Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data
Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, for high precision genetic analysis, the complicated genetic segregation mode in polyploid organisms requires high-coverage NGS data and elaborate analytical algorithms. In the present study, we propose a simple strategy for the genetic mapping of polyploids using low-coverage NGS data. The validity of the strategy was investigated using simulated data. Previous studies indicated that accurate allele dosage estimation from low-coverage NGS data (read ...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Yamamoto, E., Shirasawa, K., Kimura, T., Monden, Y., Tanaka, M., Isobe, S. Tags: Investigations Source Type: research
Genome-Wide Characterization and Comparative Analysis of MYB Transcription Factors in Ganoderma Species
In this study, five medicinal macrofungi of genus Ganoderma were subjected to a genome-wide comparative analysis of MYB genes. A total of 75 MYB genes were identified and classified into four types: 1R-MYBs (52), 2R-MYBs (19), 3R-MYBs (2) and 4R-MYBs (2). Gene structure analysis revealed varying exon numbers (3-14) and intron lengths (7-1058 bp), and noncanonical GC-AG introns were detected in G. lucidum and G. sinense. In a phylogenetic analysis, 69 out of 75 MYB genes were clustered into 15 subgroups, and both single-copy orthologous genes and duplicated genes were identified. The promoters of the MYB genes harbored mult...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Wang, L., Huang, Q., Zhang, L., Wang, Q., Liang, L., Liao, B. Tags: Investigations Source Type: research
Quantifying Influences on Intragenomic Mutation Rate
We report work to quantify the impact on the probability of human genome polymorphism both of recombination and of sequence context at different scales. We use population-based analyses of data on human genetic variants obtained from the public Ensembl database. For recombination, we calculate the variance due to recombination and the probability that a recombination event causes a mutation. We employ novel statistical procedures to take account of the spatial auto-correlation of recombination and mutation rates along the genome. Our results support the view that genomic diversity in recombination hotspots arises largely f...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Simon, H., Huttley, G. Tags: Investigations Source Type: research
Genomic Prediction with Genotype by Environment Interaction Analysis for Kernel Zinc Concentration in Tropical Maize Germplasm
Zinc (Zn) deficiency is a major risk factor for human health, affecting about 30% of the world’s population. To study the potential of genomic selection (GS) for maize with increased Zn concentration, an association panel and two doubled haploid (DH) populations were evaluated in three environments. Three genomic prediction models, M (M1: Environment + Line, M2: Environment + Line + Genomic, and M3: Environment + Line + Genomic + Genomic x Environment) incorporating main effects (lines and genomic) and the interaction between genomic and environment (G x E) were assessed to estimate the prediction ability (rMP) for e...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Mageto, E. K., Crossa, J., Perez-Rodriguez, P., Dhliwayo, T., Palacios-Rojas, N., Lee, M., Guo, R., San Vicente, F., Zhang, X., Hindu, V. Tags: Genomic Prediction Source Type: research
Bayesian and Machine Learning Models for Genomic Prediction of Anterior Cruciate Ligament Rupture in the Canine Model
Anterior cruciate ligament (ACL) rupture is a common, debilitating condition that leads to early-onset osteoarthritis and reduced quality of human life. ACL rupture is a complex disease with both genetic and environmental risk factors. Characterizing the genetic basis of ACL rupture would provide the ability to identify individuals that have high genetic risk and allow the opportunity for preventative management. Spontaneous ACL rupture is also common in dogs and shows a similar clinical presentation and progression. Thus, the dog has emerged as an excellent genomic model for human ACL rupture. Genome-wide association stud...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Baker, L. A., Momen, M., Chan, K., Bollig, N., Lopes, F. B., Rosa, G. J. M., Todhunter, R. J., Binversie, E. E., Sample, S. J., Muir, P. Tags: Genomic Prediction Source Type: research
A Forward Genetic Approach to Mapping a P-Element Second Site Mutation Identifies DCP2 as a Novel Tumor Suppressor in Drosophila melanogaster
The use of transposons to create mutations has been the cornerstone of Drosophila genetics in the past few decades. Second-site mutations caused by transpositions are often devoid of transposons and thereby affect subsequent analyses. In a P-element mutagenesis screen, a second site mutation was identified on chromosome 3, wherein the homozygous mutants exhibit classic hallmarks of tumor suppressor mutants, including brain tumor and lethality; hence the mutant line was initially named as lethal (3) tumorous brain [l(3)tb]. Classical genetic approaches relying on meiotic recombination and subsequent complementation with chr...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Mishra, R., Kunar, R., Mandal, L., Alone, D. P., Chandrasekharan, S., Tiwari, A. K., Tapadia, M. G., Mukherjee, A., Roy, J. K. Tags: Mutant Screen Report Source Type: research
A Set of Diverse Genes Influence the Frequency of White-Opaque Switching in Candida albicans
The fungal species Candida albicans is both a member of the human microbiome and a fungal pathogen. C. albicans undergoes several different morphological transitions, including one called white-opaque switching. Here, cells reversibly switch between two states, "white" and "opaque," and each state is heritable through many cell generations. Each cell type has a distinct cellular and colony morphology and they differ in many other properties including mating, nutritional specialization, and interactions with the innate immune system. Previous genetic screens to gain insight into white-opaque switching have focused on certai...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Brenes, L. R., Lohse, M. B., Hartooni, N., Johnson, A. D. Tags: Mutant Screen Report Source Type: research
De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii
We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 – 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these sp...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Heraghty, S. D., Sutton, J. M., Pimsler, M. L., Fierst, J. L., Strange, J. P., Lozier, J. D. Tags: Genome Report Source Type: research
Genomic Analysis of Diverse Members of the Fungal Genus Monosporascus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate
The genus Monosporascus represents an enigmatic group of fungi important in agriculture and widely distributed in natural arid ecosystems. Of the nine described species, two (M. cannonballus and M. eutypoides) are important pathogens on the roots of members of Cucurbitaceae in agricultural settings. The remaining seven species are capable of colonizing roots from a diverse host range without causing obvious disease symptoms. Recent molecular and culture studies have shown that members of the genus are nearly ubiquitous as root endophytes in arid environments of the Southwestern United States. Isolates have been obtained fr...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Robinson, A. J., Natvig, D. O., Chain, P. S. G. Tags: Genome Report Source Type: research
Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]
In this study, we report a high-quality Ng assembly using 10X Genomics linked-reads with 670X sequencing depth. The current assembly has a genome size of 259,040,977 bp in 3,160 scaffolds with 38.05% G-C and a 98.6% BUSCO completeness score. 97% of the RNA reads are perfectly aligned to the genome, indicating high quality in contiguity and completeness. A total of 14,777 genes are annotated in the Ng genome, and 72% of the annotated genes have a one-to-one ortholog in the Nv genome. We reported 5 million Ng-Nv SNPs which will facility mapping and population genomic studies in Nasonia. In addition, 42 Ng-specific genes were...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Wang, X., Kelkar, Y. D., Xiong, X., Martinson, E. O., Lynch, J., Zhang, C., Werren, J. H., Wang, X. Tags: Genome Report Source Type: research
Corrigendum
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research
The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models
It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequ...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Vollmar, S., Wellmann, R., Borda-Molina, D., Rodehutscord, M., Camarinha-Silva, A., Bennewitz, J. Tags: Investigations Source Type: research
Contractions of the C-Terminal Domain of Saccharomyces cerevisiae Rpb1p Are Mediated by Rad5p
We report that contractions require the post-replication repair factor Rad5p but, unlike expansions, not the homologous recombination factors Rad51p and Rad52p. Sequence analysis of contraction events reveals that deleted regions are flanked by microhomologies. We also find that G-quadruplex forming sequences predicted by the QGRS Mapper are enriched on the noncoding strand of the CTD compared to the body of RPB1. Formation of G-quadruplexes in the CTD coding region could block the replication fork, necessitating post-replication repair. We propose that contractions of the CTD result when microhomologies misalign during Ra...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Stewart, T., Exner, A. E., Patnaik, P., Fuchs, S. M. Tags: Investigations Source Type: research
Dissecting the Genetic Architecture of Cystatin C in Diversity Outbred Mice
Plasma concentration of Cystatin C (CysC) level is a biomarker of glomerular filtration rate in the kidney. We use a Systems Genetics approach to investigate the genetic determinants of plasma CysC concentration. To do so we perform Quantitative Trait Loci (QTL) and expression QTL (eQTL) analysis of 120 Diversity Outbred (DO) female mice, 56 weeks of age. We performed network analysis of kidney gene expression to determine if the gene modules with common functions are associated with kidney biomarkers of chronic kidney diseases. Our data demonstrates that plasma concentrations and kidney mRNA levels of CysC are associated ...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Huda, M. N., VerHague, M., Albright, J., Smallwood, T., Bell, T. A., Que, E., Miller, D. R., Roshanravan, B., Allayee, H., Manuel de Villena, F. P., Bennett, B. J. Tags: Multiparental Populations Source Type: research
An Investigation into the Genetic History of Japanese Populations of Three Starfish, Acanthaster planci, Linckia laevigata, and Asterias amurensis, Based on Complete Mitochondrial DNA Sequences
Crown-of-thorns starfish, Acanthaster planci (COTS), are common in coral reefs of Indo-Pacific Ocean. Since they are highly fecund predators of corals, periodic outbreaks of COTS cause substantial loss of healthy coral reefs. Using complete mitochondrial DNA sequences, we here examined how COTS outbreaks in the Ryukyu Archipelago, Japan are reflected by the profile of their population genetics. Population genetics of the blue starfish, Linckia laevigata, which lives in the Ryukyu Archipelago, but not break out and the northern Pacific sea star, Asterias amurensis, which lives in colder seawater around the main Islands of J...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Inoue, J., Hisata, K., Yasuda, N., Satoh, N. Tags: Investigations Source Type: research
