| Orchidaceae plants have more than 700 genera and 20,000 species,and they are distributed in tropical and subtropical regions of the world.A few species are also produced in temperate regions.In our country there are 171 genera and 1,247 species of orchids and many subspecies,varieties and variants.Orchidaceae are perennial monocotyledons and belong to the third largest family of angiosperms.Orchidaceae also have high ornamental,economic and medicinal values.Cymbidium and Paphiopedilum plants are the main group of orchids,and both contain a large number of medicinal and ornamental plants.Orchidaceae is an evolutionary and complex family.So far,the research and understanding of the kinship between the various taxa in the family is still incomplete.Due to the lack of understanding of the genome of orchid plants,it has become a bottleneck in orchid research.It is known from various studies that the chloroplast genome is more suitable for studying the phylogenetic relationship of plants,because the chloroplast genome has the characteristics of small sequence length,single parental inheritance,low nucleotide replacement rate,and simple and conservative genome structure.In this study,we sequenced and assembled the complete chloroplast genome sequences of six species of Paphiopedilum and two species of Cymbidium.In addition,we downloaded the chloroplast genome sequences of eleven other species of Orchidaceae from Gen Bank,including three published Paphiopedilum sequences on the Internet.The comparative analysis of the chloroplast genome of Paphiopedilum was carried out by using informatics methods,and several data sets and related software were also used establish the phylogenetic relationship between them.The main contents and results of this study are as follows:1.Comparative analysis and phylogenetic analysis of chloroplast genomes of nine Paphiopedilum species.The results of the analysis show that the nine Paphiopedilum species have basically similar genetic structures,and their chloroplast genomes are all DNA molecules with circular tetrads,but there are also obvious differences;The chloroplast genome of six species of Paphiopedilum is 154,699 bp to 162,682 bp in length,with an average length of 157,561 bp,encoding 122 functional genes,including 76 protein genes(CDS),38 t RNA genes and 8 r RNA genes;By analyzing the IR / SC boundary of chloroplast genomes of nine species of Paphiopedilum,the results showed that the expansion and contraction of IR region existed in the chloroplast genomes of nine species of Paphiopedilum;The results of variation analysis showed that there were significant differences in trn P-UGG-psa J,psb B-psb T,ycf2-trn L-CAA,psa C-trn L-UAG,rpl32-ccs A,and two highly variable genes(rps15 and psa C)were found.These regions are of great significance to further study the genetic diversity and phylogeny of Paphiopedilum;The phylogenetic trees of 20 species based on various methods show that nine species of Paphiopedilum are grouped into one branch,and each branch has a high support rate.The research results can help us to understand more clearly the genetic relationship of nine Paphiopedilum species.2.Chloroplast genome analysis of two Cymbidium speciesIn this study,two chloroplast genomes(C.bicolor and C.qiubeiense)of Cymbidium were assembled and annotated,and simple analysis was carried out;The length of chloroplast genome of two Cymbidium species is 156,528 bp and 156,594 bp;Phylogenetic trees were established by using chloroplast genomes of two Cymbidium species and 11 different genera of other Orchidaceae to determine the position of two Cymbidium species in the phylogenetic relationship of Orchidaceae. |
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