Modelling segmental duplications in the human genome

Human lncRNAs harbor conserved modules embedded in different sequence contexts

We analyzed the structure of human long non-coding RNA (lncRNAs) genes to investigate whether the non-coding transcriptome is organized in modular domains, as is the case for protein-coding genes. To this aim, we compared all known human lncRNA exons and identified 340 pairs of exons with high sequence and/or secondary structure similarity but embedded in a dissimilar sequence context. We grouped these pairs in 106 clusters based on their reciprocal similarities. These shared modules are highly conserved between humans and the four great ape species, display evidence of purifying selection and likely arose as a result of recent segmental duplications. Our analysis contributes to the understanding of the mechanisms driving the evolution of the non-coding genome and suggests additional strategies towards deciphering the functional complexity of this class of molecules.

When is an SNP not an SNP?

Genomic duplications are important sources of structural change and gene innovation. In humans, the most recent and highly identical sequences (>90% homology, >1 kb long) are known as segmental duplications (SDs). Single-nucleotide variants or single-nucleotide polymorphisms within SDs have not been systematically assessed due to limitations around mapping short-read sequencing data. Single-nucleotide variant rs62486260 was flagged in a study of familial renal stone disease but it was unclear whether it was real or an artifact resulting from the presence of a SD. We describe in silico and wet-lab approaches to investigate this, using segment-specific long-PCR assays, followed by short PCR for Sanger sequencing. Our conclusion was that rs62486260 is an artifact. Our approach can be generalized to deal with other such situations.

Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies

Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate copies. These high-recurrence duplications correspond to gene retrocopies. We identified 3,892 candidate retrocopies from 1,316 parental genes in the canFam4 assembly and find that ∼8.82% of duplicated base pairs involve a retrocopy, confirming this mechanism as a major driver of gene duplication in canines. Similar patterns are found across eight other recent canine genome assemblies, with metrics supporting a greater quality of the PacBio HiFi mCanLor1.2 assembly. Comparison between the wolf and other canine assemblies found that 92% of retrocopy insertions are shared between assemblies. By calculating the number of generations since genome divergence, we estimate that new retrocopy insertions appear, on average, in 1 out of 3,514 births. Our analyses illustrate the impact of retrogene formation on canine genomes and highlight the variable representation of duplicated sequences among recently completed canine assemblies.

Anesthetic Considerations for Patients with Hereditary Neuropathy with Liability to Pressure Palsies: A Narrative Review

Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant demyelinating neuropathy characterized by an increased susceptibility to peripheral nerve injury from trauma, compression, or shear forces. Patients with this condition are unique, necessitating distinct considerations for anesthesia and surgical teams. This review describes the etiology, prevalence, clinical presentation, and management of HNPP and presents contemporary evidence and recommendations for optimal care for HNPP patients in the perioperative period. While the incidence of HNPP is reported at 7-16:100,000, this figure may be an underestimation due to underdiagnosis, further complicating medicolegal issues. With the subtle nature of symptoms associated with HNPP, patients with this condition may remain unrecognized during the perioperative period, posing significant risks. Several aspects of caring for this population, including anesthetic choices, intraoperative positioning, and monitoring strategy, may deviate from standard practices. As such, a tailored approach to caring for this unique population, coupled with meticulous preoperative planning, is crucial and requires a multidisciplinary approach.

Genome-wide analysis and expression divergence of protein disulfide isomerase (PDI) gene family members in chickpea (Cicer arietinum) under salt stress

Chickpea (Cicer arietinum ) is a grain crop that is an important source of protein, vitamins, carbohydrates and minerals. It is highly sensitive to salt stress, and salt damage to cellular homeostasis and protein folding affects production. Plants have several mechanisms to prevent cellular damages under abiotic stresses, such as proteins in the endoplasmic reticulum (protein isulfide somerases (PDIs) and PDI-like proteins), which help prevent the build-up of mis-folded proteins that are damaged under abiotic stresses. In this study, we completed initial comprehensive genome-wide analysis of the chickpea PDI gene family. We found eight PDI genes are distributed on six out of eight chromosomes. Two pairs of paralogous genes were found to have segmental duplications. The phylogenetic analysis showed that the PDI s have a high degree of homology in C. arietinum, Cicer reticulatum, Lens culinaris, Phaseolus acutifolius, Pisum sativum and Oryza sativa . The gene structure analysis displayed that CaPDI1-CaPDI8 have 9-12 exons except for CaPDI5 , which has 25 exons. Subcellular localisation indicated accumulation of CaPDIs in endoplasmic reticulum. Protein-conserved motifs and domain analysis demonstrated that thioredoxin domains of PDI family is present in all CaPDIs. CaPDI proteins have strong protein-protein interaction. In silico expression analysis showed that four out of eight PDI genes (CPDI2, CaPDI6, CaPDI7 and CaPDI8 ) were expressed under salt stress. Of these, expression of CaPDI2 and CaPDI8 was the highest. This work indicated that PDI genes are involved in salt stress tolerance in chickpea and the CaPDIs may be further studied for their role of inducing salt tolerance.