Single-Molecule Real-Time Transcript Sequencing of Turnips Unveiling the Complexity of the Turnip Transcriptome
To generate the full-length transcriptome of Xinjiang green and purple turnips, Brassica rapa var. Rapa, using single-molecule real-time (SMRT) sequencing. The samples of two varieties of Brassica rapa var. Rapa at five developmental stages were collected and combined to perform SMRT sequencing. Meanwhile, next generation sequencing was performed to correct SMRT sequencing data. A series of analyses were performed to investigate the transcript structure. Finally, the obtained transcripts were mapped to the genome of Brassica rapa ssp. pekinesis Chiifu to identify potential novel transcripts. For green turnip (F01), a total...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Zhuang, H., Wang, Q., Han, H., Liu, H., Wang, H. Tags: Genome Report Source Type: research
Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741)
Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 M...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Nock, C. J., Baten, A., Mauleon, R., Langdon, K. S., Topp, B., Hardner, C., Furtado, A., Henry, R. J., King, G. J. Tags: Genome Report Source Type: research
Solyntus, the New Highly Contiguous Reference Genome for Potato (Solanum tuberosum)
With the rapid expansion of the application of genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), the third largest food crop in the world, the related species S. phureja, designated "DM", has been used as the most popular reference genome for the last 10 years. Here, we introduce the de novo sequenced genome of Solyntus as the next standard reference in potato genome studies. A true Solanum tuberosum made up of 116 contigs that is also highly homozygous, diploid, vigorous and self-compatible, Solyntus provides a more direct and contiguous refer...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: van Lieshout, N., van der Burgt, A., de Vries, M. E., ter Maat, M., Eickholt, D., Esselink, D., van Kaauwen, M. P. W., Kodde, L. P., Visser, R. G. F., Lindhout, P., Finkers, R. Tags: Genome Report Source Type: research
High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
Social wasps of the genus Vespula have spread to nearly all landmasses worldwide and have become significant pests in their introduced ranges, affecting economies and biodiversity. Comprehensive genome assemblies and annotations for these species are required to develop the next generation of control strategies and monitor existing chemical control. We sequenced and annotated the genomes of the common wasp (Vespula vulgaris), German wasp (Vespula germanica), and the western yellowjacket (Vespula pensylvanica). Our chromosome-level Vespula assemblies each contain 176–179 Mb of total sequence assembled into 25 scaffold...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Harrop, T. W. R., Guhlin, J., McLaughlin, G. M., Permina, E., Stockwell, P., Gilligan, J., Le Lec, M. F., Gruber, M. A. M., Quinn, O., Lovegrove, M., Duncan, E. J., Remnant, E. J., Van Eeckhoven, J., Graham, B., Knapp, R. A., Langford, K. W., Kronenberg, Tags: Genome Report Source Type: research
Reference Genome for the Highly Transformable Setaria viridis ME034V
We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural varia...
Source: G3: Genes Genomes Genetics - October 4, 2020 Category: Genetics & Stem Cells Authors: Thielen, P. M., Pendleton, A. L., Player, R. A., Bowden, K. V., Lawton, T. J., Wisecaver, J. H. Tags: Genome Report Source Type: research
Corrigendum
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research
Genetic Basis of Natural Variation in Spontaneous Grooming in Drosophila melanogaster
Spontaneous grooming behavior is a component of insect fitness. We quantified spontaneous grooming behavior in 201 sequenced lines of the Drosophila melanogaster Genetic Reference Panel and observed significant genetic variation in spontaneous grooming, with broad-sense heritabilities of 0.25 and 0.24 in females and males, respectively. Although grooming behavior is highly correlated between males and females, we observed significant sex by genotype interactions, indicating that the genetic basis of spontaneous grooming is partially distinct in the two sexes. We performed genome-wide association analyses of grooming behavi...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Yanagawa, A., Huang, W., Yamamoto, A., Wada-Katsumata, A., Schal, C., Mackay, T. F. C. Tags: Investigations Source Type: research
Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum
We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium discoideum, a key model organism in molecular, cellular, evolutionary and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 x 10–11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance ...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Kucukyildirim, S., Behringer, M., Sung, W., Brock, D. A., Doak, T. G., Mergen, H., Queller, D. C., Strassmann, J. E., Lynch, M. Tags: Investigations Source Type: research
SIR2 Expression Noise Can Generate Heterogeneity in Viability but Does Not Affect Cell-to-Cell Epigenetic Silencing of Subtelomeric URA3 in Yeast
Chromatin structure clearly modulates gene expression noise, but the reverse influence has never been investigated, namely how the cell-to-cell expression heterogeneity of chromatin modifiers may generate variable rates of epigenetic modification. Sir2 is a well-characterized histone deacetylase of the Sirtuin family. It strongly influences chromatin silencing, especially at telomeres, subtelomeres and rDNA. This ability to influence epigenetic landscapes makes it a good model to study the largely unexplored interplay between gene expression noise and other epigenetic processes leading to phenotypic diversification. Here, ...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Liu, J., Mosser, L., Botanch, C., Francois, J.-M., Capp, J.-P. Tags: Investigations Source Type: research
Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus
Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM productio...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Tabima, J. F., Trautman, I. A., Chang, Y., Wang, Y., Mondo, S., Kuo, A., Salamov, A., Grigoriev, I. V., Stajich, J. E., Spatafora, J. W. Tags: Investigations Source Type: research
Can a Population Targeted by a CRISPR-Based Homing Gene Drive Be Rescued?
CRISPR-based homing gene drive is a genetic control technique aiming to modify or eradicate natural populations. This technique is based on the release of individuals carrying an engineered piece of DNA that can be preferentially inherited by the progeny. The development of countermeasures is important to control the spread of gene drives, should they result in unanticipated damages. One proposed countermeasure is the introduction of individuals carrying a brake construct that targets and inactivates the drive allele but leaves the wild-type allele unaffected. Here we develop models to investigate the efficiency of such br...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Rode, N. O., Courtier-Orgogozo, V., Debarre, F. Tags: Investigations Source Type: research
A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions
The world is facing a global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Kim, D.-K., Knapp, J. J., Kuang, D., Chawla, A., Cassonnet, P., Lee, H., Sheykhkarimli, D., Samavarchi-Tehrani, P., Abdouni, H., Rayhan, A., Li, R., Pogoutse, O., Coyaud, E., van der Werf, S., Demeret, C., Gingras, A.-C., Taipale, M., Raught, B., Jacob, Y Tags: Investigations Source Type: research
speck, First Identified in Drosophila melanogaster in 1910, Is Encoded by the Arylalkalamine N-Acetyltransferase (AANAT1) Gene
The pigmentation mutation speck is a commonly used recombination marker characterized by a darkly pigmented region at the wing hinge. Identified in 1910 by Thomas Hunt Morgan, speck was characterized by Sturtevant as the most "workable" mutant in the rightmost region of the second chromosome and eventually localized to 2-107.0 and 60C1-2. Though the first speck mutation was isolated over 110 years ago, speck is still not associated with any gene. Here, as part of an undergraduate-led research effort, we show that speck is encoded by the Arylalkylamine N-acetyltransferase 1 (AANAT1) gene. Both alleles from the Morgan lab co...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Spana, E. P., Abrams, A. B., Ellis, K. T., Klein, J. C., Ruderman, B. T., Shi, A. H., Zhu, D., Stewart, A., May, S. Tags: Investigations Source Type: research
