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Αλέξανδρος Γ. Σφακιανάκης

Monday, October 5, 2020

 

Reference Genome for the Highly Transformable Setaria viridis ME034V
Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. 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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
"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....
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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,...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
Assessment of the Potential for Genomic Selection To Improve Husk Traits in Maize
Husk has multiple functions such as protecting ears from diseases, infection, and dehydration during development. Additionally, husks comprised of fewer, shorter, thinner, and narrower layers allow faster moisture evaporation of kernels prior to harvest. Intensive studies have been conducted to identify appropriate husk architecture by understanding the genetic basis of related traits, including husk length, husk layer number, husk thickness, and husk width. However, marker-assisted selection is...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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,...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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)...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions
Within the budding yeasts, the opportunistic pathogen Candida glabrata and other members of the Nakaseomyces clade have developed virulence traits independently from C. albicans and C. auris. To begin exploring the genetic basis of C. glabrata virulence and its innate resistance to antifungals, we launched the Hermes transposon from a plasmid and sequenced more than 500,000 different semi-random insertions throughout the genome. With machine learning, we identified 1278 protein-encoding genes (25%...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
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...
G3: Genes, Genomes, Genetics current issue
Mon Oct 05, 2020 23:47
Effects of collagen membranes with different properties in peri‐implant dehiscence defects
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
6 mm vs 11 mm implants supporting mandibular full‐arch fixed prostheses: 4‐year ad‐interim report of a multicenter randomized controlled trial
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Regeneration of peri‐implant dehiscence defects using a synthetic biomaterial. A randomized controlled clinical trial
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Macrophage polarization in peri‐implantitis lesions
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
The effect of soft tissue thickness on crestal bone loss of early loaded implants
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Effect of intraoral conditions on precision and trueness of full‐arch digital implant impressions
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Up to 10 years analysis of implant‐supported and tooth‐implant‐supported fixed restorations ‐ a RCT
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Anti‐fibronectin Aptamers improve physiologic coagulum patterns and osteoblastic cells behavior
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Osteogenic and antimicrobial behaviour of surface functionalized titanium implant with gold nanoparticles. An in vitro study
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Improvement in wettability and crystallinity by reactive plasma on nanostructured titanium surfaces for implants
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Linear and volumetric augmentation in anterior maxilla using autogenous symphysis bone graft
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Marginal bone level and biologic width dynamics in tissue‐level and bone‐level implants
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Critical defect healing assessment in rat calvaria using a titanium‐reinforced polytetrafluoroethylene membrane
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
12 years of clinical experience with gold shaded titanium abutments
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Time efficiency and quality of outcomes in a centralized digital workflow for the fabrication of implant crowns
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Vitality of Retromolar Bone Grafts ‐ A Critical Appraisal of the Current Histomorphometric Approach
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
The peri‐implant mucosa at implants with two different geometries of the transmucosal area: a randomized controlled experimental in vivo investigation
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Two short implants versus one short implant with a cantilever ‐ 5‐year results of a randomized clinical trial
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Immediate provisionalization of Astra Tech implants in healed and extraction sites: 1 to 11‐year results
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17
Advanced surgical navigation system using augmented reality technology
Clinical Oral Implants Research
Mon Oct 05, 2020 11:17

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