From Autotrophism To Parasitism:Sequence Variation And Evolution Of Chloroplast Genomes In Orobanchaceae Species

The family Orobanchaceae including full autotrophic,hemi-parasitic,and holoparasitic species,has been becoming a key taxa to study the plastome evolution of different lifestyles.To the present,the chloroplast genome researches of Orobanchaceae plants mainly focus on parasitic species.Exploring the evolutionary patterns of chloroplast genomes in hemiparasitic groups would help to understand the effects of the transformation of the nutrient patterns from the autotrophic to parasitic plants.As a hemi-parasitic group of Orobanchaceae,Pedicularis L.is widely distributed in diverse environments with important medicinal values.In this study,four de novo assembled plastomes of Pedicularis,together with others in Orobanchaceae published,were analyzed to investigate the evolutionary history of chloroplast genomes at genus and family level.The main results are as follows:(1)The chloroplast genomes of four species of Pedicularis are from 152,907 bp(P.muscicola)to 153,547 bp(P.longiflora)in length,annotated to 133 genes,including 88 protein-coding genes,37 tRNA genes and 8 rRNA genes,of which 115 appear as single copy genes.Genes ndhD and ndhF are pseudogenes in Pedicularis oederi,Pedicularis muscicola and Pedicularis longiflora;Gene ndhH is a pseudogene in Pedicularis muscicola and Pedicularis longiflora.The amino acid composition and GC content of the protein coding regions of four Pedicularis species are similar,preferring to use A/T bases.Comparative chloroplast genomics analysis showed that repeat sequences appeared frequently in the high variable regions in the four chloroplast genomes of Pedicularis.Taking the autotrophic plant Lindenbergia philippensis as a reference,the collinear analysis showed that the SSC region of the chloroplast genome of Pedicularis had rearrangement.The rearrangement of the SSC region results in a change in the gene order at the IR/SC boundary.Phylogenetic analysis indicated that there was a deep split between heterotrophic and autotrophic plants,and Pedicularis was a monophyletic clade,but the interspecific relationships within the genus was still uncertain.(2)We analyzed and compared the sequence variation of the complete chloroplast genome of 25 species from 17 genera of the family Orobanchaceae,and explored the evolution of the chloroplast genome during the transition from autotrophy to parasitism.The chloroplast genome sizes of semi-parasitic plants are similar to those of autotrophic plants,but some species have slightly reduced or expanded,while the chloroplast genome of whole parasitic plants varies widely,from 45 kb(Conopholis americana)to 150 kb(Lathraea squamaria).As for the chloroplast genome structure,the SSC region of all hemi-parasitic plants had rearrangement,and the LSC region of some hemi-parasitic plants also were rearrangeed;In the holoparasitic plants,the structure of the chloroplast genome changed to varying degrees,for example,rearrangement,fragment loss,and some are not even typical four-segment structures.In terms of gene content,there were 113 single-copy genes in the autotrophic plants of Orobanchaceae,but the number of genes shared among the 25 species was 33.The number of genes in hemi-parasitic plants was similar to that of autotrophic plants,but the ndh genes were pseudogeneticized or even lost.While in holoparasitic plants,gene reduction,gene loss and pseudogenation were common: most photosynthesis-related genes were lost or pseudogenized,and transcription-related genes or other genes were also pseudogenized or lost to various degrees.The variation analysis of the chloroplast genome of three living types showed that the chloroplast genome of autotrophic plants had a low variability,mainly in the SC region;the hemi-parasitic plant had a high mutation rate in the SSC region;and the holoparasitic plant had a high mutation rate in the whole chloroplast genome.By analyzing the codon usage bias of the protein coding region,it was shown that the overall codon usage bias was affected by the base mutation,but the rpl/s gene was subjected to selection pressure in the hemi-parasitic and holoparasitic species.The selection pressure analysis of common genes in 25 species showed that matK and rps18 genes were positively selected and had positive selection sites.Phylogenetic analysis indicated that the autotrophic plants were located at the base of the family Orobanchaceae,and the parasitic plants were monophyletic,and the holoparasitic plants were multiple originated,which could provide a brief reference for the phylogenetic research of Orobanchaceae.