Paeonia ludlowii is indigenous to Tibet and has an important ecological and economic value in China. In Tibet, P. ludlowii has been used in folk medicine with relative success. Plant microbial endophytes play an important role in plant growth, health and ecological function. The diversity of endophytic bacteria associated with P. ludlowii remains poorly understood. In this study, the structure of the endophytic bacterial communities associated with different tissues, including fruits, flowers, leaves, stems, and roots, and rhizosphere soils was analyzed with Illumina MiSeq sequencing of bacterial 16S rDNA. A total of 426,240 sequences and 4847 operational taxonomic units (OTUs) were obtained. The OTUs abundance of roots was higher than that of other tissues; however, the OTUs abundance was similar among different deep soil samples. In the plant tissues, Cyanobacteria was the most abundant bacterial phylum, followed by Proteobacteria; however, the most abundant phyla were Proteobacteria and Acidobacteria in soil samples from three different layers. In addition, the diversity and richness of the microorganisms in the soil were very similar to those in roots but higher than those in other tissues of P. ludlowii . Predictive metagenome analysis revealed that endophytic bacteria play critical functional roles in P. ludlowii . This conclusion could facilitate the study of the ecological functions of endophytic bacteria and their interactions with P. ludlowii to analyze the reasons why this important medicinal plant is becoming endangered.

IntroductionIn 1936, the Englishman Ludlow discovered Paeonia ludlowii during his investigation in Tibet. In 1953, he published an article in the British "Botanical Magazine" naming Paeonia ludlowii 1 . It is a deciduous shrub of the genus Paeonia in the family Ranunculaceae, a subspecies of Paeonia delavayi, and it is endemic to Tibet 2 . It is distributed only in a narrow range of approximately 100 km in length in Brahmaputra Canyon at an altitude of 2900 3200 m; it is one of the eight peony species in China 3,4 . However, the distribution range of Paeonia ludlowii is narrow, its population is small, and it is considered endangered, as it is included in the "Chinese Red List of Species" 5,6 . China issued the Announcement of the Ministry of Health on Approving Acer truncatum kernel oil and Peony seed oil as New Food Resources on March 22, 2011, approving Peony seed oil as a new food resource 7 ; thus, peony seed oil has officially become an edible oil from a woody plant in China. According to the literature, P. ludlowii can be used as a new material for the development of oil peony varieties 8 .

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Rheum species present a significant economic value. Traditional Chinese medicine rhubarb is an important medicinal material in China. It has a long history of use, with a record of use as early as two thousand years ago. Here, we determined the complete chloroplast genome sequences of Rheum nobile and Rheum acuminatum and comprehensively compared them to two other available Rheum cp genomes at the genome scale. The results revealed cp genomes ranging in size from 159,051 to 161,707 bp with a similar typical quadripartite and circular structure. The genome organization, gene numbers, gene order, and GC contents of these four Rheum cp genomes were similar to those of many angiosperm cp genomes. Repeats and microsatellites were detected in the R. nobile and R. acuminatum cp genomes. The Mauve alignment revealed that there were no rearrangements in the cp genomes of the four Rheum species. Thirteen mutational hotspots for genome divergence were identified, which could be utilized as potential markers for phylogenetic studies and the identification of Rheum species. The phylogenetic relationships of the four species showed that the members of Rheum cluster into a single clade, indicating their close relationships. Our study provides valuable information for the taxonomic, phylogenetic, and evolutionary analysis of Rheum.