RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum

Background RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton. Results Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes. Conclusions Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton.

A polygenic score for educational attainment partially predicts voter turnout

Twin and adoption studies have shown that individual differences in political participation can be explained, in part, by genetic variation. However, these research designs cannot identify which genes are related to voting or the pathways through which they exert influence, and their conclusions rely on possibly restrictive assumptions. In this study, we use three different US samples and a Swedish sample to test whether genes that have been identified as associated with educational attainment, one of the strongest correlates of political participation, predict self-reported and validated voter turnout. We find that a polygenic score capturing individuals’ genetic propensity to acquire education is significantly related to turnout. The strongest associations we observe are in second-order midterm elections in the United States and European Parliament elections in Sweden, which tend to be viewed as less important by voters, parties, and the media and thus present a more information-poor electoral environment for citizens to navigate. A within-family analysis suggests that individuals’ education-linked genes directly affect their voting behavior, but, for second-order elections, it also reveals evidence of genetic nurture. Finally, a mediation analysis suggests that educational attainment and cognitive ability combine to account for between 41% and 63% of the relationship between the genetic propensity to acquire education and voter turnout.

Multi-omics Analyses Provides Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis galbana

Isochrysis galbana is considered an ideal bait for functional foods and nutraceuticals in humans because of its high fucoxanthin (Fx) content. However, multi-omics analysis of the regulation networks for Fx biosynthesis in I. galbana has not been reported. In this study, we report a high-quality genome sequence of I. galbana LG007, which has a 92.73 Mb genome size, with a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenomic inferences confirmed the monophyly of Haptophyta, with I. galbana sister to Emiliania huxleyi and Chrysochromulina tobinii. Evolutionary analysis revealed an estimated divergence time between I. galbana and E. huxleyi of ~ 133 million years ago (Mya). Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion, including IgPLMT, IgOAR1 and Δ-4 desaturase. Metabolome analysis showed that the content of carotenoid in I. galbana cultured under green light (7d-G) for 7 days was higher than that of white light (7d-W), and β-carotene was the main carotenoids, accounting for 79.09% of the total carotenoids. Comprehensive analysis of multi-omics analysis revealed that β-carotene, antheraxanthin, zeaxanthin and Fx content was increased by green light induction, which was significantly correlated with the expression of IgMYB98, IgZDS, IgPDS, IgLHCX2, IgZEP, IgLCYb, and IgNSY. These findings contribute to understanding Fx biosynthesis and its regulation, providing a valuable reference for food and pharmaceutical applications.

Molecular evolution of PCSK family: Analysis of natural selection rate and gene loss

Proprotein convertases subtilisin kexins are serine endoproteases, playing critical roles in the biological functions, including lipid, glucose, and bile acid metabolism, as well as cell proliferation, migration, and metastasis. Experimental studies have demonstrated the physiological functions of PCSKs and their association with diseases; however, studies on the evolutionary history and diversification of these proteins are missing. In the present research, a bioinformatics study was conducted on the molecular evolution of several PCSKs family members and gene loss events across placental mammalian. In order to detect evolutionary constraints and positive selection, the CodeML program of the PAML package was used. The results showed the positive selection to occur in PCSK1, PCSK3, PCSK5, and PCSK7. A decelerated rate of evolution was observed in PCSK7, PCSK3, and MBTPS1 in Carnivores compared to the rest of phylogeny, and an accelerated evolution of PCSK1, PCSK7, and MBTPS1 in Muridae family of rodents was found. Additionally, our results indicated pcsk9 gene loss in 12 species comprising Carnivores and bats (Chiroptera). Future studies are required to evaluate the functional relevance and selective evolutionary advantages associated with these modifications in PCSK proteins during evolution.

High-Risk Screening for Fabry Disease: A Nationwide Study in Japan and Literature Review

Fabry disease (FD) is an X-linked inherited disorder caused by mutations in the GLA gene, which encodes the lysosomal enzyme α-galactosidase A (α-Gal A). FD detection in patients at an early stage is essential to achieve sufficient treatment effects, and high-risk screening may be effective. Here, we performed high-risk screening for FD in Japan and showed that peripheral neurological manifestations are important in young patients with FD. Moreover, we reviewed the literature on high-risk screening in patients with renal, cardiac, and central neurological manifestations. Based on the results of this study and review of research abroad, we believe that FD can be detected more effectively by targeting individuals based on age. In recent years, the methods for high-risk screening have been ameliorated, and high-risk screening studies using GLA next-generation sequencing have been conducted. Considering the cost-effectiveness of screening, GLA sequencing should be performed in individuals with reduced α-Gal A activity and females with certain FD manifestations and/or a family history of FD. The findings suggest that family analysis would likely detect FD patients, although GLA sequencing of asymptomatic family members requires adequate genetic counseling.

Anxiety and depression: population distribution and family associations

Aim. The aim of the study was to characterize the population distribution of psychiatric phenotypes according to anxiety and depression. Methods. The level of anxiety and depression was assessed with the HADS Hospital Anxiety and Depression Scale test. Students in grades 9-11 of secondary schools in Kharkiv, as well as their parents, were tested. We tested 306 persons from 115 families. Results. The frequency of depression among men in the Kharkiv population is 9%, among women 11%, among boys 15%, among girls 22%; the frequency of increased anxiety among men is 14%, among women 22%, among boys 19%, among girls 44%. There is a positive relationship between anxiety and depression in older men and women, expressed by the association coefficient in men rDT =0.45, in women rDT =0.79. The relatives revealed a similarity in psychological types, described by the association index for depression in mother/daughter pairs r = 0.40, mother/son r = 0.03, father/daughter r = 0.20, father/son r = 0.40; for anxiety: mother/daughter r = 0.15, mother/son r = 0.05, father/daughter r = 0.24, father/son r = 0.01. Conclusions. Individuals of the younger generation are more likely to have signs of anxiety and depression than those of their parents' generation. The parent-offspring phenotype relationship is stronger in same-sex couples compared to opposite-sex couples. Keywords: depression, anxiety, population distribution, family analysis.

Zinc finger transcription factor ZAT family genes confer multi-tolerances in Gossypium hirsutum L.

ZAT (Zinc Finger of Arabidopsis thaliana) proteins are composed of a plant-specific transcription factor family, which play an important role in plant growth, development, and stress resistance. To study the potential function of ZAT family in cotton, the whole genome identification, expression, and structure analysis of ZAT gene family were carried out. In this study, our analysis revealed the presence of 115, 56, 59, and 115 ZAT genes in Gossypium hirsutum, G. raimondii, G. arboreum and G. barbadense, respectively. According to the number of domains and phylogenetic characteristics, we divided ZAT genes of four Gossypium species into 4 different clades, and further divided them into 11 subfamilies. The results of collinearity analysis showed that segmental duplication was the main method to amplify the cotton ZAT genes family. Analysis of cis-elements of promoters indicated that most GhZAT genes contained cis-elements related to plant hormones and abiotic stress. According to heatmap analysis, the expression patterns of GhZAT genes under different stresses indicated that GhZAT genes were significantly involved in the response to cold, heat, salt, and PEG stress, possibly through different mechanisms. Among the highly expressed genes, we cloned a G. hirsutum gene GhZAT67. Through virus-induced gene silencing (VIGS), we found that its expression level decreased significantly after being silenced. Under alkaline treatment, the wilting degree of silenced plants was even greater than the wild type, which proved that GhZAT67 gene was involved in the response to alkaline stress.

Molecular characteristics of S-RNase alleles as the determinant of self-incompatibility in the style of Fragaria viridis

Strawberry (Fragaria spp.) is a member of the Rosoideae subfamily in the family Rosaceae. The self-incompatibility (SI) of some diploid species is a key agronomic trait that acts as a basic pollination barrier; however, the genetic mechanism underlying SI control in strawberry remains unclear. Two candidate S-RNases (Sa- and Sb-RNase) identified in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were confirmed to be SI determinants at the S locus following genotype identification and intraspecific hybridization using selfing progenies. Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria; however, none of the compatible species contained S-RNase. Although the results of interspecific hybridization experiments showed that F. viridis (SI) styles could accept pollen from F. mandshurica (self-compatible), the reciprocal cross was incompatible. Sa and Sb-RNase contain large introns, and their noncoding sequences (promotors and introns) can be transcribed into long noncoding RNAs (lncRNAs). Overall, the genus Fragaria exhibits S-RNase-based gametophytic SI, and S-RNase loss occurs at the S locus of compatible germplasms. In addition, a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species. Furthermore, the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.

A comprehensive analysis of copy number variation in a Turkish dementia cohort

Background Copy number variants (CNVs) include deletions or multiplications spanning genomic regions. These regions vary in size and may span genes known to play a role in human diseases. As examples, duplications and triplications of SNCA have been shown to cause forms of Parkinson’s disease, while duplications of APP cause early onset Alzheimer’s disease (AD). Results Here, we performed a systematic analysis of CNVs in a Turkish dementia cohort in order to further characterize the genetic causes of dementia in this population. One hundred twenty-four Turkish individuals, either at risk of dementia due to family history, diagnosed with mild cognitive impairment, AD, or frontotemporal dementia, were whole-genome genotyped and CNVs were detected. We integrated family analysis with a comprehensive assessment of potentially disease-associated CNVs in this Turkish dementia cohort. We also utilized both dementia and non-dementia individuals from the UK Biobank in order to further elucidate the potential role of the identified CNVs in neurodegenerative diseases. We report CNVs overlapping the previously implicated genes ZNF804A, SNORA70B, USP34, XPO1, and a locus on chromosome 9 which includes a cluster of olfactory receptors and ABCA1. Additionally, we also describe novel CNVs potentially associated with dementia, overlapping the genes AFG1L, SNX3, VWDE, and BC039545. Conclusions Genotyping data from understudied populations can be utilized to identify copy number variation which may contribute to dementia.