constructed from the above sequence fragments,and it was suggested that the gene sequence of mat K,ndh D and rpo C2,acc D,pet D,ndh A,rpo B,acc D,pet A-psb J and other sequence fragments can be used as DNA barcodes.2)Comparative genome analysis of ChloroplastsIt is helpful to understand the phylogenetic relationship between the genome of Chloroplast and the chestnut Chloroplast by recording and downloading the whole genome sequence of the Chloroplast species published in the beginning of this study and statistically analyzing the sequence characteristics.The chloroplast genomes of various families of Fagaceae showed similarities and differences in the number of sequence genes,gene types,gene order,and GC content of each subarea.The Chinese chestnut was used as the reference sequence to find the rearrangement phenomenon in the IR region in the collinear analysis of the fungus.However,the analysis of the variation of the Fistula objective showed that the SC region had greater variation than the IR region,and the IR region was more conservative.To partition the chestnut plants,use five data sets(whole cp genome,protein-coding regions,LSC,SSC,IR)to build a phylogenetic tree,and to build a phylogenetic tree of the entire sequence of the chloroplast genomes of all known species of Fagaceae.Provide a reference for the phylogeny of Castanea and Fagaceae.