Indian Journal of Skin Allergy

Advancements in sequencing technologies have dramatically transformed genomics research by enabling the analysis of genetic information with unprecedented scale and efficiency. Next-generation sequencing (NGS), renowned for its high-throughput capabilities, has significantly reduced costs and expanded the scope of sequencing applications. Among these, sequencing by synthesis (SBS) on Illumina systems is predominant, favored for its accuracy and cost-effectiveness. However, emerging technologies like Element Biosciences’ sequencing by Avidity (AVITI) are beginning to challenge this dominance. In this study, we sequenced and genotyped a library of 40 cannabis samples using both the AVITI and Illumina NovaSeq systems, observing an 81.2% overlap with 98.9% concordance in genotype calls. AVITI stands out for its flexibility and reduced per-base costs, presenting a viable option particularly for mid-sized laboratories. As the scientific community continues to seek ways to lower genotyping expenses, the combination of the AVITI system with NanoGBS library preparation offers a cost-effective solution adaptable to a wide range of project sizes.

Yellow/stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a major biotic stress in global wheat production. Introgression lines derived from the Triticum spelta accessions PI348764 and IARI276 showed high levels of yellow rust resistance at seedling and adult plant stage. The Yr5 gene located on 2B chromosome was previously the only stripe rust resistance gene described in T. spelta gene pool. By genotyping parental and introgressed material with markers linked with the Yr5 gene, we demonstrate that PI348764 likely carries Yr5, and that it appears to be absent from IARI276. By employing a combination of methods, including screening for adult plant resistance and seedling resistance at multiple field trials; bulked segregant analysis (BSA) on F5 families, and genotyping using wheat Breeders' 35K array; we show that YrIARI276 is a novel stripe rust resistance gene with putative chromosomal locations on 1BL, 1DL, 5AL or 7BL. Furthermore, genetic analysis revealed that YrIARI276 showed a goodness of fit to Mendelian ratios for a single dominant gene. As the gene is distinct from Yr5 and the chromosomal location is unique from earlier reported Yr genes, it will be useful in improving diversity of Yr gene repertoire in disease resistance breeding programmes.

The voles of the Microtus thomasi / M. atticus species complex (Arvicolinae) display extensive karyotypic variation, in the number of autosomes and the morphology of sex chromosomes. We analysed the satellitome of M. thomasi and identified 17 satDNA families, corresponding to 6.704% of the genome. Homogenization and divergence analyses showed that some satDNA families are more homogeneous, indicative of recent amplification, while others displayed higher variation, suggesting ancient amplification. Twelve of satDNA families are conserved across Arvicolinae with a substantial variation in the abundance and the composition. These results supports the "library" hypothesis, where a shared collection of satDNAs exists across related species, with differential amplification driving species-specific genomic profiles. Localization analysis demonstrated that an increased number of satDNA families are localized in the pericentromeric and the heterochromatic regions of autosomes and sex chromosomes. Our results suggest that the heterochromatin of the X and Y chromosomes co-evolved and that satDNA families might have contributed to the chromosomal rearrangements involved in the karyotypic variation and sex chromosome polymorphism of the chromosomal races. Our study contribute to a deeper understanding of the evolutionary mechanisms underlying karyotype diversification in Microtus species, which exhibit some of the highest rates of karyotypic variation among mammals.

We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (<i>Bombus bellicosus</i>). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (<i>B. pascuorum</i>). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees which suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.

Urochloa P. Beauv. (formerly classified as Brachiaria (Trin.) Griseb.) is a genus of African perennial grasses that is extensively cultivated in tropical countries for cattle nutrition. Three of the most economically relevant species, Urochloa brizantha, U. decumbens, and U. ruziziensis, form the ‘brizantha’ agamic complex, which includes allopolyploid series with distinct subgenomes. Investigating the composition and organization of repetitive DNA, a major component of grass genomes, can provide insights into their genomic relationships and evolutionary history. This study aimed to characterize the repetitive DNA landscape of selected Urochloa species belonging to the ‘brizantha’ agamic complex; identify and compare major repeat classes across species and evaluate their potential as cytogenetic markers on mitotic chromosomes using fluorescent in situ hybridization (FISH). Clustering analysis revealed that repetitive DNA constitutes 56–65% of the genomes, with Ty3/Gypsy retrotransposons, particularly the Athila and Retand lineages, representing the most abundant repeat class. U. decumbens exhibited the highest proportion of Ty3/Gypsy retrotransposons, while U. ruziziensis had the highest satellite DNA content. The chromosomal location of representative satellites (UroSat-1a, UroSat-2a, and UroSat-3) was determined in all three species via FISH. UroSat-1a was detected in all centromeres, while UroSat-2a and UroSat-3 signals varied in number and position. Our findings validate the use of satDNA as cytogenetic markers in the Urochloa ‘brizantha’ agamic complex and revealed genomic relationships among different species and ploidy levels.

Our comprehension of avian karyotypes still needs to be improved, especially for Suliform birds. To enhance understanding of chromosomal evolution in this order, we conducted conventional and molecular cytogenetic analysis in five species, named Sula dactylatra, S. leucogaster, S. sula (Sulidae), Fregata magnificens (Fregatidae), and Nannopterum brasilianum (Phalacrocoracidae). The diploid chromosome number for S. dactylatra and S. leucogaster was established as 2n = 76 in males, and 2n = 75 in females, but S. sula displayed a karyotype of 2n = 76 chromosomes in males. The disparity in diploid chromosome numbers between male and female Sula is due to a multiple sex chromosome system of the Z1Z1Z2Z2/Z1Z2W type. We propose that the emergence of this multiple-sex chromosome system resulted from a Robertsonian translocation involving the W chromosome and the smallest microchromosome. F. magnificens exhibited a diploid number 76 (2n = 76), while N. brasilianum displayed a diploid number of 74 (2n = 74) in both sexes. The ribosomal cluster was located in one microchromosome pair in S. dactylatra, S. leucogaster, S. sula, and F. magnificens and in four pairs in N. brasilianum. Our findings provide evidence of a conserved multiple-sex chromosome system within the Sula genus, shedding light on the high karyotype diversity in Suliformes.

Polyamine oxidase (PAOs) are enzymes associated with polyamine catabolism and play important roles in growth and development and stress tolerance of plants. In the present study, genome-wide discovery and analysis of the PAO family in sorghum was done utilizing model PAO of Arabidopsis. Six PAO genes were found using publicly available genomic data. Sorghum has the PAO gene representatives distributed throughout four chromosomes (chr1, 3, 6, and 7), and most members have 8 to 9 exons. The molecular weights of PAO proteins range from 53 to 63 kDa. PAO proteins have a theoretical PI between 5.2 and 8.1. The identification and characterization of PAO gene members in sorghum laying the foundation for further experimental studies elucidating their roles in growth, development, and stress responses, ultimately contributing to our understanding of plant biology, with significant implications for plant breeding by providing valuable insights into potential targets for enhancing stress tolerance and improving crop performance.

<i>Aegilops speltoides</i> (2n=2x=14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of <i>Aegilops</i> from the <i>Sitopsis</i> section and wheat and found that <i>Ae. speltoides</i> is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from <i>Ae. speltoides</i> more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and <i>Ae. speltoides</i> and develop <i>Ae. speltoides</i> chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low coverage sequence data was analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in <i>Ae. speltoides</i> and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. <i>Ae. speltoides</i> had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting <i>Ae. speltoides</i> chromatin in the wheat background using fluorescent <i>in situ</i> hybridization.

India harbours a substantial population of 9.43 million dogs, showcasing diverse phenotypes and utility. Initiatives focusing on awareness, conservation and informed breeding can greatly enhance the recognition and welfare of the unique Indian canine heritage. This study describes the design and development of a high density SNP array for genomic characterization of Indian dogs. Paired-end (150bp) DNA sequences from four diverse dog populations were generated with 10X coverage, following the standard pipeline of Axiom Array technology for chip design. More than 23 million raw SNPs were initially identified, with 629,597 SNP markers ultimately tiled on the Indian canine array (Axiom_Shwaan) after stringent filtering and processing. With an inter-marker distance of 3.8 kb the Axiom_Shwaan greatly increases the canine genome coverage. The array was validated by genotyping 186 samples representing 11 dog breeds/populations from India. The high call rate (99%) of SNPs on the designed chip indicates its suitability for use in Indian dog populations, reflecting sufficient genetic diversity. The principal component and phylogenetic analyses delineated the native dog breeds into discrete groups. This high-density SNP array will empower future applications in population genetics, breed/selection signature identification, development of trait-specific biomarkers and genome-wide data mining for various canine abilities.

Benzo (a) pyrene produced by food during high-temperature process enters the body through ingestion, which causes food safety issues to the human body. In order to alleviate the harm of foodborne benzo (a) pyrene to human health, a strain that can degrade benzo (a) pyrene was screened from Kefir, a traditional fermented product in Xinjiang. Bacillus cereus M72-4 is a Gram-positive bacteria sourced from Xinjiang traditional fermented product Kefir, under Benzo(a)pyrene stress conditions, there was 69.39% degradation rate of 20 mg/L Benzo(a)pyrene by strain M72-4 after incubation for 72 h. The whole genome of M72-4 sequenced using PacBio sequencing technology in this study. The genome size was 5754801 bp and a GC content was 35.24%, a total of 5719 coding genes were predicted bioinformatically. Through functional database annotation, it was found that the strain has a total of 219 genes involved in the transportation and metabolism of hydrocarbons, a total of 9 metabolic pathways related to the degradation and metabolism of exogenous substances, and a total of 67 coding genes.According to the KEGG database annotation results, a key enzyme related to Benzo(a)pyrene degradation, catechol 2,3-dioxygenase, was detected in the genome data of Bacillus cereus M72-4, encoding genes dmpB and xylE, respectively; There are also monooxygenases and dehydrogenases. Therefore, it can be inferred that this strain mainly degrades Benzo(a)pyrene through Benzoate metabolic.

The actin cytoskeleton is a dynamic mesh of filaments that provide structural support for cells and respond to external deformation forces. Active sensing of these forces is crucial for the function of the actin cytoskeleton, and some actin crosslinkers accomplish it. One such crosslinker is filamin, a highly conserved actin crosslinker dimeric protein with an elastic region capable of responding to mechanical changes in the actin cytoskeleton. Filamins are required across various cells and tissues. In Drosophila early and recent studies have provided many details about filamin functions. This review centers on the two Drosophila filamins encoded by the cheerio and jitterbug genes. We examine the structural and evolutionary aspects of filamin genes in flies, contrasting them with those of other model organisms. Then, we synthesize phenotypic data across diverse cell types. Additionally, we outline the genetic tools available for both genes. We also propose to divide filamins into typical and atypical based on the number of actin-binding domains and their relationship with other filamins.

<i>Crematogaster</i> Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical <i>Crematogaster</i>, several taxonomical issues remain unresolved. While cytogenetic approaches can help to delimit species, cytogenetic data are only available for 18 taxa. In this study, classical and molecular cytogenetic analyses were performed on five <i>Crematogaster</i> species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2n=22 chromosomes were observed in <i>Crematogaster erecta</i> Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. <i>Crematogaster</i> aff. erecta had 2n=28, while<i> C. limata</i> Smith, 1858, <i>C. tenuicula</i> Forel, 1904 and <i>Crematogaster </i>sp. had 2n = 38. The telomeric motif (TTAGG)<sub>n</sub> was found in all five species, and the (TCAGG)<sub>n</sub> motif was detected in the telomeres of <i>C. limata</i>. This peculiar motif was also detected in the centromeric regions of <i>C. erecta</i> cytotype I. The microsatellite (GA)<sub>n</sub> was dispersed in the chromosomes of all species studied which also had a single intrachromosomal rDNA site. The cytogenetic results revealed notable interspecific and intraspecific variation, which suggests different chromosomal rearrangements involved in the origin of these variations, also highlighting the taxonomic value of cytogenetic data on <i>Crematogaster</i>.

Brassica napus, commonly known as rapeseed or canola, is an economically valuable oilseed crop grown throughout Canada that currently faces several challenges due to industrial farming practices as well as a changing climate. Calcium-dependent protein kinases (CDPKs) are key regulators of stress signaling in multiple plant species. CDPKs sense changes in cellular calcium levels via a calmodulin-like domain and are able to respond to these changes via their protein kinase domain. In this mini-review, we provide a quick guide to BnaCDPKs. We present an updated phylogeny of the BnaCDPK family in relation to CDPKs from Arabidopsis thaliana and Oryza sativa and we provide a standardized nomenclature for the large BnaCDPK family that contains many co-orthologs. We analyze expression patterns of BnaCDPKs across tissue types and in response to abiotic and biotic stresses, and we summarize known functions of BnaCDPKs. We hope this guide is useful to anyone interested in exploring the prospect of harnessing the potential of BnaCDPKs in the generation of elite cultivars of B. napus.

Successful resistance to disease-causing pathogens is underpinned by properly regulated immune signalling and defence responses in plants. The plant immune system is controlled at multiple levels of gene and protein regulation—from chromatin-associated epigenetic processes to protein post-translational modifications. Optimal fine-tuning of plant immune signalling and responses is important to prevent plant disease development, which is being exacerbated by a globally changing climate. In this review, we focus on how changing climatic factors mechanistically intercept plant immunity at different levels of regulation (chromatin, transcriptional, post-transcriptional, translational, and post-translational). We specifically highlight recent studies that have provided molecular insights into critically important climate-sensitive nodes and mechanisms of the plant immune system. We then propose several potential future directions to build climate-resilient plant disease resistance using cutting-edge biotechnology. Overall, this conceptual understanding and promising biotechnological advances provide a foundational platform towards novel approaches to engineer plant immune resilience.