Differential Gene Expression Between Polymorphic Zooids of the Marine Bryozoan Bugulina stolonifera
Bryozoans are a diverse phylum of marine and freshwater colonial invertebrates containing approximately 6,300 described living species. Bryozoans grow by budding new physiologically connected colony members (zooids) from a founding individual that forms from a metamorphosed larva. In some species these zooids come in different shapes and sizes and are specialized to serve different tasks within the colony. A complex interaction of genotype, environment, and developmental pathway shapes zooid fate, however, the specific mechanisms underlying the establishment of this division of labor remain unknown. Here, the first charact...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Treibergs, K. A., Giribet, G. Tags: Investigations Source Type: research
Effect of Salt Stress on Mutation and Genetic Architecture for Fitness Components in Saccharomyces cerevisiae
Mutations shape genetic architecture and thus influence the evolvability, adaptation and diversification of populations. Mutations may have different and even opposite effects on separate fitness components, and their rate of origin, distribution of effects and variance-covariance structure may depend on environmental quality. We performed an approximately 1,500-generation mutation-accumulation (MA) study in diploids of the yeast Saccharomyces cerevisiae in stressful (high-salt) and normal environments (50 lines each) to investigate the rate of input of mutational variation (Vm) as well as the mutation rate and distributio...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Kozela, C., Johnston, M. O. Tags: Investigations Source Type: research
Recombinational Repair of Nuclease-Generated Mitotic Double-Strand Breaks with Different End Structures in Yeast
In this study sequence-diverged ectopic substrates were used to assess whether the frequent Pol -mediated removal of a mismatch 8 nucleotides from a 3' end affects recombination outcomes and whether the presence of a 3' vs. 5' overhang at the break site alters outcomes. Recombination outcomes monitored were the distributions of recombination products into crossovers vs. noncrossovers, and the position/length of transferred sequence (heteroduplex DNA) in noncrossover products. A terminal mismatch that was 22 nucleotides from the 3' end was rarely removed and the greater distance from the end did not affect recombination out...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Gamble, D., Shaltz, S., Jinks-Robertson, S. Tags: Investigations Source Type: research
The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere
Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50 = 13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Compton, A., Liang, J., Chen, C., Lukyanchikova, V., Qi, Y., Potters, M., Settlage, R., Miller, D., Deschamps, S., Mao, C., Llaca, V., Sharakhov, I. V., Tu, Z. Tags: Investigations Source Type: research
Alternative Splicing During the Chlamydomonas reinhardtii Cell Cycle
In this study, we used existing longitudinal RNA-seq data obtained during the light-dark cycle to investigate the changes in the alternative splicing pattern and found that 3277 genes (19.75% of 17,746 genes) undergo alternative splicing. These splicing events include Alternative 5' (Alt 5'), Alternative 3' (Alt 3') and Exon skipping (ES) events that are referred as alternative site selection (ASS) events and Intron retention (IR) events. By clustering analysis, we identified a subset of events (26 ASS events and 10 IR events) that show periodic changes in the splicing pattern during the cell cycle. About two-thirds of the...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Pandey, M., Stormo, G. D., Dutcher, S. K. Tags: Investigations Source Type: research
Effects of Different Strategies for Exploiting Genomic Selection in Perennial Ryegrass Breeding Programs
Genomic selection (GS) is a potential pathway to accelerate genetic gain for perennial ryegrass (Lolium perenne L.). The main objectives of the present study were to investigate the level of genetic gain and accuracy by applying GS in commercial perennial ryegrass breeding programs. Different scenarios were compared to a conventional breeding program. Simulated scenarios differed in the method of selection and structure of the breeding program. Two scenarios (Phen-Y12 and Phen) for phenotypic selection and three scenarios (GS-Y12, GS and GS-SP) were considered for genomic breeding schemes. All breeding schemes were simulat...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Esfandyari, H., Fe, D., Tessema, B. B., Janss, L. L., Jensen, J. Tags: Genomic Prediction Source Type: research
Rapid Self-Selecting and Clone-Free Integration of Transgenes into Engineered CRISPR Safe Harbor Locations in Caenorhabditis elegans
Precision genome editing for model organisms has revolutionized functional analysis and validation of a wide variety of molecular systems. To date, the capacity to insert single-copy transgenes into the model nematode Caenorhabditis elegans has focused on utilizing either transposable elements or CRISPR-based safe harbor strategies. These methods require plate-level screening processes to avoid selecting heritable extrachromosomal arrays or rely on co-CRISPR markers to identify knock-in events. As a result, verification of transgene insertion requires anti-array selection screening methods and PCR genotyping. These approac...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Stevenson, Z. C., Moerdyk-Schauwecker, M. J., Jamison, B., Phillips, P. C. Tags: Investigations Source Type: research
Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality
With the development of high-throughput genotyping techniques, selection signatures in the genome of domestic pigs have been extensively interrogated in the last decade. The Duroc, a major commercial pig breed famous for its fast growth rate and high lean ratio, has not been extensively studied focusing on footprints of intensively artificial selection in their genomes by a lot of re-sequencing data. The goal of this study was to investigate genomic regions under artificial selection and their contribution to the unique phenotypic traits of the Duroc using whole-genome resequencing data from 97 pigs. Three complementary me...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Yu, J., Zhao, P., Zheng, X., Zhou, L., Wang, C., Liu, J.-F. Tags: Investigations Source Type: research
Genomic Studies Reveal Substantial Dominant Effects and Improved Genomic Predictions in an Open-Pollinated Breeding Population of Eucalyptus pellita
This study demonstrates the importance of genomic approaches in OP families to study nonadditive effects. To capture the LD between markers and the quantitative trait loci (QTL) it may be important to use informative markers from candidate genes. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Thavamanikumar, S., Arnold, R. J., Luo, J., Thumma, B. R. Tags: Genomic Prediction Source Type: research
Assessment of the Potential for Genomic Selection To Improve Husk Traits in Maize
In this study, we compared four GS models on a maize association population with 498 inbred lines belonging to four subpopulations, including 27 lines in stiff stalk, 67 lines in non-stiff stalk, 193 lines in tropical-subtropical, and 211 lines in mixture subpopulations. Genomic Best Linear Unbiased Prediction with principal components as cofactor, performed the best and was selected to examine the impact of interaction between sampling proportions and subpopulations. We found that predictions on inbred lines in a subpopulation were benefited from excluding individuals from other subpopulations for training if the training...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Cui, Z., Dong, H., Zhang, A., Ruan, Y., He, Y., Zhang, Z. Tags: Genomic Prediction Source Type: research
A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding
A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus x domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level seq...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Zurn, J. D., Driskill, M., Jung, S., Main, D., Yin, M. H., Clark, M. C., Cheng, L., Ashrafi, H., Aryal, R., Clark, J. R., Worthington, M., Finn, C. E., Peace, C., Iezzoni, A., Bassil, N. Tags: Investigations Source Type: research
Mutator Foci Are Regulated by Developmental Stage, RNA, and the Germline Cell Cycle in Caenorhabditis elegans
RNA interference is a crucial gene regulatory mechanism in Caenorhabditis elegans. Phase-separated perinuclear germline compartments called Mutator foci are a key element of RNAi, ensuring robust gene silencing and transgenerational epigenetic inheritance. Despite their importance, Mutator foci regulation is not well understood, and observations of Mutator foci have been largely limited to adult hermaphrodite germlines. Here we reveal that punctate Mutator foci arise in the progenitor germ cells of early embryos and persist throughout all larval stages. They are additionally present throughout the male germline and in the ...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Uebel, C. J., Agbede, D., Wallis, D. C., Phillips, C. M. Tags: Investigations Source Type: research
Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation
MicroProteins are a class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or which they relate to. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterized microProteins in Arabidopsis thaliana, studies from more complex plant geno...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Bhati, K. K., Kruusvee, V., Straub, D., Chandran, A. K. N., Jung, K.-H., Wenkel, S. Tags: Investigations Source Type: research
A Nested Association Mapping Panel in Arabidopsis thaliana for Mapping and Characterizing Genetic Architecture
Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate ...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Brock, M. T., Rubin, M. J., DellaPenna, D., Weinig, C. Tags: Multiparental Populations Source Type: research
Genome-Wide Duplication of Allotetraploid Brassica napus Produces Novel Characteristics and Extensive Ploidy Variation in Self-Pollinated Progeny
In this study, we explored the influences of additional WGD on the allopolyploid Brassica napus. Compared to tetraploid B. napus, octoploid B. napus (AAAACCCC, 2n = 8x =76) showed significant differences in phenotype, reproductive ability and the ploidy of self-pollinated progeny. Genome duplication also altered a key reproductive organ feature in B. napus, that is, increased the number of pollen apertures. Unlike autopolyploids produced from the diploid Brassica species, the octoploid B. napus produced from allotetraploid B. napus had a relatively stable meiotic process, high pollen viability and moderate fertility under ...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Yin, L., Zhu, Z., Luo, X., Huang, L., Li, Y., Mason, A. S., Yang, J., Ge, X., Long, Y., Wang, J., Zou, Q., Tao, L., Kang, Z., Tang, R., Wang, M., Fu, S. Tags: Investigations Source Type: research
