Complete chloroplast genome of the medicinal plant Evolvulus alsinoides: comparative analysis, identification of mutational hotspots and evolutionary dynamics with species of Solanales.

Evolvulus alsinoides, belonging to the family Convolvulaceae, is an important medicinal plant widely used as a nootropic in the Indian traditional medicine system. In the genus Evolvulus, no research on the chloroplast genome has been published. Hence, the present study focuses on annotation, characterization, identification of mutational hotspots, and phylogenetic analysis in the complete chloroplast genome (cp) of E. alsinoides. Genome comparison and evolutionary dynamics were performed with the species of Solanales. The cp genome has 114 genes (80 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes) that were unique with total genome size of 157,015 bp. The cp genome possesses 69 RNA editing sites and 44 simple sequence repeats (SSRs). Predicted SSRs were randomly selected and validated experimentally. Six divergent hotspots such as trnQ-UUG, trnF-GAA, psaI, clpP, ndhF, and ycf1 were discovered from the cp genome. These microsatellites and divergent hot spot sequences of the Taxa 'Evolvulus' could be employed as molecular markers for species identification and genetic divergence investigations. The LSC area was found to be more conserved than the SSC and IR region in genome comparison. The IR contraction and expansion studies show that nine genes rpl2, rpl23, ycf1, ycf2, ycf1, ndhF, ndhA, matK, and psbK were present in the IR-LSC and IR-SSC boundaries of the cp genome. Fifty-four protein-coding genes in the cp genome were under negative selection pressure, indicating that they were well conserved and were undergoing purifying selection. The phylogenetic analysis reveals that E. alsinoides is closely related to the genus Cressa with some divergence from the genus Ipomoea. This is the first time the chloroplast genome of the genus Evolvulus has been published. The findings of the present study and chloroplast genome data could be a valuable resource for future studies in population genetics, genetic diversity, and evolutionary relationship of the family Convolvulaceae. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01051-w.

Data on large cardamom transcriptome associated with Chirke disease.

Large cardamom (Amomum subulatum Roxburg), is an ancient spice native to North-Eastern India and Southeast Asia, which belongs to the family Zingiberaceae under the order Scitaminae. Large cardamom is mostly affected by a viral disease termed Chirke caused by Large Cardamom Chirke Virus (LCCV). These disease has spread due to drastic changes in the ecosystem, inadequate rain in dry months and absence of good agricultural practices by the farmers resulting in aphid infestations. In the present study, using HiSeq™ 2000 RNA sequencing technology transcriptome sequencing was performed for both control (disease not expressed) and diseased large cardamom leaf tissues. RNA-seq generated 77260968 (7.72 GB) and 72239708 (7.22 GB) paired raw reads for large cardamom control and diseased samples respectively. The raw data were submitted to the NCBI SRA database under the accession numbers SRX2529373 and SRX2529372 and the assembled transcriptomes were submitted to TSA under the accession numbers GIAV01000000 and GIAW01000000 for the control and diseased samples respectively. The raw reads were quality trimmed and assembled de novo using TRINITY assembler which created 156822 (control) and 148953 (diseased) contigs with N50 values 2107 (control) and 2182 (diseased). The data were used to identify the significantly differentially expressed genes between control and diseased samples.

Data on small cardamom transcriptome associated with capsule rot disease.

Small cardamom (Elettaria cardamomum (L.) Maton, also known as the 'Queen of Spices' is a rhizomatous herbaceous monocot from the family Zingiberaceae. In the present study, using HiSeq™ 2000 RNA sequencing technology, transcriptome sequencing was performed for both control and disease stressed small cardamom leaf tissues. RNA-seq generated 46,931,637 (101 base) and 31,682,496 (101 base) raw reads and totally 9.93GB and 6.63GB of sequence data for cardamom control and stressed samples respectively. The raw data were submitted to NCBI SRA database of under the accession numbers SRX2512359 and SRX2512358 for the control and diseased samples respectively. The raw reads were quality filtered and assembled using TRINITY de novo assembler which created 1,11,495 (control) and 91,096 (diseased) contigs with N50 values 3013 (control) and 2729 (stressed). The data was further used to identify significantly differentially expressed unigenes between control and stressed samples. Assembled unigenes were further annotated and evaluated in silico to predict the function using publicly available databases and gene annotation tools.

Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom.

Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families, including monocot/tissue-specific and 14 novel miRNAs in both genotypes. Significant differences in miRNA family abundance between the libraries were observed in read frequencies. A total of 19 miRNAs (from known miRNAs) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known miRNA families in wild and 1025 potential targets for 42 known miRNA families in cultivar genotypes. The differential expression analysis revealed that most miRNAs identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars. Potential targets predicted for the newly identified miRNAs from the miRNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT-PCR confirmed miRNAs were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm miRNA-mRNA target pairing using RNA ligase-mediated 5' Rapid Amplification of cDNA Ends (5'RLM-RACE) PCR.

Data on identification of conserved and novel miRNAs in Elettaria cardamomum.

Elettaria cardamomum (L.) Maton, or small cardamom referred as 'queen of spices', is a perennial herbaceous rhizomatous monocot of the family Zingiberaceae. Cardamom seeds and fruits are the economically significant parts and effectively used as a traditional medicine, food additive and flavoring agent. In the present study, using Ion Proton next generation sequencing technology we performed the small RNA sequencing, conserved and novel miRNA predictions of a wild and five cultivar genotypes of cardamom. Small RNA sequencing generated a total of 5,451,328 and 2,756,250 raw reads for wild and cultivar cardamom respectively. The raw data was submitted to SRA database of NCBI under the accession numbers and SRX2273863 (wild) and SRX2273862 (cultivars). The raw reads were quality filtered and predicted conserved and novel miRNAs for wild and cultivar cardamom. The predicted miRNAs, miRNA-targets and functional annotations might provide valuable insights into differences between wild progenitor and cultivated cardamom.

Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom).

Elettaria cardamomum (L.) Maton, known as 'queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild) and SRX1141276 (cultivars). The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

Intraspecific variations in cardamom (Elettaria cardamomum Maton): assessment of genomic diversity by flow cytometry, cytological studies and ISSR analysis.

BACKGROUND: The main goal of the work was to analyse intraspecific variation in Elettaria cardamomum Maton (cardamom) using genome size, cytological studies and molecular marker data. Nuclear DNA content and molecular marker details furnish data on genome size and genetic diversity respectively among the studied accessions and both complement each other for evolutionary and taxonomic studies. RESULTS: The relative 2C genome size and total number of base pairs of cardamom was determined through flow cytometric analysis using propidium iodide staining. The nuclear DNA content was estimated in various sections of the species representing individuals from wild and cultivar genotypes following Zea mays L. CE-777 (2C = 5.43 pg) as internal reference standard. Chromosome number from growing root tip was examined following standard protocols. Twenty-six ISSR primers that generated polymorphic bands were used for genetic diversity analysis of the thirty accessions of cardamom. Estimated nuclear 2C DNA content ranged from 2.57 to 3.22 pg demonstrating 1.25-fold variation. The mean amount of 2C nuclear DNA of the cardamom was calculated as 2.87 pg which is equivalent of 2806 Mbp as the diploid genome size. The chromosome number was found to be 2n = 48. Among the thirty accessions of cardamom studied using ISSR markers, C53 (feral from Bonacaud) showed a very prominent level of genetic diversity and was lowest for C96 (Avinash-I, a released variety from Indian Institute of Spices Research, Kozhikode). CONCLUSION: These analyses revealed the existence of genetic variability within the studied cardamom accessions. The plant specimens also differed significantly in their genome size. However, the genetic variability parameters did not show any correlation with genome size.

Combined surgical method of orbital and periorbital hemangioma treatment in infants.

PURPOSE: To analyze the results of application of combined surgical treatment in different forms of hemangioma in infants. MATERIALS AND METHODS: One hundred seventy-four children with different forms of orbital and periorbital hemangiomas aged 1-16 months (mean age 5.2 + 1.97 months) were operated on at the pediatric ophthalmology department. Fast growth of hemangioma, both superficial (intradermal) and deep (subdermal and orbital) localization, significant deformity of eyelids, with narrowing of eye fissure were the indications for surgical treatment. The combined-staged method, including cryosurgery of superficial intradermal lesions and surgical excision of subdermal and/or orbital parts of the tumor in different combinations depending on the form and depth of hemangioma spreading, was applied. RESULTS: Usage of cryodestruction usually on the first stage of treatment allowed gentle scarring of the angiomatously changed skin areas. Surgical excision of the deep part of the tumor eliminated disfigurement and visual axis occlusion, avoiding amblyopia development. Good cosmetic and anatomic result was achieved in 90.4% of cases. CONCLUSION: Combined surgical method of treatment of progressive capillary hemangiomas by using cryosurgery and surgical excision in infants allows the choice of optimum tactics depending on features of the course and clinical picture in each individual case and provides achievement of high cosmetic and functional result of treatment. The early beginning of treatment in cases of fast progressing of the tumor allows prevention of extensive skin affection and amblyopia development.

Clinical and anatomical substantiation of levator resection in the complex surgical treatment of BPES.

OBJECTIVE: To describe the clinical and anatomical results of the complex one-stage surgical treatment of BPES by means of levator resection. MATERIALS AND METHODS: 51 children (73 eyes) aged 3-16 years with BPES were operated on by the newly developed one-stage technique at the Pediatric Ophthalmology Department of the Filatov Institute of Eye Diseases and Tissue Therapy. The surgical technique included shortening of the internal canthal ligament, resection of the tarsus and levator muscle, and skin plasty. The new surgical technique is based on new data on the topography of the upper eyelid and anterior part of the orbit obtained by MRI-onward protrusion of the orbital septum with increased volume of the pre-aponeurotic fat pad; thickening of the suborbicularis fat layer; shortening and thickening of the mobile part of the upper eyelid; and slight expression and low position of the palpebral fold. RESULTS: Elimination of ptosis and epicanthus was achieved in all cases (eye fissure widening of up to 7-11 mm, average 8.8 +/- 1.04 mm, and lengthening of up to 21-30 mm, average 24.7 +/- 2.87 mm). Increased levator function to 3-10 mm (average 5.6 +/- 0.19 mm) was also achieved after surgery. Control MRI investigation confirmed the normalization of the topography of the eyelid and orbital structures. CONCLUSION: The newly developed surgical technique for BPES correction by means of levator resection permits one to obtain high cosmetic and functional results based on improvement of the topography of the upper eyelid and orbital structures.