Comparative Chloroplast Genomics Of Patchouliol-type And Pogostone-type Of Pogostemon Cablin

Pogostemon cablin(Blanco)Benth.(Labiatae)is a perennial herbaceous plant with significant economic and medicinal importance.Based on the main components of patchouli oil,P.cablin has been divided into two chemotypes: Patchouliol-type and Pogostone-type.Traditionally,the patchoulol-type is mainly used in the perfume industry,whereas the pogostone-type cultivars are considered medicinal plants in China.However,the rapid development of Guangzhou has driven the local real estate industry,and the planting area of the pogostone-type P.cablin,which was originally widely planted in Shipai and Tangxia,has been drastically reduced.It has completely disappeared,which directly leads to a significant reduction in the production of the pogostone-type P.cablin.In addition,some farmers have mixed the two types of P.cablin,resulting in mixed varieties in the production area and use the Patchouliol-type to replace the pogostone-type for medicine.So,it is difficult to ensure the quality and yield of P.cablin from the source.In the present study,20 complete plastomes of two chemotypes were sequenced and successfully assembled.By comparing the genome junction,codon usage bias and simple repeated sequences,the characteristics of two chemotypes P.cablin were revealed.The phylogenetic tree was constructed based on the whole chloroplast genome,and the phylogenetic relationship of P.cablin was elucidate.Plastomes of all sequenced P.cablin contained a LSC region,a SSC region and two IRs regions.The overall sizes of assembled complete plastomes of Patchouliol-type and Pogostone-type were 152,462 bp and152,461 bp,and the total GC content was 38.2%.The plastome of P.cablin possessed 114 unique genes(80 coding genes,30 t RNAs and 4r RNAs)without gene deletion,translocation and inversion.In the LSC/IRa junction,IRa expanded into the rps19,and the IRb/LSC junction was located between the rpl2 and trn H.In the SSC/IRb junction,the ycf1 crosses the SSC/IRb junction,and the IRa/SSC junction is located on the ndh F.The total number of SSR was 74 in P.cablin complete plastomes,mainly distributed in large single copy region and composed of A/T.Moreover,the codon bias analysis showed that there were 50,820 codons in the complete plastomes,but the number of the same codon in the two chemical types was different.In addition,seven optimal codons—UUG,GUA,UCU,CCU,CCC,GCA,AGG—were selected from the complete plastomes.The phylogeneic analyses based on the whole plastomes showed that Patchouliol-type and Pogostone-type of P.cablin are one branch respectively,and the sister group relationship of the two branches is highly supported.