The Mitochondrial Genome Of Cistanche Genus In China

Cistanche is an all-parasitic medicinal plant of the Orobanchaceae family and an endangered species distributed in the arid desert area of northwest China.Its fleshy stems with scale leaves have the effects of invigorating the kidney and replenishing blood.At present,the Cistanche industry has formed a scale of several billions,making important contributions to the economic development of the western region.The research team has completed the research on the chloroplast genomes of four species of Cistanche in China.In order to protect its genetic resources and enrich its genetic information,this study used young fleshy stems as materials to treat the four species of Cistanche in the northwestern China:Cistanche deserticola,Cistanche salsa,Cistanche sinensis,and Cistanche tubulosa were sequenced,assembled,and analyzed for mitochondrial genomes.The main results are as follows:1.Three-generation Nanopore high-throughput sequencing was used to sequence the Cistanche genome to obtain 216 Gb data,and second-generation Illumina sequencing was used to obtain 20 Gb data.After Blastn comparison,mitochondrial reads were screened and connected into 37 contigs.The contigs were assembled into primary sequences to obtain the mitochondrial genome of Cistanche.2.The mitochondrial genome size obtained by splicing and assembling is:C.deserticola 2043 Kb,C.salsa 2100 Kb,C.senensis 1392 Kb and C.tubulosa 2536 Kb.The base composition ratios are A(27.44-27.80%),T(27.59-28.03%),C(22.15-22.53%)and G(22.03-22.43%).3.The mitochondrial genome of Cistanche is diverse.The mitochondrial genome of C.deserticola is composed of 11 linear contigs,C.salsa is composed of 8 linear contigs,C.sinensis is composed of 6 linear contigs and 1 circular contigs,and C.tubulosa is composed of 11 linear contigs.Mitochondrial genome comparison showed that there were a lot of recombination events.C.deserticola and C.salsa were recombined less,and the others recombined more.4.Gene annotation analysis showed that the mitochondrial genome of Cistanche contains 33 intact protein-coding genes,3 ribosomal RNA genes,and 23 transport RNA genes.In addition,15 protein-coding genes were transferred from the chloroplast genome to the mitochondrial genome.5.There are many repetitive sequences in the mitochondrial genome of Cistanche,33-72 simple repetitive sequences,22-68 tandem repetitive sequences and 320-875 interspersed repetitive sequences were detected.6.Phylogenetic analysis showed that the four species of Cistanche were clustered together and the internal support rate was 100.C.deserticola and C.salsa were clustered together,and C.salsa and C.tubulosa were clustered together.7.Analysis of selection pressure and mutation sites showed that the ccmC gene was positively selected on the clade of C.salsa,with 5 mutation sites;the matR gene was positively selected on the clade of C.deserticola,and there were also 5 mutation sites.