An alternative suite of universal primers for genotyping in multiplex PCR

Population status and genetic assessment of mugger (Crocodylus palustris) in a tropical regulated river system in North India

For rewilding the depleted crocodylian populations in India, a targeted 'one-species one area' based conservation approach was adopted in the early-1970s. Suitable habitats were identified and designated as protected areas, specifically targeted to recover a particular crocodylian species. A ~ 610 km stretch of Chambal River in the Ganga River Basin was declared as National Chambal Sanctuary to restore the 'Critically Endangered' gharial (Gavialis gangeticus), where active management of mugger (Crocodylus palustris) was discouraged. In the present study, we examined the population trends, occupancy, and genetic status of mugger by conducting population monitoring and genetic assessment to understand the status of potentially competitive mugger in the Sanctuary. Our finding suggests that the mugger population has notably increased and colonised the Sanctuary. We observed a moderate level of genetic diversity in the mugger, which was relatively higher compared to the gharial in the Sanctuary. The rapid colonization of ecological generalist mugger raises concerns about potential competition with ecological specialist gharial threatening its long-term sustainability. Considering the coexistence dynamics between the species, it is essential to extend adaptive management strategies for mugger to ensure successful recovery of gharial population in the Sanctuary.

Population genetics of the critically endangered three-striped turtle, Batagur dhongoka, from the Ganga river system using mitochondrial DNA and microsatellite analysis

The three-striped roofed (Batagur dhongoka) is a semi-aquatic turtle that belongs to family Geoemydidae. Due to anthropogenic pressure, it has been facing an intense decline of over 80% in its distribution range in the past 50 years. It is considered as 'Critically Endangered' so effective conservation strategies are needed to protect the species by determining their genetic diversity and population genetic structure. This study investigates the genetic diversity, population structure and demographic pattern of B. dhongoka from two Turtle Rescue and Rehabilitation Centre established near Ganga river using mitochondrial cytochrome b (Cyt b: 1140 bp) ; control region (CR: 451 bp) and ten nuclear microsatellite loci. mtDNA results show low levels of nucleotide diversity (π = 0.0022) in B. dhongoka haplotypes and provide evidence for a low substitution rate. The demographic pattern estimated by the Bayesian skyline plot (BSP) analysis indicates historical stability followed by growth in the effective population size, with a recent reduction in population size from ~ 2 thousand years ago. The microsatellite findings show a moderate level of observed heterozygosity (Ho: 0.49). Bayesian-based clustering analysis revealed weak genetic structures in B. dhongoka and presence of admixed assignations suggesting close genetic relationships. These findings shed light on B. dhongoka's genetic status and underline the necessity of comprehensive rehabilitation and relocation programs and conservation and management techniques to ensure the species' long-term survival. In order to ensure the effective protection and conservation of B. dhongoka, the Government of India has taken a proactive measure by incorporating it into Schedule I of the Wildlife (Protection) Act, 1972, as amended in 2022.

Himalayan upliftment and Shiwalik succession act as a cradle for divergence in Bengal monitor lizard Varanus bengalensis (Reptilia: Varanidae) in India

The Himalayan foothills and associated environment are well-known for driving the rapid diversification of many species and the formation of biodiversity hotspots. The effects of environmental change since the Miocene have accelerated species diversification, and hence are useful for studying population genetic structure, and evolutionary relationships via genetic approaches. To date, the effects of climatic fluctuations on the biogeography of large-bodied lizards have not been assessed comprehensively. Herein, we examine the diversification of Varanus bengalensis, focusing on its genetic structure to provide insights into how landscape structure and climatic fluctuations have shaped species differentiation. We confirm the existence of two distinct lineages within V. bengalensis distributed across the Himalayan foothills and the remainder of mainland India. Divergence analyses revealed the split between the Himalayan foothills and the remainder of the mainland lineages of V. bengalensis in the mid-Pliocene ~3.06 Ma, potentially as a consequence of the Siwalik broadening and climatic fluctuations across the Himalayan foothills. The results suggest recognition of a new lineage of V. bengalensis from the Himalayan foothills as a distinctive evolutionarily significant unit.

Subtype Screening of blaIMP Genes Using Bipartite Primers for DNA Sequencing

Genes conferring carbapenem resistance have spread worldwide among gram-negative bacteria. Subtyping of these genes has epidemiological value due to the global cross-border movement of people. Subtyping of bla_IMP genes that frequently detected in Japan appears to be important in public health settings; however, there are few useful tools for this purpose. We developed a subtyping screening tool based on PCR direct sequencing, which targets the internal sequences of almost all bla_IMP genes. The tool used bipartite multiplex primers with M13 universal sequences at the 5'-end. According to in silico analysis, among the 78 known IMP-type genes, except for bla_IMP-81, 77 detected genes were estimated to be differentiated. In vitro evaluation indicated that sequences of amplicons of IMP-1, IMP-6, IMP-7, and IMP-20 templates were identical to their respective subtypes. Even if the amplicons were small or undetectable through the first PCR, sufficient amplicons for DNA sequencing were obtained through a second PCR using the M13 universal primers. In conclusion, our tool can be possibly used for subtype screening of bla_IMP, which is useful for the surveillance of bacteria with bla_IMP in clinical and public health settings or environmental fields.

MultiplexSSR: A pipeline for developing multiplex SSR-PCR assays from resequencing data

Next-generation sequencing has greatly promoted the investigation of single nucleotide polymorphisms, while studies of simple sequence repeats are sharply decreasing. However, simple sequence repeats still present some advantages in conservation genetics. In this study, an end-to-end pipeline referred to as MultiplexSSR was established to develop multiplex PCR assays in batches with highly polymorphic simple sequence repeats for capillary platforms from resequencing data. The distribution of single sequence repeats in the genome, the error profiles of genotypes and allelotypes, and the increase in the allele length range depending on the number of individuals were investigated. A total of 98% of single sequence repeats presented lengths of less than 100 bp. The error rate of the genotyping and allelotyping of dimeric patterns was ten times higher than those for other patterns. The error rate of allelotyping was less than that of genotyping. The allele length range reached approximate saturation with 10 individuals. This pipeline uses allele numbers to select highly polymorphic loci, masks loci with variation, and applies in silico PCR to improve primer specificity. The application of the developed multiplex SSR-PCR assays validated the pipeline's robustness, showing higher polymorphism and stability for the developed simple sequence repeats and a lower cost for genotyping and providing low-depth resequencing data from less than a dozen individuals for the development of markers. This pipeline fills the gap between next-generation sequencing and multiplex SSR-PCR.

Development of a Novel Phenotypic Roadmap to Improve Blueberry Quality and Storability

Improved fruit quality and prolonged storage capability are key breeding traits for blueberry (Vaccinium spp.) fruit. Until now, breeding selection was mostly oriented on the amelioration of agronomic traits, such as flowering time, chilling requirement, or plant structure. Up until now, however, the storage effect on fruit quality has not been extensively studied, mostly because objective and handy phenotyping tools to evaluate quality traits were not available. In this study we are proposing a novel phenotyping protocol to support breeding selection and quality control within the entire blueberry production chain. Volatile organic compounds (VOCs) and texture traits, were measured by Proton Transfer Reaction- Time of Flight- Mass Spectrometry (PTR-ToF-MS) and a texture analyzer respectively, taking into consideration the influence of prolonged storage. The exploitation of the genetic variability existing within the investigated blueberry germplasm collection (including both southern and northern highbush, hybrids, and rabbiteyes) allowed the identification of the best performing cultivars, based on texture and VOCs variability, to be used as superior parental lines for future breeding programs. The comprehensive characterization of blueberry aroma allowed the identification of a wide array of spectrometric features, mostly related to aldehydes, alcohols, terpenoids, and esters, that can be used as putative biomarkers to rapidly evaluate the blueberry aroma variations related to genetic differences and storability. In addition, this study revealed a lack of straightforward relationship between harvest and postharvest quality features, that might be genotype-dependent.

Amanitaahmadii, a new species of Amanita subgenus Amanitina section Validae from Pakistan

A new species from coniferous forests in Pakistan, Amanitaahmadii, is described on the basis of morpho-anatomy and molecular data set analyses. This species is characterized by its medium-sized to large basidiomata, grayish brown to brown pileal surface and rimose pileus margin with gray to dark brown verrucose veil remnants, a cream stipe with bulbous base having grayish brown or brown longitudinal striations above the annulus, a scaly surface towards the base, globose to broadly ellipsoid and amyloid basidiospores, and the absence of clamped septa in all tissues. Molecular phylogenetic analyses based on ITS and LSU sequences confirmed its identity as a new taxon nested within subgen. Amanitinasect.Validae.

Rapid genotyping of 25 autosomal STRs in a Japanese population using fluorescent universal primers containing locked nucleic acids

Amplification of fluorescently labeled products is one of the most popular methods for genotyping genetic variations. Two-step amplification using fluorescent universal primers simultaneously produces multiple targeted fragments labeled with fluorescent dyes, and this strategy is applicable to large-scale, cost-effective genotyping. In this study, we developed a fast PCR-based, multiple short tandem repeat (STR) genotyping method using fluorescent universal primers containing locked nucleic acids (LNAs). Four amplification reactions, each assaying six or seven markers and using 0.5-1.0 ng of genomic DNA, produced obvious Fam-labeled peaks in all 26 loci tested (25 autosomal STRs and amelogenin). The overall amplification time was 37 min. Moreover, fluorescent signals for the 25 STRs obtained from LNA-containing primers were 1.5-9.0 fold higher compared to those from non-LNA primers. Using genomic DNA from 120 Japanese individuals, 16 out of the 25 STRs had observed heterozygosity greater than 0.7. Some of these 25 STRs also had high discriminatory power, similar to that of the 13 core STRs in the Combined DNA Index System dataset. The probability of incorrectly assigning a match based on the accumulated matching probability for these 25 STRs is 1.2 × 10(-22), and their combined use can provide robust information for Japanese forensics.