Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals

A Novel nonsense mutation (c.414G>A; p.Trp138*) in CLDN14 causes hearing loss in Yemeni families : a case report

Non-syndromic hearing loss (NSHL) is a hereditary disorder that affects many populations. Many genes are involved in NSHL and the mutational load of these genes often differs among ethnic groups. Claudin-14 (CLDN14), a tight junction protein, is known to be associated with NSHL in many populations. In this study, we aimed to identify the responsible variants in 3 different Yemeni families affected with NSHL. Firstly, clinical exome sequencing (CES) performed for 3 affected patients from these different families identified a new nonsense variant (c.414G > A) in CLDN14. This variant was then confirmed by Sanger sequencing and PCR-RFLP. Subsequently, four microsatellite markers were used to genotype these families, which revealed a founder effect for this variant. Overall, this study illustrates the implication of the CLDN14 gene in the Yemeni population with NSHL and identifies a new founder variant

Identification of a novel frameshift mutation in the ILDR1 gene in a UAE family, mutations review and phenotype genotype correlation.

Autosomal recessive non-syndromic hearing loss is one of the most common monogenic diseases. It is characterized by high allelic and locus heterogeneities that make a precise diagnosis difficult. In this study, whole-exome sequencing was performed for an affected patient allowing us to identify a new frameshift mutation (c.804delG) in the Immunoglobulin-Like Domain containing Receptor-1 (ILDR1) gene. Direct Sanger sequencing and segregation analysis were performed for the family pedigree. The mutation was homozygous in all affected siblings but heterozygous in the normal consanguineous parents. The present study reports a first ILDR1 gene mutation in the UAE population and confirms that the whole-exome sequencing approach is a robust tool for the diagnosis of monogenic diseases with high levels of allelic and locus heterogeneity. In addition, by reviewing all reported ILDR1 mutations, we attempt to establish a genotype phenotype correlation to explain the phenotypic variability observed at low frequencies

Plant Tissues as Biomonitoring Tools for Environmental Contaminants

Environmental toxins pose significant threats to ecosystems and human health. Monitoring and assessing these toxins are crucial for effective environmental management and public health protection. Recently, plant species have garnered increasing attention as potential bioindicators for identifying and evaluating ecological toxins. Since plants often come into touch with harmful compounds in soil, water, and the atmosphere, they are particularly valuable for analyzing how human activities influence the terrestrial ecosystem, the aquatic system, and the atmosphere. This review paper emphasizes using plant species as a resource for tracking environmental pollution and analyzing contaminants. We focused on plants because they are significant indicators of soil, water, and air quality changes. Many plants have been used as bio-indicators to assess and predict pollution, toxicity, and environmental changes. These include Allium cepa, Vicia faba, Pisum sativum, Zea mays, Nicotiana tabacum, lichens, and mosses. The idea of bioindicators is discussed in the current paper, with a focus on plants as possible candidates for bioindicators for toxin assessment and related outcomes

Electropherograms.

<p>Homozygous normal individual (A), Heterozygous individual (B), and affected individual with the c.804delG pathogenic variant in the <i>ILDR1</i> gene (NM_001199799.1) (C).</p

Identification of a novel frameshift mutation in the <i>ILDR1</i> gene in a UAE family, mutations review and phenotype genotype correlation

<div><p>Autosomal recessive non-syndromic hearing loss is one of the most common monogenic diseases. It is characterized by high allelic and locus heterogeneities that make a precise diagnosis difficult. In this study, whole-exome sequencing was performed for an affected patient allowing us to identify a new frameshift mutation (c.804delG) in the Immunoglobulin-Like Domain containing Receptor-1 (<i>ILDR1)</i> gene. Direct Sanger sequencing and segregation analysis were performed for the family pedigree. The mutation was homozygous in all affected siblings but heterozygous in the normal consanguineous parents. The present study reports a first <i>ILDR1</i> gene mutation in the UAE population and confirms that the whole-exome sequencing approach is a robust tool for the diagnosis of monogenic diseases with high levels of allelic and locus heterogeneity. In addition, by reviewing all reported <i>ILDR1</i> mutations, we attempt to establish a genotype phenotype correlation to explain the phenotypic variability observed at low frequencies.</p></div

<i>ILDR1</i> reported mutations, described effects and predicted consequences using insilico analysis.

<p><i>ILDR1</i> reported mutations, described effects and predicted consequences using insilico analysis.</p

Significant transcriptomic changes are associated with differentiation of bone marrow-derived mesenchymal stem cells into neural progenitor-like cells in the presence of bFGF and EGF

IntroductionMesenchymal stem cells (MSCs) isolated from bone marrow have different developmental origins, including neural crest. MSCs can differentiate into neural progenitor-like cells (NPCs) under the influence of bFGF and EGF. NPCs can terminally differentiate into neurons that express beta-III-tubulin and elicit action potential. The main aim of the study was to identify key genetic markers involved in differentiation of MSCs into NPCs through transcriptomic analysis.MethodTotal RNA was isolated from MSCs and MSCs-derived NPCs followed by cDNA library construction for transcriptomic analysis. Sample libraries that passed the quality and quantity assessments were subjected to high throughput mRNA sequencing using NextSeq (R) 500. Differential gene expression analysis was performed using the DESeq2 R package with MSC samples being a reference group. The expression of eight differentially regulated genes was counter validated using real-time PCR.ResultsIn total, of the 3,252 differentially regulated genes between MSCs and NPCs with two or more folds, 1,771 were upregulated genes, whereas 1,481 were downregulated in NPCs. Amongst these differential genes, 104 transcription factors were upregulated, and 45 were downregulated in NPCs. Neurogenesis related genes were upregulated in NPCs and the main non-redundant gene ontology (GO) terms enriched in NPCs were the autonomic nervous system, cell surface receptor signalling pathways), extracellular structure organisation, and programmed cell death. The main non-redundant GO terms enriched in MSCs included cytoskeleton organisation cytoskeleton structural constituent, mitotic cell cycle), and the mitotic cell cycle process Gene set enrichment analysis also confirmed cell cycle regulated pathways as well as Biocarta integrin pathway were upregulated in MSCs. Transcription factors enrichment analysis by ChEA3 revealed Foxs1 and HEYL, amongst the top five transcription factors, inhibits and enhances, respectively, the NPCs differentiation of MSCs.ConclusionsThe vast differences in the transcriptomic profiles between NPCs and MSCs revealed a set of markers that can identify the differentiation stage of NPCs as well as provide new targets to enhance MSCs differentiation into NPCs.Funding Agencies|University of Sharjah [1602145036-P]; Malaysia Toray Science Foundation [304/PPSP/6150142/M126]</p

Pedigree of the affected family, Audiogram and PCR-RFLP analysis.

<p>(A) Pedigree of the affected family with nonsyndromic hearing loss. Arrow denotes the proband. (B) Audiogram of the proband individual II-1 exhibiting bilateral, severe to profound sensorineural hearing loss. (C) Results of PCR-RFLP analysis of DNA of the affected family with nonsyndromic hearing loss. A 993 bp PCR fragment is digested with FauI restriction enzyme. The wildtype DNA is cleaved into four fragments 538, 222, 136 and 97 bp, whereas the c.804delG mutant allele is cleaved into three fragments 635, 222 and 136 bp in length. MW: DNA Ladder (100bp DNA Ladder, REF G2101) (Promega, USA); ND: undigested PCR product.</p