Draft genome of Korthalsia laciniosa (Griff.) Mart., a climbing rattan elucidates its phylogenetic position

Korthalsia laciniosa (Griff.) Mart. is a climbing rattan used as a source of durable and flexible cane. In the present study, the draft genome of K. laciniosa was sequenced, de novo assembled and annotated. Genome-wide identification of MADS-Box transcription factors revealed loss of Mβ, and Mγ genes belonging to Type I subclass in the rattan lineage. Mining of the genome revealed presence of 13 families of lignin biosynthetic pathway genes and expression profiling of nine major genes documented relatively lower level of expression in cirrus when compared to leaflet and petiole. The chloroplast genome was re-constructed and analysis revealed the phylogenetic relatedness of this genus to Eugeissona, in contrast with its present taxonomic position. The genomic resource generated in the present study will accelerate population structure analysis, genetic resource conservation, phylogenomics and facilitate understanding the unique developmental processes like gender expression at molecular level.

The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (Arecaceae)

Taxonomic complexities, like environmental plasticity and homoplasy, make precise identification challenging in Calamus, the genus of spiny climbing palms of the subfamily Calamoideae (Arecaceae). In the present study, the species discriminatory power of twelve potential DNA barcode regions (rbcL, matK, psbA-trnH, rpoC, rpoB, psbK-psbI, atpF-atpH, psbZ-trnfM, ITS1, ITS2, PRK, and RPB2) were evaluated in 21 species of Calamus from the Western Ghats region of India, using distance, tree, and similarity based statistical methods. Except for the low copy nuclear region, RPB2, none of the tested plastid loci or nuclear loci ITS, either singly or in combinations, could discriminate all the species of Calamus due to low substitution rate of plastid regions and multiple copies of ITS respectively. The RPB2 locus showed highest species resolution with 96% accuracy in similarity based analysis, indicating its potential and efficiency as a barcode locus for the genus. The putative "Calamus gamblei complex" based on overlapping morphology was successfully resolved as six distinct, though closely related, species. The analysis also indicates that C. delessertianus is a morphological variant of C. dransfieldii. In spite of being a low copy nuclear gene region, RPB2 provided an efficient barcode to delineate Calamus species and has the potential to further extend its use as a prospective barcode to other Palm genera.

DNA barcoding supports existence of morphospecies complex in endemic bamboo genus Ochlandra Thwaites of the Western Ghats, India

Ochlandra Thwaites, an economically exploited bamboo genus of the Western Ghats of India is severely affected by unsustainable extraction, natural habitat destruction and endangerment of species resources. This taxonomically challenging genus consists of a genetic mixture of 10 related polyploid species that are difficult to define and classify using traditional morphology. The present study investigated the probability of DNA barcoding using seven standard barcode regions recommended by CBOL as a supplementary tool to define true species boundaries. Distance (MEGA v.6.0) and sequence similarity (TaxonDNA) based approaches highlighted the discriminatory power of psbA-trnH intergenic spacer barcode region, but did not support true species entities. Neighbour-joining and Bayesian inference trees supported the existence of morphospecies complex in seven species of the genus owing to weak reproductive barriers amongnaturally coexisting species. Morphological affinities existing within genus might have stemmed from natural interspecific hybridization events and consequent reticulate evolution in morphospecies complex of genus Ochlandra.

Narrow gene pool can threaten the survival of Calamus nagbettai R. R. Fernald & Dey: a highly, endemic dioecious rattan species in the Western Ghats of India

Rattans, the spiny climbing palms of Arecaceae (Palmae) family exhibit high endemism to the biodiversity hot spots in India. Of the five rattan genera, Calamus is the only genus found in peninsular India with 15 of 21 species, endemic to the Western Ghats. The extensive utilization of rattans owing to their strength, durability and huge demand has resulted in depletion of their natural resources. Of the 15 endemic species, C. nagbettai is the most affected species on account of endemism, low population size and restricted distribution with fragmented populations. The present study revealed high amount of genetic diversity in the surviving scattered populations of the species using microsatellite markers. High gene flow (N_m = 1.498) observed across the populations resulted in low genetic differentiation (14%). A clear genetic admixture could be seen in Kerala as well as one of the Karnataka's populations while the remaining two populations were genetically distinct. UPGMA, PCoA and STRUCTURE analyses showed significantly different genetic composition in Kerala population compared to other populations. Kerala and Karnataka populations of C. nagbettai were also unique in their genetic structure and allelic composition. Therefore, effective management and conservation strategies have to be implemented to preserve the rarealleles with adaptive potential to protect this economically valuable Calamus species from endangerment. Over exploitation, low seed set and poor regeneration, as well as habitat fragmentation can further threaten the survival of this endemic, narrowly distributed dioecious rattan species in the Western Ghats region.

Development and validation of a headspace gas chromatographic method for the determination of residual solvents in arterolane (RBx11160) maleate bulk drug

Objective:

Arterolane maleate is an antimalarial drug currently under Phase III clinical evaluation, and presents a simple, economical and scalable synthesis, and does not suffer from safety problems. Arterolane maleate is more active than artemisinin; and is cheap to produce. It has a longer lifetime in the plasma, so it stays active longer in the body. To provide quality control over the manufacture of any API, it is essential to develop highly selective analytical methods. In the current article we are reporting the development and validation of a rapid and specific Head space gas chromatographic (HSGC) method for the determination of organic volatile impurities (residual solvents) in Arterolane Maleate bulk drug.

Materials and Methods:

The method development and its validation were performed on Perkin Elmer's gas chromatographic system equipped with Flame Ionization detector and head space analyzer. The method involved a thermal gradient elution of ten residual solvents present in arterolane maleate salt in RTx-624, 30 m × 0.32 mm, 1.8 μ column using nitrogen gas as a carrier. The flow rate was 0.5 ml/min and flame ionization detector (FID) was used.

Results:

During method validation, parameters such as precision, linearity, accuracy, limit of quantification and detection and specificity were evaluated, which remained within acceptable limits.

Conclusions:

The method has been successfully applied for the quantification of the amount of residual solvents present in arterolane maleate bulk drug.The method presents a simple and reliable solution for the routine quantitative analysis of residual solvents in Arterolane maleate bulk drug.

Genetic Diversity Assessment of Rarely Cultivated Traditional Indica Rice (Oryza sativa L.) Varieties

Random amplified polymorphic DNA fingerprinting was performed to assess the genetic diversity among rarely cultivated traditional indica rice (Oryza sativa L.) varieties collected from a tribal hamlet of Kerala State, India. A total of 664 DNA bands amplified by 15 primers exhibited 72.9% polymorphism (an average of 32.3 polymorphic bands per primer). The varieties Jeerakasala and Kalladiyaran exhibited the highest percent (50.19%) polymorphism, while Thondi and Adukkan showed the lowest (9.85%). Adukkan (78 bands) and Jeerakasala (56 bands) yielded the highest and the lowest number of amplicons, respectively. Unweighted Pair Group Method with Arithmetic mean analysis using the Dice similarity coefficient showed the highest value of similarity coefficient between the varieties Adukkan and Thondi, both shared higher level of similarity (0.81), followed by Kanali and Thondi (0.88). Of the three subclusters, the varieties of Adukkan, Thondi, Kanali, Mannuveliyan, Thonnuranthondi, and Chennellu grouped together with a similarity of 0.77. The second group represented by Navara, Gandhakasala, and Jeerakasala with a similarity coefficient of 0.76 formed a cohesive group. The variety Kalladiyaran formed an isolated position that joined the second cluster. The Principal Coordinate Analysis also showed separation of Kalladiyaran from the other varieties.