Systematic Integration And Application Of Bioinformatics Analysis Methods For Chloroplast Genomes In Plants

Chloroplasts are the primary site of photosynthesis in plant cells.They are semiautonomous organelles that contain a complete set of genetic information and can perform self-expression and replication.With the rapid development of sequencing technology and bioinformatics technology,more and more plant chloroplast genomes have been studied and applied.The chloroplast genome can be used to identify plant classification,explore phylogenetic relationships,and infer phylogeography,etc.This study systematically summarizes the analysis methods and procedures of plant chloroplast genome biological information,and selected dicotyledonous plant Litsea,monocotyledonous plant Musa and basal group Nymphaea as research objects based on Angiosperms Phylogeny Group(APG IV),and carries out the practical application of chloroplast genome bioinformatics analysis methods as well as the analysis and report of 30 plant chloroplast genomes.The main conclusions of this study are as follows:(1)Genome feature analysis shows that the chloroplast genomes of Litsea,Musa and Nymphaea have a typical quadripartite structure,including a large single copy region(LSC),a small single copy region(SSC)and two identical inverted repeat regions(IRs);the species of chloroplast genes are basically the same,including 78 protein-coding genes,37 t RNA genes and 4 r RNA genes;codons usually change the first or second nucleotide,which changes amino acids from hydrophilic to hydrophobic;the AT content in repeat sequences is higher than the GC content,and the number of direct repeats and palindromic repeats is higher than that of reverse repeats and complementary repeats.(2)The rpl16 and ycf2 genes of Litsea have undergone strong positive selection pressure,and rpl16 is the only high-variance protein-coding gene.Phylogenetic analysis based on the data of complete chloroplast genomes and 64 proteincoding genes suggests that L.moupinensis is a sister group of L.rubescens,L.chunii and L.tsinlingensis.(3)The protein-coding genes of Musa are relatively stable during the evolutionary process,but two genes(ycf1 and ycf2)are under positive selection;due to the contraction and expansion of the IRb region,the rps19 gene is completely located in the IRb region or exists in multiple copies;the phylogenetic tree of Musa divided it into two subgenera,Musa L.sect.Musa and Musa sect.Callimusa.(4)The result of the phylogenetic tree of Nymphaeales further divided it into three families: Hydatellaceae,Cabombaceae and Nymphaeaceae.Meanwhile,Nymphaeaceae can be divided into five subfamilies,or three subfamilies Brachyceras-Anecphya,Ltos-Hydrocallis and Nymphaea are more appropriate.The divergence time tree of Nymphaeales re-estimated the origin time of angiosperms and Nymphaeaceae,the origin time of angiosperms is about 228 Ma,the divergence time of Nymphaeaceae is about 131 Ma.In conclusion,this paper provides methodological guidance for studying the chloroplast genome,as well as further sequence information for the taxonomic study of the genera Litsea,Musa and Nymphaea,and provides a molecular basis for interspecific phylogenetic developmental questions.