Comparative And Phylogenetic Analysis Of The Complete Chloroplast Genomes Of Cistanche

The Cistanche plant of Orobanchaceae is an important group of plant resources in China.At present,the annual sales of Cistanche-related products in China has exceeded 100 million yuan.The Cistanche industry has formed a certain scale and has become an important component of the economic development of the western region.Chloroplasts,as organelles for photosynthesis and energy conversion,play an important role in maintaining the survival of the Earth's living things.Chinese taxonomists have different opinions on the classification of Cistanche.In order to better provide omics reference data for the classification and identification of Cistanche.In this paper,the whole chloroplast genome of four parasitic species of Cistanche(C.deserticola,C.tubulosa,C.salsa and C.sinensis)in northwest China was sequenced,assembled and analyzed.Phylogeny,differentiation time and molecular markers were analyzed.Results:(1)The chloroplast genome of four Cistanche plants belongs to a typical annular quartile structure.(2)The chloroplast genome size was 109 495 bp in C.deserticola,75 375 bp in C.tubulosa,111 710 bp in C.salsa and 111 500 bp in C.sinensis.(3)The gene loss in the chloroplast genome of four Cistanche plants are mainly in photosynthesis and energy production genes.(4)The study found for the first time that Ribosomal RNA genes in C.tubulosa were single copies,suggesting that C.tubulosa may be experiencing more severe gene loss.(5)Sliding window analysis showed that the average nucleotide diversity among the chloroplast genomes of Cistanche species was 0.309 866,which was much higher than that of other genera.(6)Using the mVISTA software to analyze the sequence similarity of five chloroplast genomes of Cistanche.The results showed that C.deserticola and C.tubulosa were similar;C.sinensis,C.tubulosa and C.phelypaea were similar.Among them,C.sinensis differs greatly from C.deserticola and C.salsa in the non-coding region.It is speculated that the genetic evolution of C.sinensis may be different from C.deserticola and C.salsa,or that C.sinensis is experiencing a different evolution process from C.deserticola and C.salsa.(7)Phylogenetic trees were constructed based on 15 common genes in the chloroplast genome of Orobanchaceae plants:clpP?matK?rpl16?rpl2?rpl20?rpl33?rpl36?rps11?rps14?rps18?rps3?rps4?rps7?rps8 and rps2.The results showed that five species of Cistanche were clustered on one branch.In the genus Cistanche,it can be roughly divided into two branches,one is C.sinensis living alone.This indicates that C.sinensis is more differentiated than the other four Cistanch Cispecies in the same genus.(8)Molecular clock(differentiation time)of Cistanche species was studied by BEAST software.The results showed that the formation time of Cistanche species was different.The first species to form was C.sinensis,which took the lead in differentiation 27.0 223 million years ago(Mya).(9)The Ecoprimer software was used to analyze the chloroplast genomes of five species of Cistanche,and 20 pairs of potential molecular markers were designed for accurate identification of Cistanche species.