The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat
Gene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we used an independent RNA-Seq dataset to test the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analyzed the RNA-Seq data against the RefSeqv1.0 genome and identified a set of differentially expressed genes (DEGs) between the wild-type and...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Harrington, S. A., Backhaus, A. E., Singh, A., Hassani-Pak, K., Uauy, C. Tags: Investigations Source Type: research
On the Distribution of Tract Lengths During Adaptive Introgression
Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximatin...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Shchur, V., Svedberg, J., Medina, P., Corbett-Detig, R., Nielsen, R. Tags: Investigations Source Type: research
Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative
Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. ...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Nyine, M., Adhikari, E., Clinesmith, M., Jordan, K. W., Fritz, A. K., Akhunov, E. Tags: Investigations Source Type: research
Locating the Sex Determining Region of Linkage Group 12 of Guppy (Poecilia reticulata)
We describe two families with recombinants between the X and Y chromosomes, which confirm that the male-determining locus is in the region identified by all previous studies, near the terminal pseudo-autosomal region (PAR), which crosses over at a very high rate in males. We correct the PAR marker order, and assign two unplaced scaffolds to the PAR. We also detect a duplication, with one copy in the male-determining region, explaining signals of sex linkage in a more proximal region. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Charlesworth, D., Bergero, R., Graham, C., Gardner, J., Yong, L. Tags: Investigations Source Type: research
Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans Gene Expression Data
Identification of co-expressed sets of genes (gene modules) is used widely for grouping functionally related genes during transcriptomic data analysis. An organism-wide atlas of high-quality gene modules would provide a powerful tool for unbiased detection of biological signals from gene expression data. Here, using a method based on independent component analysis we call DEXICA, we have defined and optimized 209 modules that broadly represent transcriptional wiring of the key experimental organism C. elegans. These modules represent responses to changes in the environment (e.g., starvation, exposure to xenobiotics), genes...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Cary, M., Podshivalova, K., Kenyon, C. Tags: Investigations Source Type: research
Maize Introgression Library Provides Evidence for the Involvement of liguleless1 in Resistance to Northern Leaf Blight
This study demonstrates the power of an introgression library combined with high density marker coverage to resolve quantitative trait loci. Furthermore, the role of liguleless1 in leaf architecture and in resistance to northern leaf blight has important applications in crop improvement. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Kolkman, J. M., Strable, J., Harline, K., Kroon, D. E., Wiesner-Hanks, T., Bradbury, P. J., Nelson, R. J. Tags: Multiparental Populations Source Type: research
Genomic Prediction and Selection for Fruit Traits in Winter Squash
This study is one of the first empirical studies to evaluate gain from a multi-trait genomic selection model in a resource-limited horticultural crop. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Hernandez, C. O., Wyatt, L. E., Mazourek, M. R. Tags: Genomic Prediction Source Type: research
Detecting New Allies: Modifier Screen Identifies a Genetic Interaction Between Imaginal disc growth factor 3 and combover, a Rho-kinase Substrate, During Dorsal Appendage Tube Formation in Drosophila
Biological tube formation underlies organ development and, when disrupted, can cause severe birth defects. To investigate the genetic basis of tubulogenesis, we study the formation of Drosophila melanogaster eggshell structures, called dorsal appendages, which are produced by epithelial tubes. Previously we found that precise levels of Drosophila Chitinase-Like Proteins (CLPs), encoded by the Imaginal disc growth factor (Idgf) gene family, are needed to regulate dorsal-appendage tube closure and tube migration. To identify factors that act in the Idgf pathway, we developed a genetic modifier screen based on the finding tha...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Espinoza, C. Y., Berg, C. A. Tags: Mutant Screen Report Source Type: research
A Genetic Screen Links the Disease-Associated Nab2 RNA-Binding Protein to the Planar Cell Polarity Pathway in Drosophila melanogaster
Mutations in the gene encoding the ubiquitously expressed RNA-binding protein ZC3H14 result in a non-syndromic form of autosomal recessive intellectual disability in humans. Studies in Drosophila have defined roles for the ZC3H14 ortholog, Nab2 (aka Drosophila Nab2 or dNab2), in axon guidance and memory due in part to interaction with a second RNA-binding protein, the fly Fragile X homolog Fmr1, and coregulation of shared Nab2-Fmr1 target mRNAs. Despite these advances, neurodevelopmental mechanisms that underlie defective axonogenesis in Nab2 mutants remain undefined. Nab2 null phenotypes in the brain mushroom bodies (MBs)...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Lee, W.-H., Corgiat, E., Rounds, J. C., Shepherd, Z., Corbett, A. H., Moberg, K. H. Tags: Mutant Screen Report Source Type: research
Construction of Pseudomolecules for the Chinese Chestnut (Castanea mollissima) Genome
In this study, we generated a high-quality C. mollissima genome assembly by combining 90x Pacific Biosciences long read and 170x high-throughput chromosome conformation capture data. The assembly was 688.93 Mb in total, with a contig N50 of 2.83 Mb. Most of the assembled sequences (99.75%) were anchored onto 12 chromosomes, and 97.07% of the assemblies were accurately anchored and oriented. A total of 33,638 protein-coding genes were predicted in the C. mollissima genome. Comparative genomic and transcriptomic analyses provided insights into the genes expressed in specific tissues, as well as those associated with burr dev...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Wang, J., Tian, S., Sun, X., Cheng, X., Duan, N., Tao, J., Shen, G. Tags: Genome Report Source Type: research
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions
Globe artichoke (Cynara cardunculus var. scolymus; 2n2x=34) is cropped largely in the Mediterranean region, being Italy the leading world producer; however, over time, its cultivation has spread to the Americas and China. In 2016, we released the first (v1.0) globe artichoke genome sequence (http://www.artichokegenome.unito.it/). Its assembly was generated using ~133-fold Illumina sequencing data, covering 725 of the 1,084 Mb genome, of which 526 Mb (73%) were anchored to 17 chromosomal pseudomolecules. Based on v1.0 sequencing data, we generated a new genome assembly (v2.0), obtained from a Hi-C (Dovetail) genomic library...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Acquadro, A., Portis, E., Valentino, D., Barchi, L., Lanteri, S. Tags: Genome Report Source Type: research
A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem
Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infe...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Fokkens, L., Guo, L., Dora, S., Wang, B., Ye, K., Sanchez-Rodriguez, C., Croll, D. Tags: Genome Report Source Type: research
De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration
Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype–phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly-contiguous assembly for C. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete ...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Sin, S. Y. W., Lu, L., Edwards, S. V. Tags: Genome Report Source Type: research
Hybrid Genome Assembly and Evidence-Based Annotation of the Egg Parasitoid and Biological Control Agent Trichogramma brassicae
Trichogramma brassicae (Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by a Wolbachia infection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybrid de novo strategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorous ab initio-, homology-, and...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Ferguson, K. B., Kursch-Metz, T., Verhulst, E. C., Pannebakker, B. A. Tags: Genome Report Source Type: research
Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing to Isolate Stress Tolerance and Aflatoxin Production
Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae. However, less progress has been made for A. flavus. As part of the effort of the USDA-ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL3357 was sequenced and resulted in a scaffold-level genome released in 2005. Our goal has been biologically driven, focusing on two areas: isolate variation in aflatoxin production and drought stress exacerbating aflatoxin production by A. flavus. Therefore, we developed two refere...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Fountain, J. C., Clevenger, J. P., Nadon, B., Youngblood, R. C., Korani, W., Chang, P.-K., Starr, D., Wang, H., Isett, B., Johnston, H. R., Wiggins, R., Agarwal, G., Chu, Y., Kemerait, R. C., Pandey, M. K., Bhatnagar, D., Ozias-Akins, P., Varshney, R. K., Tags: Genome Report Source Type: research
