Diversity and ethnomycological importance of mushrooms from Western Himalayas, Kashmir.

BACKGROUND: Wild edible mushrooms (WEM) are economically significant and used in traditional medicines worldwide. The region of Jammu and Kashmir (Western Himalayas) is enriched with the diversity of edible mushrooms, collected by the rural people for food and income generation. This is the first detailed study on diversity and ethno-medicinal uses of mushrooms from the State of Jammu and Kashmir. METHODS: Consecutive surveys were conducted to record ethnomycological diversity and socio-economic importance of wild edible mushrooms value chain in rural areas of Azad Jammu and Kashmir during 2015-2019. Ethnomycological data were collected with a semi-structured questionnaire having a set of questions on indigenous mycological knowledge and collection and retailing of wild edible mushrooms. A total of 923 informants from the study area provided the results identifying the gender, type of mushroom species, medicinal uses, and marketing of mushrooms. Diversity of mushrooms was studied by using quadrat and transect methods. Principal component analysis (PCA) and detrended correspondence analysis (DCA) were also applied to the dataset to analyse the relationship between species distribution, the underlying environmental factors, and habitat types. PCA identified the major species-specific to the sites and put them close to the sites of distribution. RESULTS: A total of 131 mushroom species were collected and identified during 2015-2019 from the study area. Ninety-seven species of mushrooms were reported new to the State of Azad Jammu and Kashmir. The dominant mushroom family was Russulaceae with 23 species followed by Agaricaceae, 16 species. Major mushroom species identified and grouped by the PCA were Coprinus comatus, Lactarius sanguifluus, Amanita fulva, Armillaria gallica, Lycoperdon perlatum, Lycoperdon pyriforme, and Russula creminicolor. Sparassis crispa, Pleurotus sp, and Laetiporus sulphureus were recorded most edible and medicinally significant fungi. Morels were also expensive and medicinally important among all harvested macro-fungal species. These were reported to use against common ailments and various health problems. CONCLUSIONS: Collection and retailing of WEM contribute to improving the socio-economic status, providing alternative employment and food security to rural people of the area. These mushrooms are used as a source of food and traditional medicines among the rural informants and could be used as a potential source of antibacterial and anticancer drugs in the future.

A census of nuclear cyanobacterial recruits in the plant kingdom.

The plastids and mitochondria of the eukaryotic cell are of endosymbiotic origin. These events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. Previous studies demonstrated that the invasion of land affected plastids and mitochondria differently and that the paths of mitochondrial integration differed between animals and plants. Other studies examined the reasons why a set of proteins remained encoded in the organelles and were not transferred to the nuclear genome. However, our understanding of the functional relations of the transferred genes is insufficient. In this paper, we report a high-throughput phylogenetic analysis to identify genes of cyanobacterial origin for plants of different levels of complexity: Arabidopsis thaliana, Chlamydomonas reinhardtii, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorffii, Sorghum bicolor, Oryza sativa, and Ostreococcus tauri. Thus, a census of cyanobacterial gene recruits and a study of their function are presented to better understand the functional aspects of plastid symbiogenesis. From algae to angiosperms, the GO terms demonstrated a gradual expansion over functionally related genes in the nuclear genome, beginning with genes related to thylakoids and photosynthesis, followed by genes involved in metabolism, and finally with regulation-related genes, primarily in angiosperms. The results demonstrate that DNA is supplied to the nuclear genome on a permanent basis with no regard to function, and only what is needed is kept, which thereby expands on the GO space along the related genes.

Gastroprotective Effect of Freeze Dried Stripped Snakehead Fish (Channa striata Bloch.) Aqueous Extract against Aspirin Induced Ulcerogenesis in Pylorus Ligated Rats.

Channa striata (Bloch.) is a fresh water fish belonging to the family Channidae. The stripped snakehead fish possesses wide range of medicinal properties. In view of traditional use of C. striata for wound healing, the present study was undertaken to investigate the beneficial effects of orally administered freeze dried aqueous extract of Channa striata (AECS) in experimentally induced gastric ulcers in Wistar rats. Aspirin induced ulcerogenesis in pyloric ligation model was used for the assessment of antiulcer activity and Ranitidine (50 mg/kg) was employed as the standard drug. The various gastric parameters like volume of gastric juice, pH, free and total acidities, ulcer index, and levels of antioxidant enzymes like catalase, superoxide dismutase, and lipid peroxidation marker malondialdehyde were determined. AECS at concentrations of 40% and 50% w/v significantly decreased the volume of gastric juice and increased the levels of catalase while considerable decrease in free and total acidities and increase in superoxide dismutase were observed with the treatment of standard drug and AECS (50% w/v). All the test doses of AECS markedly decreased ulcer index and malondialdehyde compared to the standard drug whereas AECS 30% w/v did not alter volume of gastric juice, pH, free and total acidities, catalase, and superoxide dismutase. From these findings, it can be concluded that AECS is devoid of acid neutralizing effects at lower doses and possesses antisecretory and antiulcer activities and this could be related to its antioxidant mechanism.

Identification of differentially expressed genes relevant to corm formation in Sagittaria trifolia.

Sagittaria trifolia is a good model of wetland plants to elucidate the formation of corm. However, few studies have been conducted to uncover the complexity of gene expression involved in corm formation. In this study, high-throughput tag-sequencing based on Solexa Genome Analyzer Platform was applied to monitor the changes in gene expression with three libraries of differentially expressed genes (DEGs) (C1 library: stolon stage, C2 library: initial swelling stage and C3 library: swelling stage) during corm formation in Sagittaria trifolia. Approximately 6.0 million tags were sequenced, and 5854021, 5983454, and 5761079 clean tags including 138319, 116804, and 101739 distinct tags were obtained after removal of low quality tags from each library, respectively. About 46% distinct tags were unambiguous tags mapping to the reference genes, and 33% were unambiguous tag-mapped genes. Totally, 20575, 19807, and 18438 were annotated in C1, C2, and C3 libraries, respectively, after mapping their functions in existing databases. In addition, we found that profiling of gene expression in C1/C2 and C2/C3 libraries were different among most of the selected 20 DEGs. Most DEGs in C1/C2 libraries were relevant to hormone synthesis and response; energy metabolism and stress response, while most of the genes in C2/C3 libraries were involved in carbohydrate metabolism. All up-regulated transcriptional factors and 16 important genes relevant to corm formation in three libraries were also identified. To further analyze the expression of 9 genes, from the results of tag-sequencing, qRT-PCR was applied. In summary, this study provides a comprehensive understanding of gene expression, during the formation of corm in Sagittaria trifolia.

Isolation and functional characterization of a salt responsive transcriptional factor, LrbZIP from lotus root (Nelumbo nucifera Gaertn).

Basic leucine zipper transcription factor (bZIP) is involved in signaling transduction for various stress responses. Here we reported a bZIP transcription factor (accession: JX887153) isolated from a salt-resistant lotus root using cDNA-AFLP approach with RT-PCR and RACE-PCR method. Full-length cDNA which consisted of a single open reading frame encoded a putative polypeptide of 488 amino acids. On the basis of 78, 76, and 75 % sequence similarity with the bZIPs from Medicago truncatula (XP_003596814.1), Carica papaya (ABS01351.1) and Arabidopsis thaliana (NP_563810.2), we designed it as LrbZIP. Semi quantitative RT-PCR results, performed on the total RNA extracted from tips of lotus root, showed that LrbZIP expression was increased with 250 mM NaCl treatment for 18 h. Effects of low temperature on the expression of LrbZIP was also studied, and its expression was significantly enhanced with a 4 °C treatment for 12 h. In addition, LrbZIP expression was strongly induced by treatment with exogenous 100 µM ABA. To evaluate its function across the species, tobacco (Nicotiana tabacum L.) was transformed with LrbZIP in a binary vector construct. Transgenic plants exhibited higher resistance as compared with the control according to the results of the root growth, chlorophyll content and electrolyte leakage when exposed to NaCl treatment. In addition, LrCDPK2, LrLEA, and TPP also showed enhanced expression in the transgenic plants. Overall, expression of LrbZIP was probably very important for salt-resistant lotus root to survive through salt stress.

AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots.

The transcription factor family intimately regulates gene expression in response to hormones, biotic and abiotic factors, symbiotic interactions, cell differentiation, and stress signalling pathways in plants. In this study, 170 AP2/ERF family genes are identified by phylogenetic analysis of the rice genome (Oryza sativa l. japonica) and they are divided into a total of 11 groups, including four major groups (AP2, ERF, DREB, and RAV), 10 subgroups, and two soloists. Gene structure analysis revealed that, at position-6, the amino acid threonine (Thr-6) is conserved in the double domain AP2 proteins compared to the amino acid arginine (Arg-6), which is preserved in the single domain of ERF proteins. In addition, the histidine (His) amino acid is found in both domains of the double domain AP2 protein, which is missing in single domain ERF proteins. Motif analysis indicates that most of the conserved motifs, apart from the AP2/ERF domain, are exclusively distributed among the specific clades in the phylogenetic tree and regulate plausible functions. Expression analysis reveals a widespread distribution of the rice AP2/ERF family genes within plant tissues. In the vegetative organs, the transcripts of these genes are found most abundant in the roots followed by the leaf and stem; whereas, in reproductive tissues, the gene expression of this family is observed high in the embryo and lemma. From chromosomal localization, it appears that repetition and tandem-duplication may contribute to the evolution of new genes in the rice genome. In this study, interspecies comparisons between rice and wheat reveal 34 rice loci and unveil the extent of collinearity between the two genomes. It was subsequently ascertained that chromosome-9 has more orthologous loci for CRT/DRE genes whereas chromosome-2 exhibits orthologs for ERF subfamily members. Maximum conserved synteny is found in chromosome-3 for AP2 double domain subfamily genes. Macrosynteny between rice and Arabidopsis, a distant, related genome, uncovered 11 homologs/orthologs loci in both genomes. The distribution of AP2/ERF family gene paralogs in Arabidopsis was most frequent in chromosome-1 followed by chromosome-5. In Arabidopsis, ERF subfamily gene orthologs are found on chromosome-1, chromosome-3, and chromosome-5, whereas DRE subfamily genes are found on chromosome-2 and chromosome-5. Orthologs for RAV and AP2 with double domains in Arabidopsis are located on chromosome-1 and chromosome-3, respectively. In conclusion, the data generated in this survey will be useful for conducting genomic research to determine the precise role of the AP2/ERF gene during stress responses with the ultimate goal of improving crops.

Isolation and characterization of an endosperm-specific promoter from wheat (Triticum aestivum L.).

Genes coding for avenin-like proteins (ALP) represent a new family of wheat storage protein genes. To find a wheat endosperm-specific promoter, a 1644-bp fragment upstream of the ALP type-B gene (GenBank accession number JN622144) was isolated. The important promoter elements of the ALP type-B gene were ascertained through sequence analysis which revealed that this fragment contains the TATA and CAAT boxes, which are important elements in gene expression. A prolamin box containing an endosperm motif and a GCN4-like motif (GLM) is present at about 300 bp upstream of the translation start site. The promoter sequence has two ESP-like elements and one of them is followed by an RY motif with the nucleotides CATG overlapping. The RY motif is considered the core functional sequence in a promoter. In an attempt to confirm the promoter activity, a series of 5'-deletions of the promoter were fused with the beta-glucuronidase (GUS) gene, and the constructs were stably introduced into tobacco plants. GUS staining confirmed that the AVL type-B promoter is an endosperm-specific promoter in tobacco seeds. Quantitative analysis of GUS expression in transgenic plants showed that even the shortest 5'-deletion, i.e. a 290-bp promoter sequence within the prolamin box, was sufficient to drive GUS expression in the endosperm. The highest expression level was found in transgenic plants containing the 5'-deletion vector construct pALP-8. This suggests that the ESP-like element overlapping with the RY motif may play a crucial role in the regulatory function of the promoter.

Stable chloroplast transformation of immature scutella and inflorescences in wheat (Triticum aestivum L.).

Chloroplast transformation in wheat was achieved by bombardment of scutella from immature embryos and immature inflorescences, respectively. A wheat chloroplast site-specific expression vector, pBAGNRK, was constructed by placing an expression cassette containing neomycin phosphotransferase II (nptII) and green fluorescent protein (gfp) as selection and reporter genes, respectively, in the intergenic spacer between atpB and rbcL of wheat chloroplast genome. Integration of gfp gene in the plastome was identified by polymerase chain reaction (PCR) analysis and Southern blotting using gfp gene as a probe. Expression of GFP protein was examined by western blot. Three positive transformants were obtained and the Southern blot of partial fragment of atpB and rbcL (targeting site) probes verified that one of them was homoplasmic. Stable expression of GFP fluorescence was confirmed by confocal microscopy in the leaf tissues from T(1) progeny seedlings. PCR analysis of gfp gene also confirmed the inheritance of transgene in the T(1) progeny. These results strengthen the feasibility of wheat chloroplast transformation and also give a novel method for the introduction of important agronomic traits in wheat through chloroplast transformation.

Isolation and heterologous transformation analysis of a pollen-specific promoter from wheat (Triticum aestivum L.).

The promoter of a pollen-specific gene TaPSG719 was isolated from wheat (Triticum aestivum L.) by inverse-PCR (IPCR). Sequence analysis revealed that the promoter contains two cis-acting elements (AGAAA and GTGA) known to confer anther/pollen-specific gene expression which suggests that the promoter of TaPSG719 gene is a pollen-specific one. To ascertain the regulatory function of TaPSG719 promoter, two deleted fragments (-1,776 to -1 bp and -1,019 to -1 bp) were fused to the beta-glucuronidase (GUS) gene and transformed into tobacco plants. Similar GUS expression patterns were observed in all transformed plants and its activity was detected exclusively in pollen. No GUS activity in any other floral or vegetative tissue was observed. The results confirm that TaPSG719 promoter is pollen-specific and active during the middle stages of pollen development till anther matured, and it can drive pollen-specific gene expression across the species.