The Conserved ASCL1/MASH-1 Ortholog HLH-3 Specifies Sex-Specific Ventral Cord Motor Neuron Fate in Caenorhabditis elegans
Neural specification is regulated by one or many transcription factors that control expression of effector genes that mediate function and determine neuronal type. Here we identify a novel role for one conserved proneural factor, the bHLH protein HLH-3, implicated in the specification of sex-specific ventral cord motor neurons in C. elegans. Proneural genes act in early stages of neurogenesis in early progenitors, but here, we demonstrate a later role for hlh-3. First, we document that differentiation of the ventral cord type C motor neuron class (VC) within their neuron class, is dynamic in time and space. Expression of V...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Perez, L. M., Alfonso, A. Tags: Investigations Source Type: research
Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed
Mutation rate estimates for vegetatively reproducing organisms are rare, despite their frequent occurrence across the tree of life. Here we report mutation rate estimates in two vegetatively reproducing duckweed species, Lemna minor and Spirodela polyrhiza. We use a modified approach to estimating mutation rates by taking into account the reduction in mutation detection power that occurs when new individuals are produced from multiple cell lineages. We estimate an extremely low per generation mutation rate in both species of duckweed and note that allelic coverage at de novo mutation sites is very skewed. We also find no s...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Sandler, G., Bartkowska, M., Agrawal, A. F., Wright, S. I. Tags: Investigations Source Type: research
A Multivariate Poisson Deep Learning Model for Genomic Prediction of Count Data
The paradigm called genomic selection (GS) is a revolutionary way of developing new plants and animals. This is a predictive methodology, since it uses learning methods to perform its task. Unfortunately, there is no universal model that can be used for all types of predictions; for this reason, specific methodologies are required for each type of output (response variables). Since there is a lack of efficient methodologies for multivariate count data outcomes, in this paper, a multivariate Poisson deep neural network (MPDN) model is proposed for the genomic prediction of various count outcomes simultaneously. The MPDN mod...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Montesinos-Lopez, O. A., Montesinos-Lopez, J. C., Singh, P., Lozano-Ramirez, N., Barron-Lopez, A., Montesinos-Lopez, A., Crossa, J. Tags: Genomic Prediction Source Type: research
New Strains for Tissue-Specific RNAi Studies in Caenorhabditis elegans
RNA interference is a powerful tool for dissecting gene function. In Caenorhabditis elegans, ingestion of double stranded RNA causes strong, systemic knockdown of target genes. Further insight into gene function can be revealed by tissue-specific RNAi techniques. Currently available tissue-specific C. elegans strains rely on rescue of RNAi function in a desired tissue or cell in an otherwise RNAi deficient genetic background. We attempted to assess the contribution of specific tissues to polyunsaturated fatty acid (PUFA) synthesis using currently available tissue-specific RNAi strains. We discovered that rde-1 (ne219), a c...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Watts, J. S., Harrison, H. F., Omi, S., Guenthers, Q., Dalelio, J., Pujol, N., Watts, J. L. Tags: Investigations Source Type: research
Genetic and Physical Localization of the Gene Controlling Leaf Pigmentation Pattern in Medicago truncatula
In Medicago truncatula, some ecotypes form a black or purple stain in the middle of adaxial leaf surface due to accumulation of anthocyanins. However, this morphological marker is missing in some other ecotypes, although anthocyanin biosynthesis pathway is not disrupted. Genetic analysis indicated that the lack of the leaf spot of anthocyanins accumulation is a dominant trait, which is controlled by a single gene, LPP1. Genetic mapping indicated that the LPP1 gene was delimited to a 280 kb-region on Chromosome 7. A total of 8 protein-coding genes were identified in the LPP1 locus through gene annotation and sequence analys...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Yu, X., Qin, Q., Wu, X., Li, D., Yang, S. Tags: Investigations Source Type: research
Analysis of Gal4 Expression Patterns in Adult Drosophila Females
Precise genetic manipulation of specific cell types or tissues to pinpoint gene function requirement is a critical step in studies aimed at unraveling the intricacies of organismal physiology. Drosophila researchers heavily rely on the UAS/Gal4/Gal80 system for tissue-specific manipulations; however, it is often unclear whether the reported Gal4 expression patterns are indeed specific to the tissue of interest such that experimental results are not confounded by secondary sites of Gal4 expression. Here, we surveyed the expression patterns of commonly used Gal4 drivers in adult Drosophila female tissues under optimal condit...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Weaver, L. N., Ma, T., Drummond-Barbosa, D. Tags: Investigations Source Type: research
Origins and Evolutionary Patterns of the 1.688 Satellite DNA Family in Drosophila Phylogeny
Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The 1.688 satDNA, also known as the 359 bp satellite, is one of the most abundant repetitive sequences in Drosophila melanogaster and has been linked to several different biological functions. We investigated the presence and evolution of the 1.688 satDNA in 16 Drosophila genomes. We find that the 1.688 satDNA family is much more ancient than previously appreciated, being shared among part of the melanogaster group that diverged from a common ancestor ~27 Mya. We found that the 1.688...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: de Lima, L. G., Hanlon, S. L., Gerton, J. L. Tags: Investigations Source Type: research
Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny
We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Catchen, J., Amores, A., Bassham, S. Tags: Investigations Source Type: research
Multiple Loci Control Variation in Plasticity to Foliar Shade Throughout Development in Arabidopsis thaliana
The shade avoidance response is a set of developmental changes exhibited by plants to avoid shading by competitors, and is an important model of adaptive plant plasticity. While the mechanisms of sensing shading by other plants are well-known and appear conserved across plants, less is known about the developmental mechanisms that result in the diverse array of morphological and phenological responses to shading. This is particularly true for traits that appear later in plant development. Here we use a nested association mapping (NAM) population of Arabidopsis thaliana to decipher the genetic architecture of the shade avoi...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Ta, J., Palmer, C., Brock, M., Rubin, M., Weinig, C., Maloof, J., Runcie, D. Tags: Investigations Source Type: research
Maximum a posteriori Threshold Genomic Prediction Model for Ordinal Traits
Due to the ever-increasing data collected in genomic breeding programs, there is a need for genomic prediction models that can deal better with big data. For this reason, here we propose a Maximum a posteriori Threshold Genomic Prediction (MAPT) model for ordinal traits that is more efficient than the conventional Bayesian Threshold Genomic Prediction model for ordinal traits. The MAPT performs the predictions of the Threshold Genomic Prediction model by using the maximum a posteriori estimation of the parameters, that is, the values of the parameters that maximize the joint posterior density. We compared the prediction pe...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Montesinos-Lopez, A., Gutierrez-Pulido, H., Montesinos-Lopez, O. A., Crossa, J. Tags: Genomic Prediction Source Type: research
Transcriptome Analysis of the Chicken Follicular Theca Cells with miR-135a-5p Suppressed
In this study, primary chicken follicular theca cells were isolated and then transfected with gga-miR-135a-5p inhibitor. Transcriptome sequencing was performed in chicken follicular theca cells with or without transfection. Differentially expressed genes (DEGs) were analyzed using bioinformatics. A dual-luciferase reporter assay was used to verify the target relationship between gga-miR-135a-5p and predicted targets within the DEGs. Compared with the normal chicken follicle theca cells, 953 up-regulated and 1060 down-regulated genes were detected in cells with gga-miR-135a-5p inhibited. The up-regulated genes were signific...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Zhou, Y., Liu, J., Lei, Q., Han, H., Liu, W., Cunwei, T., Li, F., Cao, D. Tags: Investigations Source Type: research
RPL-4 and RPL-9 Mediated Ribosome Purifications Facilitate the Efficient Analysis of Gene Expression in Caenorhabditis elegans Germ Cells
This study provides a solid basis upon which future germ cell TRAP experiments can be built, and it highlights the need for rigorous testing when adopting such methods to a new biological system. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Nousch, M. Tags: Investigations Source Type: research
The Utility of Resolving Asthma Molecular Signatures Using Tissue-Specific Transcriptome Data
An integrative analysis focused on multi-tissue transcriptomics has not been done for asthma. Tissue-specific DEGs remain undetected in many multi-tissue analyses, which influences identification of disease-relevant pathways and potential drug candidates. Transcriptome data from 609 cases and 196 controls, generated using airway epithelium, bronchial, nasal, airway macrophages, distal lung fibroblasts, proximal lung fibroblasts, CD4+ lymphocytes, CD8+ lymphocytes from whole blood and induced sputum samples, were retrieved from Gene Expression Omnibus (GEO). Differentially regulated asthma-relevant genes identified from eac...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Ghosh, D., Ding, L., Bernstein, J. A., Mersha, T. B. Tags: Investigations Source Type: research
The Landscape of Genomic Imprinting at the Porcine SGCE/PEG10 Locus from Methylome and Transcriptome of Parthenogenetic Embryos
The objective of this study was to, using porcine parthenogenetic embryos, investigate imprinting status of genes within the genomic region spans between the COL1A2 and ASB4 genes in chromosome 9. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) were conducted with normal and parthenogenetic embryos, and methylome and transcriptome were analyzed. As a result, differentially methylated regions (DMRs) between the embryos were identified, and parental allele-specific expressions of the SGCE and PEG10 genes were verified. The pig imprinted interval was limited between SGCE and PEG10, since both the COL1A2 ...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Ahn, J., Hwang, I.-S., Park, M.-R., Cho, I.-C., Hwang, S., Lee, K. Tags: Investigations Source Type: research
Polygenic Scores for Height in Admixed Populations
Polygenic risk scores (PRS) use the results of genome-wide association studies (GWAS) to predict quantitative phenotypes or disease risk at an individual level, and provide a potential route to the use of genetic data in personalized medical care. However, a major barrier to the use of PRS is that the majority of GWAS come from cohorts of European ancestry. The predictive power of PRS constructed from these studies is substantially lower in non-European ancestry cohorts, although the reasons for this are unclear. To address this question, we investigate the performance of PRS for height in cohorts with admixed African and ...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Bitarello, B. D., Mathieson, I. Tags: Genomic Prediction Source Type: research
