The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis vectorial capacity and engineering interventions are both impeded by limitations vector's genome assembly. existing assemblies An. draft-quality contain thousands sequence gaps, potentially missing elements important for its biology evolution.

Waste collection and transportation is the contact point between waste generators management systems. A proposal for an innovative model of municipal solid (MSW) which a part system using spatial geo database, integrated in geographical information (GIS) environment presented. Pallavapuram fast-developing municipality Chennai city southern suburbs about 20 km from Chennai, state capital Tamil Nadu India. The disposal MSW was previously occurring indiscriminate irrational manner municipality....

Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids cereals and photosynthesis sought-after phenotypes protein-rich legume crops, genome grain amaranths is likely to play a critical role crop research. We have sequenced transcriptome Amaranthus hypochondriacus, diploid (2n = 32) belonging order Caryophyllales with an estimated size 466 Mb. Of 411 linkage single-nucleotide polymorphisms (SNPs) reported for 355...

The incredibly narrow protein fold bottleneck, which separates the billions of unique proteins on one side to deliver diverse biological functions other, arises from folds tolerating mutations during evolution. One such fold, called beta-trefoil, is present in functionally including cytokines involved immune system. unrecognizable sequence-level diversity even among paralogs interleukin-1, within same chromosomal locus, suggests resilience this mutational on-slaught. Furthermore,...

Recently, large numbers of normal human tissues have been profiled for non-coding RNAs and more than fourteen thousand long intergenic (lincRNAs) are found expressed in tissues. The functional roles these lincRNAs (nlincRNAs) the regulation protein coding genes disease biology yet to be established. Here, we two RNA-seq datasets including cancer matched non-neoplastic from 12 individuals diverse demography both nlincRNAs. We find 130 nlincRNAs significantly regulated cancer, with 127 same...

Anopheles stephensi is the most menacing malaria vector to watch for in newly urbanising parts of world. Its fitness reported be a direct consequence adapting laying eggs over-head water tanks with street-side puddles polluted by oil and sewage. Large frequent inversions genome vectors are implicated adaptation. We report assembly strain An. type-form, collected from construction site Chennai (IndCh) 2016. The here L50 4, completes trilogy high-resolution genomes strains respect 16.5 Mbp 2Rb...

Malaria remains a major healthcare risk to growing economies like India and chromosome-level reference genome of Anopheles stephensi is critical for successful vector management understanding evolution using comparative genomics. We report assemblies an Indian strain, STE2, Pakistani strain SDA-500 by combining draft genomes the two strains homology-based iterative approach. The resulting assembly IndV3/PakV3 with L50 9/12 N50 6.3/6.9 Mb respectively, had scaffolds long enough building 90%...

Rhizoctonia solani, causing crown and root rot, is a major risk to sugar beet (Beta vulgaris L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection priority breeding programs. We report the identification single-nucleotide polymorphism (SNP) marker linked resistance using restriction site-associated DNA (RAD) sequencing two geographically discrete sets plant materials with different degrees resistance/susceptibility enable wider superior genotypes....

The identification of efficient molecular markers related to low bolting tendency is a priority in sugar beet ( Beta vulgaris L.) breeding. This study aimed identify SNP associated with by establishing genome-wide association study. An elaborate 3-year field trial comprising 13 lines identified L14 as the one exhibiting lowest along an increased survival rate after autumnal sowing. For discovery following phenotyping, contrasting phenotypes 24 non-bolting and 15 plants line were sequenced...

A large number of congenital disorders are very rare and localized to rural areas in India, a country that practices both endogamy consanguinity. Recent advances genomics can aid the identification causative genomic elements when exploring therapeutic interventions developing neonatal screening assign novel functions. Here, we report loss-of-function mutation (p.Trp370*) HACE1 gene is associated with neurodevelopmental disorder boy from remote village southern India.

The most widely used human genome reference assembly hg19 harbors minor alleles at 2.18 million positions as revealed by 1000 Genome Phase 3 dataset. Although this is less than 2% of the 89 variants reported, it has been shown that can result in 30% false positives individual genomes, thus misleading and burdening downstream interpretation. More alarming fact that, significant percentage are homozygous recessive for these alleles, with potential disease implications, masked from reporting.We...

Vector management programs rely on knowledge of the biology and genetic make-up mosquitoes. Anopheles stephensi is a major invasive urban malaria vector, distributed throughout Indian subcontinent Middle East, has recently been expanding its range in Africa. With existence three biological forms, distinctly identifiable based number ridges eggs varying vectorial competence, An. perfect species for developing isofemale lines, which can be tested insecticide susceptibility competence various...

Abstract Edible/non-toxic varieties of Jatropha curcas L. are gaining increasing attention, providing both oil as biofuel feedstock or even edible and the seed kernel meal animal feed ingredient. They a viable alternative to limitation posed by presence phorbol esters in toxic varieties. Accurate genotyping toxic/non-toxic accessions is critical breeding management. The aim this study was identify SNP markers linked toxicity J. . For discovery, NGS technology used sequence whole genomes...

Head and neck squamous cell carcinomas (HNSCC) include heterogeneous group of tumors, classified according to their anatomical site. It is the sixth most prevalent cancer globally. Among South Asian countries, India accounts for 40% HNC malignancies with significant morbidity mortality. In present study, we have performed exome sequencing analysis 51 Neck carcinoma samples. Besides known mutations in oncogenes tumour suppressors, identified novel gene signatures differentiating buccal,...

Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability high-quality genomes several mosquito vectors. Anopheles stephensi, with its three distinctly-identifiable forms at egg stage, correlating varying vector competence, offers ideal species to discover functional implicated Plasmodium resistance. Recently, strains An. stephensi type-form, known display high vectorial capacity, were reported. Here, we report a...

Prp16 is a DEAH box pre-mRNA splicing factor that triggers key spliceosome conformational switch to facilitate second step in Saccharomyces cerevisiae. However, functions are largely unexplored Schizosaccharomyces pombe, an attractive model with exon-intron architecture more relevant several other eukaryotes. Here, we generated mis-sense alleles SpPrp16 whose consequences on genome-wide uncover its nearly global role only small subset of unaffected introns. dependent and independent intron...

In the age of genomics-based crop improvement, a high-quality genome local landrace adapted to environmental conditions is critically important. Grain amaranths produce highly nutritional grains with multitude desirable properties including C4 photosynthesis sought-after in other crops. For improving agronomic traits grain amaranth and for transfer dicot crops, reference necessary. Towards this end, our lab had initiated sequencing Amaranthus (A.) hypochondriacus (A.hyp_K_white) reported...

Abstract Background The hg19 assembly of the human genome is most heavily annotated and commonly used reference to make variant calls for individual genomes. Based on phase 3 report 1000 genomes project (1000G), it now well known that many positions in represent minor alleles. Since call methods are developed under assumption harbors major alleles at all ~3 billion positions, these mask whenever an homozygous allele respective positions. Hence, important address extent impact from point view...

Microbial mats in hot springs form a dynamic ecosystem and support the growth of diverse communities with broad-ranging metabolic capacity. In this study, we used 16S rRNA gene amplicon sequencing to analyse microbial mat samples from two Al Aridhah, Saudi Arabia. Putative pathways were identified using phylogenetic investigation by reconstruction unobserved states (PICRUSt). Filamentous anoxygenic phototrophic bacteria associated phylum Chloroflexi abundant (> 50 %) both at 48 °C. mainly...

// Pushpinder Singh Bawa 1, 2, , Samathmika Ravi 1 Swagatika Paul Bibha Chaudhary and Subhashini Srinivasan Institute of Bioinformatics Applied Biotechnology, Biotech Park, Electronic City Phase I, Bangalore, India 2 Manipal University, Manipal, Karnataka, Correspondence to: Srinivasan, email: ssubha@ibab.ac.in Keywords: lncRNA; PCAT92; prostate cancer; ABCC4; ZIC2 Received: January 24, 2017     Accepted: July 18, 2018     Published: August 21, 2018...

Abstract Background The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis vectorial capacity and engineering interventions are both impeded by limitations vector’s genome assembly. existing assemblies An. draft-quality contain thousands sequence gaps, potentially missing elements important for its biology evolution. Results To access previously intractable genomic regions, we generated reference-grade assembly full...

Genome duplication event in edible dicots under the orders Rosid and Asterid, common during oligocene period, is missing for species order Caryophyllales. Despite this, grain amaranths not only survived this period but display many desirable traits rosids asterids. For example, like C4 photosynthesis, high-lysine seeds, high-yield, drought resistance, tolerance to infection resilience stress. It is, therefore, of interest look minor genome rearrangements with potential functional...