Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendron simsii (Ericaceae)

Rhododendronsimsii is one of the top ten famous flowers in China. Due to its historical value and high aesthetic, it is widely popular among Chinese people. Various colors are important breeding objectives in Rhododendron L. The understanding of the molecular mechanism of flower color formation can provide a theoretical basis for the improvement of flower color in Rhododendron L. To generate the R.simsii transcriptome, PacBio sequencing technology has been used. A total of 833,137 full-length non-chimeric reads were obtained and 726,846 high-quality full-length transcripts were found. Moreover, 40,556 total open reading frames were obtained; of which 36,018 were complete. In gene annotation analyses, 39,411, 18,565, 16,102 and 17,450 transcriptions were allocated to GO, Nr, KEGG and COG databases, correspondingly. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with Protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT) and Coding Non Coding Index (CNCI) databases and observed 6170, 2265, 4084 and 1240 lncRNAs, respectively. Based on the results, most genes were enriched in the flavonoid biosynthetic pathway. The eight key genes on the anthocyanin biosynthetic pathway were further selected and analyzed by qRT-PCR. The F3′H and ANS showed an upward trend in the developmental stages of R. simsii. The highest expression of F3′5′H and FLS in the petal color formation of R. simsii was observed. This research provided a huge number of full-length transcripts, which will help to proceed genetic analyses of R.simsii. native, which is a semi-deciduous shrub

Global pattern of leaf litter nitrogen and phosphorus in woody plants

Forest ecosystems exert an important influence on global biogeochemical cycles. A global dataset of nitrogen (N) and phosphorus (P) concentrations in leaf- litter of woody plants was compiled from the literature. Among the 677 data sets, 482 included P concentrations and the N:P ratio. At a global scale, the mean leaf-litter N and P and N:P ratio were 10.9 mg g-1, 0.85 mg g-1 and 18.3, respectively. Leaf-litter N and P were significantly correlated. When the data was grouped by continents, the highest mean N was found in Africa (19.5 mg g-1), and the lowest in North America (8.18 mg g-1). P was significantly smaller in the Asian Islands (Japan and Malaysia, 0.44 mg g-1) than on the Asian mainland. For the global dataset, leaf-litter N increased linearly with mean annual temperature and annual precipitation and decreased with latitude. Although leaf- litter P showed no significant relationship with temperature, it declined linearly with precipitation and there was a convex quadratic relationship with latitude. For the global dataset and also for different functional groups (e.g. shrubs, evergreen broadleaf, deciduous broadleaf, and conifers) the leaf-litter N:P ratio generally followed a positive linear relationship with temperature and precipitation, and showed a concave quadratic response with latitude. The differences in leaf-litter N:P ratio among functional groups and among continents should be taken into account when modeling biogeochemical cycles in different regions as well as on a global scale

PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings

Schima superba (Theaceae) is a subtropical evergreen tree and is used widely for forest firebreaks and gardening. It is a plant that tolerates salt and typically accumulates elevated amounts of manganese in the leaves. With large ecological amplitude, this tree species grows quickly. Due to its substantial biomass, it has a great potential for soil remediation. To evaluate the thorough framework of the mRNA, we employed PacBio sequencing technology for the first time to generate S. Superba transcriptome. In this analysis, overall, 511,759 full length non-chimeric reads were acquired, and 163,834 high-quality full-length reads were obtained. Overall, 93,362 open reading frames were obtained, of which 78,255 were complete. In gene annotation analyses, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Genes (COG), Gene Ontology (GO), and Non-Redundant (Nr) databases were allocated 91,082, 71,839, 38,914, and 38,376 transcripts, respectively. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT), and Coding Non-Coding Index (CNCI) databases and observed 8,551, 9,174, 20,720, and 18,669 lncRNAs, respectively. Moreover, nine genes were randomly selected for the expression analysis, which showed the highest expression of Gene 6 (Na_Ca_ex gene), and CAX (CAX-interacting protein 4) was higher in manganese (Mn)-treated group. This work provided significant number of full-length transcripts and refined the annotation of the reference genome, which will ease advanced genetic analyses of S. superba

Evaluation of Metal Tolerance of Fungal Strains Isolated from Contaminated Mining Soil of Nanjing, China

Simple Summary In this study, cadmium, chromium, and lead tolerant microbes have been isolated from contaminated mining soil and characterized. Molecular characterization of isolated fungi was performed and amplified sequences were deposited in the GenBank NCBI database. Metal tolerance of the various strains has been determined by measuring the minimum inhibitory concentrations (MICs) and the tolerance indexes of all the tested strains against Cd, Cr, and Pb. Bioaccumulation capacities of Trichoderma harzianum and Komagataella phaffi have also been assessed. These findings helped us find a novel strain of Komagataella phaffi and suggested it to be the potential mycoremediation microbe to alleviate the contamination of Cd, Cr, and Pb. Future studies of this fungal strain can help us to understand its resistance mechanism against other heavy metals, too. Rapidly increasing industry has resulted in greater discharge of hazardous chemicals in the soil. In the current study, soil samples were collected from Nanjing mine (32 degrees 09 ' 19.29 '' N 118 degrees 56 ' 57.04 '' E) and subjected to heavy metal analysis and microbe isolation. A total of 460 fungi were isolated, and five of these were yeast strains. Most of the strains exhibited tolerance to one metal. Five multimetal tolerant strains were selected and identified as Aspergillus sclerotiorum, Aspergillus aculeatus, Komagataella phaffii, Trichoderma harzianum, and Aspergillus niger. Isolated strains were grown in high concentrations of cadmium (Cd), chromium (Cr) and lead (Pb), for induced-tolerance training. The tolerance index (TI) revealed the highest Cd tolerance of novel K. phaffii strain at 5500 ppm (TI: 0.2). K. phaffii also displayed resistance at 4000 ppm against Cr (TI: 0.32) and Pb (TI: 0.32). In contrast, tolerance training for A. niger was not that successful. K. phaffii also displayed the highest bioaccumulation capacity for Cd (25.23 mg/g), Cu (21.63 mg/g), and Pb (20.63 mg/g) at 200 ppm. Scanning electron microscopy (SEM) explored the morphological changes in the mycelia of stressed fungi. Results of this study describe this delicate approach to be species and metal dependent and suggest a potential utilization of this fungal strain for the bioremediation of contaminated soils

Isolation and characterization of pathogen causing brown rot in lemon and its control by using ecofriendly botanicals

Brown rot is a common and devastating disease of different fruits and vegetables. During 2018, a profound brown rot was observed on lemon (Citrus lemon L.) in Islamabad, Pakistan and adjacent areas. This study was designed to identify disease causing pathogen of this disease. Diseased lemon fruit were collected from the orchards and disease causing pathogen was isolated. The morphology of pathogen was examined under stereoscope and compound microscope and the pathogen was identified as Alternaria alternata. For the molecular characterization of this fungus, 18S ribosomal RNA gene was sequenced and its phylogenetic analyses were performed. BLAST analysis revealed 100% similarity with A. alternate NS8, 18S ribosomal RNA gene, partial sequence (MK346034.1). This is the first report of brown rot of lemon, caused by A. alternata in Pakistan. For ecofriendly control of this disease, extracts of indigenous medicinal plants including Justacia adhatoda, Azadriachta indica, Foeniculum vulgare and Mentha spicata were used. In these plant extracts, the presence of various functional groups such as alcohols, carboxylic acids, esters, alkanes and alkenes was revealed by Fourier transform infrared spectroscopy (FTIR). Both in vitro and in vivo assay showed the significant role of aqueous plant extracts to suppress the growth of A. alternata. Among these phytoextracts, A. indica proved to be the most efficient in suppressing the growth of the pathogen and controlling disease. Findings of this study suggest the use of these plant extracts for environment friendly control of fruit rot disease

Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.Y

DataSheet_2_Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis.pdf

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.</p

DataSheet_1_Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis.pdf

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.</p