Endophytic bacterial community structure and diversity of the medicinal plant Mirabilis himalaica from different locations.

Endophytic bacteria play important roles in medicinal plant growth, abiotic stress, and metabolism. Mirabilis himalaica (Edgew.) Heimerl is known for its medicinal value as Tibetan traditional plant; however, little is known about the endophytic bacteria associated with this plant in different geographic conditions and vegetal tissues. To compare the endophytic bacterial community associated with this plant in different geographic conditions and vegetal tissues, we collected the leaves, stems, and roots of M. himalaica from five locations, Nongmu college (NM), Gongbujiangda (GB), Zhanang County (ZL), Lang County (LX), and Sangri County (SR), and sequenced the 16S rRNA V5-V7 region with the Illumina sequencing method. A total of 522,450 high-quality sequences and 4970 operational taxonomic units (OTUs) were obtained. The different tissues from different locations harbored unique bacterial assemblages. Proteobacteria and Actinobacteria were the dominant phyla in all the samples, while the dominant genera changed based on the different tissues. The endophytic bacterial structures in the leaf and stem tissues were different compared to root tissues. Redundancy analysis (RDA) showed that the endophytic bacterial community was significantly correlated with pH, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), and soil organic matter (SOM). These findings suggested that the geographic conditions, climate type, ecosystem type, and tissues determined the endophytic bacterial composition and relative abundances. This conclusion could facilitate an understanding of the relationship and ecological function of the endophytic bacteria associated with M. himalaica and provide valuable information for artificial planting of M. himalaica and identifying and applying functional endophytic bacteria.

The complete chloroplast genome sequence of Plectranthus hadiensis (Lamiaceae) and phylogenetic analysis.

Plants of the genus Plectranthus are used for the treatment of digestive problems, skin diseases, and allergies, with a wide variety of uses. Here, the complete chloroplast genome sequence of Plectranthus hadiensis (Benth. ex E.Mey) Codd. 1788 was assembled and characterized for the first time. The full length of the chloroplast genome is 152,484 bp, consisting of a small single-copy region of 17,686 bp, a large single-copy region of 83,380 bp, and a pair of inverted repeats of 51,418 bp. The overall GC content is 37.73%. The chloroplast genome contains 131 unique genes, including 87 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic tree construction based on the complete chloroplast genome sequences of 25 species (23 Nepetoideae, two Ajugoideae) of the Lamiaceae family showed that P. hadiensis exhibited the closest relationship with Isodon.

Illumina sequencing data of the complete chloroplast genome of rare species Juniperus seravschanica (Cupressaceae) from Kazakhstan.

The species of the genus Juniperus L. play an important role in Kazakhstan forest ecosystems and one of them is Juniperus seravschanica Kom. which has been listed as a rare species in the Red Book of Kazakhstan. The distribution area of J. seravschanica extends from Central Asia (Kazakhstan, Uzbekistan, Kyrgyzstan, Tajikistan, and Turkmenistan) to northern and eastern Afghanistan, northern Pakistan, Kashmir, southeastern Iran, and Oman. J. seravschanica occurred in the southern part of Kazakhstan along with the ranges Karatau, Talas Alatau, Kyrgyz Alatau, Chu-Ili, Karzhantau, and Ugam. The distribution area of J. seravschanica is constantly decreasing due to intensive logging, forest fires, and excessive cattle grazing. The species has ecological importance in the stabilization of mountain slopes against erosion, for hydrobiological regulation, and as a significant medicinal herb. The species J. excelsa M. Bieb., J. polycarpos K.Koch (var. polycarpos and var. turcomanica R.P.Adams), and J. seravschanica are morphologically very similar with some difficulties in species identification. For a better understanding of the evolutionary relationship of these species in the Juniperus genus, it is important to obtain genetic information on the highly conserved chloroplast (cp) genome. Due to the conserved genomic structure, the cp genome nucleotide sequences are widely used in species distinguishing and reconstructing phylogenetic relationships. Unfortunately, there are no publicly available nucleotide sequences of cp genomes data for J. polycarpos (var. polycarpos and var. turcomanica), J. excelsa and J. seravschanica. We report the de novo assembly of the J. seravschanica chloroplast genome by applying next-generation sequencing technology based on Illumina NovaSeq 6000. The assembled cp genome of J. seravschanica is 127,609 bp in length and contained 118 genes, including 82 protein-coding genes, 32 transfer RNA genes, and 4 ribosomal RNA genes. In total 152 simple sequence repeats were identified in the chloroplast genome sequence of J. seravschanica. The Bioproject (PRJNA883033), Sequence Read Archive (SRR21673293), and GenBank (OL684343) data were deposited at National Center for Biotechnology Information.

Genome Sequence Resource of Pectobacterium polaris QK413-1 that Causes Blackleg on Potato in Fujian Province, China.

The Pectobacterium pathogens cause soft rot and blackleg diseases on many plants and crops, including potatoes. Here, we first report a high-quality genome assembly and announcement of the P. polaris strain QK413-1, which causes blackleg disease in potatoes in China. The QK413-1 genome was sequenced and assembled using the PacBio Sequel II and Illumina sequencing platform. The assembled genome has a total size of 5,005,507 bp with a GC content of 51.81%, encoding 4,782 open reading frames, including 639 virulence genes, 273 drug resistance genes, and 416 secreted proteins. The QK413-1 genome sequence provides a valuable resource for the control of potato blackleg and research into its mechanism.

Dataset of conditioning effect of herbal extract-based plant biostimulants in pea (Pisum sativum).

Nowadays, many researchers, farmers and companies focus on the development of an environmentally friendly approach for enhancing field vegetable production and protection. Using next-generation plant biostimulants (PBs) could be effective to enhance tolerance to abiotic and biotic stresses, vegetable crop quality or nutrient efficiency which is particularly important for vegetables with a short growing season, such as Pisum sativum. Two herbal drug-containing plant conditioners Elice16Indures® (supercritical carbon dioxide extract SC-CO2) and Fitokondi® (aqueous extract) developed in the RIMPH Ltd (Hungary) were used in pea field experiments to monitor the potential of enhancing crop quality and defense response against different stress factors. Fresh leaves were collected after treatments for QuantSeq 3' mRNA sequencing at Illumina NextSeq 550 platform and libraries were investigated by genome-wide transcriptional profiling focusing on genes associated with defense response pathways. RNA quantification datasets are presented and 86 bp long sequence reads were pre-processed and assembled that were deposited in the National Center for Biotechnology Information (NCBI), Sequence Read Archive (SRA) and Transcriptome Shotgun Assembly (TSA) databases under the BioProject PRJNA870114. Functional annotation of transcripts and pairwise differential expression with enrichment analyses are presented here to support gene expression analysis experiments.

The Complete Chloroplast Genome Sequence of Machilus chuanchienensis (Lauraceae): Genome Structure and Phylogenetic Analysis.

Machilus chuanchienensis is an ecological tree distributed in southwestern China. It has a significant valuation with making Hawk tea using its leaves, an ethnic traditional tea-like beverage with a long history in Chinese tea culture. The whole chloroplast (cp) genome is an ideal model for the phylogenetic study of Lauraceae because of its simple structure and highly conserved features. There have been numerous reports of complete cp genome sequences in Lauraceae, but little is known about M. chuanchienensis. Here, the next-generation sequencing (NGS) was used to sequence the M. chuanchienensis cp genome. Then, a comprehensive comparative genome analysis was performed. The results revealed that the M. chuanchienensis's cp genome measured 152,748 base pairs (bp) with a GC content of 39.15% and coded 126 genes annotated, including comprising eight ribosomal RNA (rRNA), 36 transporter RNA (tRNA), and 82 protein-coding genes. In addition, the cp genome presented a typical quadripartite structure comprising a large single-copy (LSC; 93,811) region, a small single-copy (SSC; 18,803) region, and the inverted repeats (IRs; 20,067) region and contained 92 simple sequence repeat (SSR) locus in total. Phylogenetic relationships of 37 species indicated that M. chuanchienensis was a sister to M. balansae, M. melanophylla, and M. minutiflora. Further research on this crucial species may benefit significantly from these findings.

Genome sequencing of Colletotrichum gloeosporioides ES026 reveals plausible pathway of HupA.

BACKGROUND: Colletotrichum gloeosporioides ES026, isolated as an endophytic fungal strain, was found to produce the important medicinal compound HuperzineA (HupA). In a genetic context, ES026 showed potential in elucidating the biosynthetic pathway of HupA. METHODS AND RESULTS: The ES026 strain was sequenced using de-novo Illumina sequencing methods in this study. Assembling the cleaned data resulted in 58,594,804bp, consisting of 404 scaffolds. The G + C mol % content of this genome was 52.53%. The genome progressive-alignment with other 4 Colletotrichum strains revealed that ES026 showed closer relation with 030206, SMCG1#C and Nara gc5. More than 60 putative biosynthetic clusters were predicted with the fungal version antiSMASH4.0 program. More than 33 types I polyketide-related biosynthetic gene clusters were distributed, containing PKS and PKS-NRPS (polyketide-nonribosomal peptides) hybrid gene clusters. Another 8 NRPS biosynthetic gene clusters were distributed among the genome of ES026. The prenyltransferases, probably involved in aromatic prenyl-compounds and terpenoid biosynthesis, were analyzed using bioinformatics tools like MEGA. CONCLUSION: We predicted a new possible biosynthetic pathway for the HupA from the pipecolic acid, based on the published HupA biosynthesis proposed pathway, the biosynthesis and pipecolic acid-derived compounds. We hypothesize that a hybrid PKS-NRPS mega-enzyme was probably involved in the biosynthesis of HupA with the pipecolic acid, the building block of rapamycin, as a HupA precursor. The rapamycin is produced from a polyketide biosynthesis pathway, and the domain incorporating the pipecolic acid is studied.

Dominant microbial communities and biochemical profile of pulped natural fermented coffees growing in different altitudes.

Altitude changes the coffee fruits and beans composition before and after harvesting. We aimed to evaluate the effect of altitude on the microbial community structure associated with pulped coffee fruits under self-induced anaerobic fermentation (SIAF) and their acids, volatiles, and antioxidants biochemical profiles. The most abundant bacterial genera were Gluconobacter (800 m), Weissella (1,000 m), and Leclercia (1,200 and 1,400 m). Yeasts dominated the pulped natural fermentations within the fungal species, containing high abundances of Cystofilobasidium infirmominiatum, Wickerhamomyces anomalus, and Meyerozyma caribbica. Citric, alcohols, and caffeine were the most dominant compounds in SIAF among acids, volatiles, chemical groups, and antioxidants. High altitude coffees favor alcohols, aldehydes, and esters groups, while low altitude coffees favor phenols.

The complete chloroplast genome of Rubus rosifolius (Rosaceae), an ornamental and medicinal plant.

Rubus rosifolius belongs to the genus Rubus in the family Rosaceae and is widely distributed globally. It has white flowers and red fruits. Moreover, it has medicinal value for diseases of the stomach and other areas. However, the complete chloroplast (cp) genome of R. rosifolius remains unclear. In the present study, we sequenced the complete cp genome of R. rosifolius (GenBank accession no. OL435124), which had a typical quadripartite structure and a size of 155,650 bp. Fifteen genes (trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC, and ndhA) contained an intron, and two genes (clpP and ycf3) contained two introns. The gene rps12 showed trans-splicing. Phylogenetic analysis showed that R. rosifolius was closely related to Rubus taiwanicola, Rubus rubroangustifolius, and Rubus glandulosopunctatus.

The complete chloroplast genome sequence of Aspidopterys concava (Wall.) A. Juss. (Malpighiaceae).

Aspidopterys concava is related to a group of important medicinal plants in Malpighiaceae in southeast Asia. Here, we report the first chloroplast genome fully sequenced and annotated for Aspidopterys concava. The genome size was 160,441 bp and contained a large single-copy (LSC) region of 71,434 bp, a small single-copy (SSC) region of 53,544 bp, and a pair of inverted repeats (IRs) regions of 8943 bp. Total GC content was 37.9%. It contained 125 genes in total, comprising 82 protein-coding genes, 37 transfer RNA genes, and six ribosomal RNA genes. Phylogenetic analysis showed that A. concava was the most closely related to A. obcordata from the same genus.

The complete chloroplast genome sequence of the medicinal plant Crotalaria albida.

Crotalaria albida (C. albida) is a traditional Chinese medicinal plant that belongs to Fabaceae family. In this study, the complete chloroplast genome sequence of C. albida was sequenced. The genome is 152,743 bp in length and includes two inverted repeat regions of 25,535 bp. It was predicted to contain 127 genes in the chloroplast genome, among which 82 were protein-coding genes, 37 were tRNA genes, and 8 were rRNA genes. The maximum likelihood phylogenetic analysis based on 24 complete chloroplast genome sequences showed that C. albida was closely related to Ormosia semicastrata, Ormosia emarginata, and Ormosia xylocarpa.

The complete chloroplast genome of Crepis rigescens (Cichorioideae), a traditional Chinese medicinal plant.

Crepis rigescens, Diels 1921 is a traditional Chinese medicinal plant of Cichorioideae, which contains many chemicals, such as friedelin, ß-sitosterol, stigmasterol, chlorogenic acid, and flavonoids, and so on, which has the characteristics of high medicinal value and small side effect. Crepis rigescens was used as folk medicines for anti-bacterial, and anti-oxidation, which also had a potential curative effect in preventing cardiovascular disease and anti-tumor. Illumina paired-end reads data were used to assemble the complete chloroplast (cp) genome. 14,425,796 raw paired-end reads and the length distribution in 124,685 bp, including a large single copy (LSC) region of 82,924 bp, a small single copy (SSC) region of 18,150 bp, and a pair of inverted repeat (IRs) regions of 25,128 bp. Besides, 10 protein-coding genes (PCGs) genes and 6 tRNAs genes possess a single intron, while clpP and ycf3 have a couple of introns. Based on the concatenated coding sequences of cp PCGs, the phylogenetic analysis showed that C. rigescens and Hypochaeris radicata (MH746729) are closely related to each other within the family Cichorioideae.

Comparative transcriptomic analysis of genes in the triterpene saponin biosynthesis pathway in leaves and roots of Ardisia kteniophylla A. DC., a plant used in traditional Chinese medicine.

Ardisia kteniophylla (Primulaceae) is highly valued in traditional medicine due to its production of the pharmacologically active secondary metabolites, especially triterpenoid saponins in its roots. Although A. kteniophylla is very important in traditional medicine, the genetic basis for its production of triterpenoid saponins remains largely unknown. Therefore, we sequenced transcriptomes of A. kteniophylla to identify putative genes involved in production of triterpenoid saponins in both leaves and roots, and we used the transcriptomes to compare expression levels of these genes between the two organ systems. The production of triterpenoid saponins in plants is usually induced through hormonal signaling on account of the presence of pests. Thus, we treated plants with the hormones salicylic acid (SA) and methyl jasmonate (MeJA) and used quantitative real-time PCR (qRT-PCR) to investigate expression levels of genes involved in triterpenoid saponin biosynthesis. In total, we obtained transcriptomes for leaf and root tissues representing 52,454 unigenes. Compared with the leaf transcriptome, we found that 6092 unigenes were upregulated in the root, especially enzymes involved in the direct synthesis of triterpenoid saponins, while 6001 genes appeared downregulated, including those involved in precursory steps in the triterpenoid saponin biosynthesis pathway. Our results from qRT-PCR indicate that genes within the upstream parts of the triterpenoid saponin biosynthesis pathway may be upregulated under exposure to the applied hormones, but downstream genes are downregulated. This suggests possible conflicting effects of SA and MeJA in promoting the production of secondary metabolites on the one hand, and, on the other, limiting plant growth processes to devote energy to combating pests. We also performed an analysis of transcription factors (TFs) and found 997 unique transcripts belonging to 16 TF families. Our data may help to facilitate future work on triterpene saponins biosynthesis in A. kteniophylla with potential pharmacological and molecular breeding applications.

Time-course gene expression profiling data of Triticum aestivum treated by supercritical CO2 garlic extract encapsulated in nanoscale liposomes.

The biostimulant phytochemicals as alternatives to synthetic chemicals are gaining ground in sustainable agricultural production nowadays. The medicinal herb, garlic (Allium sativum) has a spectacular therapeutic reputation due to its antimicrobial properties. The effectiveness of supercritical carbon dioxide (SC-CO2) extraction of A. sativum could help preserve bioactive compounds and be used as a biostimulant agent. The SC-CO2 garlic was formulated in liposomes and used as a nanoscale drug delivery system to reach better efficiency of penetration and translocation. The SC-CO2 garlic extracts were used in Triticum aestivum time-course experiments to monitor conditioning effects such as improving crop quality and priming its defense responses against different pathogens. Fresh leaves were collected after SC-CO2 garlic exposure at 15 min, 24, and 48 hours for QuantSeq 3' mRNA sequencing at Illumina NextSeq 550 platform. RNA quantification datasets are presented. Raw data such as Illumina 85bp single-end read sequences and reconstructed transcripts were deposited in the NCBI SRA and TSA databases under the BioProject PRJNA808851. Functional annotation of transcripts and time-course expression data are presented here to support gene expression analysis experiments.

Data on metagenomic profiles of bacterial endophyte communities associated with Dicoma anomala.

Plants harbor varied communities of bacterial endophytes which play a crucial role in plant health and growth. Dicoma anomala is a medicinal plant that is known for its excellent ethnomedicinal uses which include treatment of coughs, fever, ulcers, and dysentery. This data in Brief article provides information on the diversity of bacterial endophytes associated with a medicinal plant, Dicoma anomala targeting the 16S rRNA gene using Illumina sequencing technology during three different seasons. Plant samples were collected in Eisleben, Limpopo province, South Africa, in the months of April, June, August and October 2018. The dataset revealed that the leaf samples collected in August had the highest species diversity as indicated by the Shannon index (4.25), Chao1 (1456.01), abundance-based coverage estimator (ACE) (1492.07) and the Simpson indices of diversity (0.05) irrespective of the species. The order of the bacterial endophyte's richness in D. anomala was April> October> June> August, from lowest to highest. The taxonomic composition analysis showed that most endophytic bacteria were composed of Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Some endophytic bacteria were found to be tissue specific. Sequences of Cutibacterium, Acinetobacter and Methylobacterium were prevalent in the leaves, whereas Amycolatopsis and Bradyrhizobium were the dominant genera in the root samples.

Characterization of the complete chloroplast genome of Fibraurea recisa Pierre 1885 (Menispermaceae), an important medicinal herb from Yunnan, China.

Fibraurea recisa Pierre 1885, which belongs to the family Menispermaceae, is an important medicinal herb in Yunnan, China. Despite its importance, genetic studies on this species remain rare. Therefore, in the current study, we assembled the complete chloroplast genome of F. recisa. Results showed that the complete genome was 161,671 bp in length, including a large single-copy region (LSC, 91,071 bp), small single-copy region (SSC, 20,858 bp), and two inverted repeat regions (IRa and IRb, 24,871 bp). The genome consisted of 124 genes, including 87 protein-coding genes, 29 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that F. recisa was most closely related to species of Tinospora within Menispermaceae. Our complete chloroplast genome of F. recisa should contribute to the genetic resource assessment of this species as well as its future conservation and utilization.

Combined Metabolome and Transcriptome Analyses of Young, Mature, and Old Rhizome Tissues of Zingiber officinale Roscoe.

Ginger (Zingiber officinale Roscoe) is known for its unique pungent taste and useability in traditional Chinese medicine. The main compounds in ginger rhizome can be classified as gingerols, diarylheptanoids, and volatile oils. The composition and concentrations of the bioactive compounds in ginger rhizome might vary according to the age of the rhizome. In this regard, the knowledge on the transcriptomic signatures and accumulation of metabolites in young (Y), mature (M), and old (O) ginger rhizomes is scarce. This study used HiSeq Illumina Sequencing and UPLC-MS/MS analyses to delineate how the expression of key genes changes in Y, M, and O ginger rhizome tissues and how it affects the accumulation of metabolites in key pathways. The transcriptome sequencing identified 238,157 genes of which 13,976, 11,243, and 24,498 were differentially expressed (DEGs) in Y vs. M, M vs. O, and Y vs. O, respectively. These DEGs were significantly enriched in stilbenoid, diarylheptanoid, and gingerol biosynthesis, phenylpropanoid biosynthesis, plant-hormone signal transduction, starch and sucrose metabolism, linoleic acid metabolism, and α-linoleic acid metabolism pathways. The metabolome profiling identified 661 metabolites of which 311, 386, and 296 metabolites were differentially accumulated in Y vs. M, Y vs. O, and M vs. O, respectively. These metabolites were also enriched in the pathways mentioned above. The DEGs and DAMs enrichment showed that the gingerol content is higher in Y rhizome, whereas the Y, M, and O tissues differ in linoleic and α-linoleic acid accumulation. Similarly, the starch and sucrose metabolism pathway is variably regulated in Y, M, and O rhizome tissues. Our results showed that ginger rhizome growth slows down (Y > M > O) probably due to changes in phytohormone signaling. Young ginger rhizome is the most transcriptionally and metabolically active tissue as compared to M and O. The transitioning from Y to M and O affects the gingerol, sugars, linoleic acid, and α-linoleic acid concentrations and related gene expressions.

Complete chloroplast genome of Dactylicapnos torulosa (Hook. & Thoms.) Hutch., a medicinal plant from southwest China and its phylogeny.

Dactylicapnos torulosa (Hook. & Thoms.) Hutch. is a commonly used medicinal plant in southwest China. In this study, we sequenced the complete chloroplast genome of D. torulosa and explored phylogenetic relationship of the species and its related species. The genome size is 166,238 bp with typical quadripartite structure. A pair of inverted repeats (IRs) of 37,115 bp are separated by a small single copy (SSC) region of 18,627 bp and a large single copy (LSC) region of 73,381 bp. In total, 107 genes are annotated, including 76 protein coding genes, 27 transport RNA, four ribosomal RNA. Moreover, 13 genes are found to contain introns. Phylogenetic analysis showed that Dactylicapnos torulosa formed a basal branch instead of gathering together with Corydalis, which was inconsistent with the traditional treatment on Fumarioideae. This study provides useful information for phylogeny and conservation of the species and its relatives.

The complete chloroplast genome sequence and phylogenetic position of Lilaeopsis chinensis (L.) Kuntze (Apiaceae).

Lilaeopsis chinensis (L.) Kuntze is a traditional Chinese medicinal plant for treating diuresis, abdominal pain and eczema. In this study, its complete chloroplast genome was assembled from the whole genome Illumina sequencing data. The circular genome is 153,162 bp long, and comprises a pair of inverted repeat regions (IRs, 25,072 bp each), a large single-copy region (LSC, 84,288 bp) and a small single-copy region (SSC, 18,730 bp). It encodes a total of 113 genes (79 protein-coding, 30 tRNA and 4 rRNA genes), with 19 of them occurring in double copies. Introns were detected in 11 protein coding genes (PCG) and 6 tRNA genes. The nucleotide composition is asymmetric (30.9% A, 19.2% C, 18.4% G and 31.5% T) with an overall A + T content of 62.4%. Phylogenetic analysis challenged the traditional taxonomic framework of the family Apiaceae, and indicated that Lilaeopsis chinensis (L.) Kuntze is closely related to Hydrocotyle verticillata.

The complete chloroplast genome of Prinsepia uniflora (Rosaceae), a medicinal plant found in northwest China.

Prinsepia uniflora Batalin 1892 is a medicinal plant widely distributed in northwest China. In this study, we report and characterize the complete chloroplast (cp) genome sequence of P. uniflora. The entire sequence is 159,179 bp in length, consisting of the large single-copy region (LSC) and small single copy region (SSC) (87,239 and 19,180 bp, respectively); these two regions are separated by a pair of 26,380-bp inverted repeat (IR) regions. The genome contains 131 genes, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 36.7%. A phylogenetic tree constructed from 18 chloroplast genomes revealed that P. uniflora was clustered with Prinsepia sinensis and Prinsepia utilis, all of which belong to the genus Prinsepia, which is supported as a sister group by a moderate bootstrap support value of 55% with the Malus and Pyrus genera.