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G3: Genes—Genomes—Genetics

Andrea Gloria-Soria, W Augustine Dunn, Xiaoqing Yu, Aurélien Vigneron, Kuang-Yao Lee, Mo Li, Brian L Weiss, Hongyu Zhao, Serap Aksoy, Adalgisa Caccone
Vector-borne diseases are responsible for more than one million deaths every year but genomic resources for most species responsible for their transmission are limited. This is true for neglected diseases such as sleeping sickness (Human African Trypanosomiasis), a disease caused by Trypanosoma parasites vectored by several species of tseste flies within the genus Glossina We describe an integrative approach that identifies statistical associations between trypanosome infection status of Glossina fuscipes fuscipes (Gff) flies from Uganda, for which functional studies are complicated because the species cannot be easily maintained in laboratory colonies, and ~73,000 polymorphic sites distributed across the genome...
January 17, 2018: G3: Genes—Genomes—Genetics
Zhaozhao Qin, Robert Johnsen, Shicheng Yu, Jeffrey Shih-Chieh Chu, David Baillie, Nansheng Chen
Using combined genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation, we identified 60 essential genes from 104 lethal mutations in two genomic regions of C. elegans totalling approximately 14 Mb on chromosome III(mid) and chromosome V(left). Five of the 60 genes had not previously been shown to have lethal phenotypes by RNA interference depletion. By analyzing the regions around the lethal missense mutations, we identified four putative new protein functional domains. Furthermore, functional characterization of the identified essential genes shows that most are enzymes, including helicases, tRNA synthetases, and kinases in addition to ribosomal proteins...
January 16, 2018: G3: Genes—Genomes—Genetics
Daoliang Lan, Xianrong Xiong, Tserang-Donko Mipam, Changxiu Fu, Qiang Li, Yi Ai, Dingchao Hou, Zhixin Chai, Jincheng Zhong, Jian Li
Jinchuan yak, a newly discovered yak breed, not only possesses a large proportion of multi-ribs but also exhibits many good characteristics, such as high meat production, milk yield and reproductive performance. However, information about their overall genetic structure, relationship with yaks in other areas, and possible origins and evolutionary processes is limited. In this study, 7,693,689 high-quality single-nucleotide polymorphisms were identified by resequencing the genome of Jinchuan yak. Principal component and population genetic structure analyses showed that Jinchuan yak was distinguished as an independent population among the domestic yak population...
January 16, 2018: G3: Genes—Genomes—Genetics
Tomasz L Mróz, Sebastian Eves-van den Akker, Agata Bernat, Agnieszka Skarzyńska, Leszek Pryszcz, Madeline Olberg, Michael J Havey, Grzegorz Bartoszewski
Cucumber (Cucumis sativus L.) has a large, paternally transmitted mitochondrial genome. Cucumber plants regenerated from cell cultures occasionally show paternally transmitted mosaic (MSC) phenotypes, characterized by slower growth, chlorotic patterns on the leaves and fruit, lower fertility, and rearrangements in their mitochondrial DNAs (mtDNAs). MSC lines 3, 12, and 16 originated from different cell cultures all established using the highly-inbred, wild-type line B. These MSC lines possess different rearrangements and under-represented regions in their mtDNAs...
January 12, 2018: G3: Genes—Genomes—Genetics
Christopher G Duncan, Hrisavgi D Kondilis-Mangum, Sara A Grimm, Pierre R Bushel, Kaliopi Chrysovergis, John D Roberts, Frederick L Tyson, B Alex Merrick, Paul A Wade
The DNA methyltransferase, Dnmt3a, is dynamically regulated throughout mammalian B cell development and upon activation by antigenic stimulation. Dnmt3a inactivation in hematopoietic stem cells has been shown to drive B cell-related malignancies, including chronic lymphocytic leukemia (CLL), and associates with specific DNA methylation patterns in transformed cells. However, while it is clear that inactivation of Dnmt3a in hematopoietic stem cells has profound functional impacts, the consequences of Dnmt3a inactivation in cells of the B lineage are unclear...
January 11, 2018: G3: Genes—Genomes—Genetics
Leandro F Moreno, Abdalla A O Ahmed, Balázs Brankovics, Christina A Cuomo, Steph B J Menken, Saad J Taj-Aldeen, Hani Faidah, J Benjamin Stielow, Marcus de M Teixeira, Francesc X Prenafeta-Boldú, Vania A Vicente, Sybren de Hoog
Rhinocladiella mackenziei accounts for the majority of fungal brain infections in the Middle East and is restricted to the arid climate zone between Saudi Arabia and Pakistan. Neurotropic dissemination caused by this fungus has been reported in immunocompromised, but also immunocompetent individuals. If untreated, the infection is fatal. Outside of humans, the environmental niche of R. mackenziei is unknown, and the fungus has been only cultured from brain biopsies. In this paper we describe the whole genome re-sequencing of two Rhinocladiella mackenziei strains from patients in Saudi Arabia and Qatar...
January 11, 2018: G3: Genes—Genomes—Genetics
Attila Gyoergy, Marko Roblek, Aparna Ratheesh, Katarina Valoskova, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz J Sánchez-Sánchez, Brian Stramer, Daria E Siekhaus
Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking...
January 10, 2018: G3: Genes—Genomes—Genetics
Yu Zhao, Jef D Boeke
Vectors encoding selectable markers have been widely used in yeast to maintain or express exogenous DNA fragments. In the fission yeast Schizosaccharomyces pombe, several engineered markers have been reported and widely used, such as ura4+ and ScLEU2 from Saccharomyces cerevisiae, which complement ura4 and leu1 mutations, respectively. These two auxotrophic markers share no homology with the Sch. pombe genome, however most others can recombine with the genomic due to sequence homology shared between the genomic and plasmid-born copies of the markers...
January 10, 2018: G3: Genes—Genomes—Genetics
Zhao-Qun Li, Long Ma, Qian Yin, Xiao-Ming Cai, Zong-Xiu Luo, Lei Bian, Zhao-Jun Xin, Peng He, Zong-Mao Chen
Moths can biosynthesize sex pheromones in the female sex pheromone glands (PGs) and can distinguish species-specific sex pheromones using their antennae. However, the biosynthesis and transportation mechanism for Type II sex pheromone components has rarely been documented in moths. In this study, we constructed a massive PG transcriptome database (14.72 giga bases) from a moth species, Ectropisgrisescens, which uses Type II sex pheromones and is a major tea pest in China. We further identified the putative sex pheromone biosynthesis and transportation related genes: 111 cytochrome P450 monooxygenases (P450s, CYPs), 25 odorant binding proteins (OBPs), and 20 chemosensory proteins (CSPs)...
January 9, 2018: G3: Genes—Genomes—Genetics
Leone De Marco, Sara Epis, Aida Capone, Elena Martin, Jovana Bozic, Elena Crotti, Irene Ricci, Davide Sassera
Yeasts of the Meyerozyma guilliermondii species complex are widespread in nature and can be isolated from a variety of sources, from the environment to arthropods to hospital patients. To date, the species complex comprises the thoroughly studied and versatile M. guilliermondii, and the hard to distinguish M. caribbica, and Candida carpophila Here we report the whole-genome sequencing and de novo assembly of four M. caribbica isolates, identified with the most recent molecular techniques, derived from four Diptera species...
January 8, 2018: G3: Genes—Genomes—Genetics
Josip Brajković, Željka Pezer, Branka Bruvo-Mađarić, Antonio Sermek, Isidoro Feliciello, Đurđica Ugarković
Satellite DNAs are tandemly repeated sequences clustered within heterochromatin. However, in some cases such as the major TCAST1 satellite DNA from the beetle Tribolium castaneum, they are found partially dispersed within euchromatin. Such organization together with transcriptional activity enables TCAST1 to modulate the activity of neighbouring genes. In order to explore if other T. castaneum repetitive families have features which could provide them with a possible gene-modulatory role we compare here the structure, organization, dispersion profiles and transcription activity of ten distinct TCAST repetitive families including TCAST1...
January 8, 2018: G3: Genes—Genomes—Genetics
Ryan Friedman, Stacey R Gish, Holly Brown, Lindsey Brier, Nicole Howard, Tamara L Doering, Michael R Brent
Received wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based on circumstantial evidence. We provide the first direct measurement of the effects of transformation on a fungal genome by sequencing the genomes of 29 transformants and 30 untransformed controls to high coverage. Contrary to the received wisdom, our results show that transformation of DNA segments flanked by long targeting sequences, followed by homologous recombination and selection for a drug marker, is extremely safe...
January 5, 2018: G3: Genes—Genomes—Genetics
Jae Young Choi, Michael D Purugganan
The domestication scenario that led to Asian rice (Oryza sativa) is a contentious topic. Here, we have reanalyzed a previously published large-scale wild and domesticated rice dataset, which were also analyzed by two studies but resulted in two contrasting domestication models. We suggest the analysis of false positive selective sweep regions and phylogenetic analysis of concatenated genomic regions may have been the sources that contributed to the different results. In the end, our result indicates Asian rice originated from multiple wild progenitor subpopulations; however, de novo domestication appears to have occurred only once and the domestication alleles were transferred between rice subpopulation through introgression...
January 4, 2018: G3: Genes—Genomes—Genetics
Christopher M Jones, Ka S Lim, Jason W Chapman, Chris Bass
The genes and genomes of insect pests are shaped by the wide array of selective forces encountered in their environments. While the molecular adaptations that evolve are beginning to be understood at the genomic and transcriptomic level they have been less well characterised at an epigenetic level. Here, we present a genome-wide map of DNA methylation, at single-nucleotide resolution for the cotton bollworm moth, Helicoverpa armigera; a globally invasive pest of agriculture. We show that methylation is almost identical in the larvae and adults of H...
January 3, 2018: G3: Genes—Genomes—Genetics
Clarissa S Santoso, Tracy L Meehan, Jeanne S Peterson, Tiara M Cedano, Christopher V Turlo, Kimberly McCall
The clearance of dead cells is a fundamental process in maintaining tissue homeostasis. Genetic studies in Drosophila melanogaster, Caenorhabditis elegans, and mammals have identified two evolutionarily conserved signaling pathways that act redundantly to regulate this engulfment process: the ced-1/-6/-7 and ced-2/-5/-12 pathways. Of these engulfment genes, only the ced-7/ABCA1 ortholog remains to be identified in D. melanogaster Homology searches revealed a family of putative ced-7/ABCA1 homologs encoding ABC transporters in D...
January 2, 2018: G3: Genes—Genomes—Genetics
Peinan Hu, Xueying Zhao, Qinghua Zhang, Weiming Li, Yao Zu
CRISPR/Cas9 system has been proven to be an efficient and precise genome editing technology in various organisms. However, the gene editing efficiencies of Cas9 proteins with a nuclear localization signal (NLS) fused to different termini and Cas9 mRNA have not been systematically compared. Here, we compared the ability of Cas9 proteins with NLS fused to the N, C, or both N and C termini and N-NLS-Cas9-NLS-C mRNA to target two sites in the tyr gene and two sites in the gol gene related to pigmentation in zebrafish...
January 2, 2018: G3: Genes—Genomes—Genetics
Nicole D Dueker, Shengru Guo, Ashley Beecham, Liyong Wang, Susan H Blanton, Marco R Di Tullio, Tatjana Rundek, Ralph L Sacco
Increased left ventricular mass (LVM) is an intermediate phenotype for cardiovascular disease (CVD) and a predictor of stroke. Using families from the Dominican Republic, we have previously shown LVM to be heritable and found evidence for linkage to chromosome 12p11. Our current study aimed to further characterize the QTL by sequencing the 1 LOD unit down region in ten families from the Dominican Republic with evidence for linkage to LVM. Within this region, we tested 5,477 common variants (CVs; minor allele frequency [MAF] ≥5%) using the QTDT test...
December 29, 2017: G3: Genes—Genomes—Genetics
Yuka Kitomi, Emari Nakao, Sawako Kawai, Noriko Kanno, Tsuyu Ando, Shuichi Fukuoka, Kenji Irie, Yusaku Uga
The volume that the root system can occupy is associated with the efficiency of water and nutrient uptake from soil. Genetic improvement of root length, which is a limiting factor for root distribution, is necessary for increasing crop production. In this report, we describe identification of two QTLs for maximal root length, QUICK ROOTING 1 (QRO1) on chromosome 2 and QRO2 on chromosome 6 in cultivated rice (Oryza sativa L.). We measured the maximal root length in 26 lines carrying chromosome segments from the long-rooted upland rice cultivar Kinandang Patong in the genetic background of the short-rooted lowland cultivar IR64...
December 26, 2017: G3: Genes—Genomes—Genetics
Laurence Signon
Paused/stalled replication forks are major threats to genome integrity; unraveling the complex pathways that contribute to fork stability/restart is crucial. Experimentally, fork stalling is induced by growth in presence of hydroxyurea (HU), which depletes the pool of deoxynucleoside triphosphates (dNTPs) and slows down replication progression in yeast. Here, I report an epistasis analysis, based on sensitivity to HU, between CLB2, the principal mitotic cyclin gene in S. cerevisiae, and genes involved in fork stability and recombination...
December 26, 2017: G3: Genes—Genomes—Genetics
Patrick Thorwarth, Eltohamy A A Yousef, Karl J Schmid
Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS) and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower (Brassica oleracea var. botrytis) by combining 174 randomly selected cauliflower genebank accessions from two different genebanks...
December 18, 2017: G3: Genes—Genomes—Genetics
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