| Cushion plant is a general term of plant groups with convergent cushion-like morphological structures,which independently originate from various linage of plant.The aerial parts of typical cushion plant usually have shortened internodes,repeatedly branched stems and branches,and closely clustered leaves throughout the plant surface,forming a compact continuous flat or hemispherical cavernous structure.The Qinghai-Tibet plateau is a hot spot for the distribution of cushion plants in china.Due to the special configuration of the plant that is extremely dwarfed and grows close to the ground,and on account of the developed root system,the specialized leaf and other unique structures,the cushion plant can well resist the strong wind,extremely cold and dry atmosphere,and maintain the steady state of micro-habitats in the cushion-shaped body.However,many studies have focused on the effect of morphological structure and physiological characteristics of cushion plants on environmental adaptability,and few have explored the intrinsic molecular adaptive mechanism exhibited by this plant group with similar phenotypes when adapting to extreme environments.In this study,three cushion plants,Saxifraga saginoides,Saxifraga sessiliflora,and Rhodiola coccinea,distributed in the Qinghai-Tibet Plateau,were taken as the main research objects.And in combination with non-cushion plants in two genus,the molecular mechanism of adaptation for cushion plants to the extreme environment in the Plateau was explored based on chloroplast genome and transcriptome sequencing analysis.The results were as follows:1.Comparative study of chloroplast genomes.The chloroplast genomes of three cushion plants,namely S.saginoides,S.sessiliflora,and R.coccinea,two non-cushion plants,R.crenulata and R.sacra,are obtained by sequencing,and the published chloroplast genomes of five saxifraga and nine Rhodiola non-cushion plants are combined to conduct the comparative chloroplast genome analysis among the cushion plants and the non-cushion plants in Saxifraga and Rhodiola,respectively.The results showed that:(1)The chloroplast genome size of Saxifraga species ranged from 146,549 to 151,066 bp,with GC content of 37.8% to 38.1%,while that of Rhodiola species ranged from 150,773 to 151,803 bp,with GC content of 37.7% to 37.8%.The chloroplast genome of Rhodiola species was more conservative in terms of genome size and GC content.However,in general,the chloroplast genome was relatively conservative within or even between the two genera.The IR boundary of all species showed no strong signs of expansion or contraction,and the genes around the boundary and their locations were relatively conservative.Protein-encoding genes in chloroplast genomes of the two genera exhibited consistent amino acid and codon usage preferences.Leucine and isoleucine are widely used,while cysteine and tryptophan are rarely used.Also,the third nucleotide of the codon encoding the same amino acid in both genera had a higher A/U frequency.(2)From the analysis of sequence characteristics,the degree of structural variation among chloroplast genomes of different species is determined by phylogenetic relationship,while the cushion phenotype of cushion plants does not have a significant impact on the sequence structural variation of chloroplast genomes.(3)Potential selected amino acid sites in atp B genes were detected in all chloroplast genomes of the high-altitude habitated species.Three cushion plants were specifically detected selected site in cem A gene,which might be related to high-altitude convergent adaptability among cushion plants.2.Comparative study of transcriptome.The transcriptome data of the following species were obtained by sequencing: high-altitude distributed cushion plants R.coccinea,non-cushion plants R.crenulata,R.sacra,relatively lower-altitude distributed species R.wallichiana in Rhodiola genus,and two high-altitude distributed cushion plants in Saxifraga,S.saginoides S.sessiliflora.The results of comparative analysis showed that:(1)The differentially expressed genes of three Rhodiola species at high altitude compared with one at low altitude shared terms or pathways such as abiotic stimulation response,photosynthesis,secondary metabolite synthesis and processing,hydrogen peroxide response,and starch and sucrose metabolism;at the same time,most of the genes related to photosynthesis and starch and sucrose metabolism were up-regulated,which acted on the processes of basic light reaction,photosystem repair,non-photochemical quenching,chloroplast avoidance movement,starch and sucrose metabolism,and trehalose synthesis,respectively,showing the plant’s common adaptability to strong light,low temperature,and other adversities in the QTP.(2)Under the same high-altitude environment,compared with the non-cushion plants R.crenulata and R.sacra,349 genes and 295 genes were detected with specific up-regulation and specific down-regulation,respectively,in cushion plant R.coccinea,of which most genes related to DNA recombination repair,production of plant secondary wall were up-regulated and most genes related to plant immunity and defense response were down-regulated.Among the analysis of differential expression in the three groups,the biological process of secondary cell wall biogenesis was specifically enriched in R.coccinea group.(3)Convergence expression signals were detected in the highly expressed genes among the three high-altitude habitated cushion plants.3.RNA editing study for chloroplast genome: based on the transcriptome and chloroplast genomic data,the chloroplast RNA editing sites of cushion plants S.saginoides,S.sessiliflora,and R.coccinea,two non-cushion plants,R.crenulata and R.sacra,were identified.the results were as follows:(1)22 common genes with editing sites were detected in Rhodiola genus,and these genes showed consistent RNA editing changes.Compared to non-cushion plants,a unique RNA editing event was detected for the ycf1 gene in the cushion plant R.coccinea.(2)22 common genes with editing sites were detected in two cushion plants of Saxifraga.RNA editing in the ycf1 gene did not occur in both species.(3)There were 14 common genes with RNA editing between the two genera,among which ndh H,ndh E,pet B,psb F,and psb Z genes shared the same amino acid changes caused by RNA editing in all species.There were also some genes with different RNA editing conversion between the two genera.For example,the editing of alanine(A)to valine(V)was identified for psb J gene in Rhodiola,while the editing of proline(P)to leucine(L)was identified in Saxifraga.(4)Seventeen genes simultaneously with RNA editing sites were detected in all three cushion plants,and these genes also had RNA editing sites in non-cushion plants.Therefore,no convergent RNA editing events were detected between the cushion plants.In summary,chloroplast genomes of both cushion and non-cushion plants within the same genus showed high conservation.Under the same environmental pressure,some similar adaptive mechanisms probably existed between the cushion plants and the related non-cushion plants habituating the high-altitude.While due to phylogenetic distance,some common different expressed genes for all high-altitude species are possibly related to the difference of phylogeny between high-altitude and low-altitude species,which requires further investigation with other samples combined.At the same time,due to the unique phenotypic structure of cushion plants,some potential convergent signals for altitude adaptation in cushion plants were detected at both the chloroplast genome and transcriptome levels.Nevertheless,further experimental validation is required for common genes identified as having potential positive amino acid sites and high expression levels in all cushion plants,in order to explore their correlation with altitude adaptation at a more specific level. |
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