Twelve quick steps for genome assembly and annotation in the classroom DOI Creative Commons
Hyungtaek Jung, Tomer Ventura, J. Sook Chung

et al.

PLoS Computational Biology, Journal Year: 2020, Volume and Issue: 16(11), P. e1008325 - e1008325

Published: Nov. 12, 2020

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting budgets individual research groups. Third-generation long-read DNA technologies are used, providing extensive genomic toolkits that were reserved for a few select model organisms. Generating high-quality assemblies annotations many aquatic species still presents significant challenges due to their large sizes, complexity, high chromosome numbers. Indeed, selecting most appropriate software platforms annotation pipelines new project can be daunting because tools often only work in limited contexts. In genomics, generating assembly/annotation has an indispensable tool better understanding biology any species. Herein, we state 12 steps help researchers get started projects by presenting guidelines broadly applicable (to species), sustainable over time, cover all aspects assembly from start finish. We review some commonly used approaches, including practical methods extract choices best library preparations. addition, discuss range potential bioinformatics pipelines, structural functional (e.g., transposable elements repetitive sequences). This paper also includes information on how build wide community project, importance data management, make results Findable, Accessible, Interoperable, Reusable (FAIR) submitting them public repository sharing with community.

Language: Английский

Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities DOI Creative Commons
Na Jia, Jinfeng Wang,

Wenqiang Shi

et al.

Cell, Journal Year: 2020, Volume and Issue: 182(5), P. 1328 - 1340.e13

Published: Aug. 18, 2020

Language: Английский

Citations

221
Molecular Evolution of the Major Arthropod Chemoreceptor Gene Families DOI Creative Commons
Hugh M. Robertson

Annual Review of Entomology, Journal Year: 2018, Volume and Issue: 64(1), P. 227 - 242

Published: Oct. 12, 2018

The evolutionary origins of the three major families chemoreceptors in arthropods-the odorant receptor (OR), gustatory (GR), and ionotropic (IR) families-occurred at base Insecta, Animalia, Protostomia, respectively. Comparison family sizes across arthropods reveals a generally positive correlation with their widely disparate complexity chemical ecology. Closely related species reveal ongoing processes gene evolution, including duplication, divergence, pseudogenization, loss, that mediate these larger patterns. Sets paralogous receptors within selection on amino acids regions likely to contribute ligand binding specificity. Ligands many ORs some GRs IRs have been identified; however, identification for more is needed, as are structures OR/GR superfamily, improve our understanding molecular evolution ecologically important arthropods.

Language: Английский

Citations

220
Gene content evolution in the arthropods DOI Creative Commons
Gregg W.C. Thomas, Elias Dohmen, Daniel Hughes

et al.

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: Jan. 23, 2020

Abstract Background Arthropods comprise the largest and most diverse phylum on Earth play vital roles in nearly every ecosystem. Their diversity stems part from variations a conserved body plan, resulting recorded adaptive changes genome. Dissection of genomic record sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Results Using 76 whole sequences representing 21 orders spanning more than 500 million years arthropod evolution, we document gene protein domain content provide temporal phylogenetic context for interpreting these innovations. We identify many novel families that arose early arthropods during diversification insects into modern orders. reveal unexpected variation patterns DNA methylation examples family coincident with appearance notable phenotypic physiological adaptations such as flight, metamorphosis, sociality, chemoperception. Conclusions These analyses demonstrate how large-scale comparative genomics can new insights genotype phenotype map generate testable hypotheses about animal diversity.

Language: Английский

Citations

211
Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus DOI Creative Commons
Felipe S. Barreto, Eric T. Watson, Thiago G. Lima

et al.

Nature Ecology & Evolution, Journal Year: 2018, Volume and Issue: 2(8), P. 1250 - 1257

Published: July 6, 2018

Abstract The copepod Tigriopus californicus shows extensive population divergence and is becoming a model for understanding allopatric differentiation the early stages of speciation. Here, we report high-quality reference genome one (~190 megabases across 12 scaffolds, ~15,500 protein-coding genes). Comparison with other arthropods reveals 2,526 genes presumed to be specific T. , an apparent proliferation involved in ion transport receptor activity. Beyond population, re-sequenced genomes seven additional populations, spanning continuum reproductive isolation. Populations show extreme mitochondrial DNA divergence, higher levels amino acid than observed taxa. Across nuclear genome, find elevated protein evolutionary rates positive selection predicted interact proteins RNA it encodes multiple pathways. Together, these results support hypothesis that rapid evolution drives compensatory within isolated thereby providing potentially important mechanism causing intrinsic

Language: Английский

Citations

189
The 40-Year Mystery of Insect Odorant-Binding Proteins DOI Creative Commons
Karen Rihani, Jean‐François Ferveur,

Loïc Briand

et al.

Biomolecules, Journal Year: 2021, Volume and Issue: 11(4), P. 509 - 509

Published: March 30, 2021

The survival of insects depends on their ability to detect molecules present in environment. Odorant-binding proteins (OBPs) form a family involved chemoreception. While OBPs were initially found olfactory appendages, recently these discovered other chemosensory and non-chemosensory organs. can bind, solubilize transport hydrophobic stimuli chemoreceptors across the aqueous sensilla lymph. In addition this broadly accepted “transporter role”, also buffer sudden changes odorant levels are hygro-reception. physiological roles expressed body tissues, such as mouthparts, pheromone glands, reproductive organs, digestive tract venom remain be investigated. This review provides an updated panorama varied structural aspects, binding properties, tissue expression functional insect OBPs.

Language: Английский

Citations

146
Functional properties of insect olfactory receptors: ionotropic receptors and odorant receptors DOI Creative Commons
Dieter Wicher, Fabio Miazzi

Cell and Tissue Research, Journal Year: 2021, Volume and Issue: 383(1), P. 7 - 19

Published: Jan. 1, 2021

Abstract The majority of insect olfactory receptors belong to two distinct protein families, the ionotropic (IRs), which are related glutamate receptor family, and odorant (ORs), evolved from gustatory family. Both types assemble heteromeric ligand-gated cation channels composed odor-specific proteins co-receptor proteins. We here present in short current view on evolution, function, regulation IRs ORs. Special attention is given how their functional properties can meet environmental ecological challenges an has face.

Language: Английский

Citations

135
Humidity sensors that alert mosquitoes to nearby hosts and egg-laying sites DOI
Willem J. Laursen, Gonzalo Budelli,

Ruocong Tang

et al.

Neuron, Journal Year: 2023, Volume and Issue: 111(6), P. 874 - 887.e8

Published: Jan. 13, 2023

Language: Английский

Citations

46
Genome sequences of four Ixodes species expands understanding of tick evolution DOI Creative Commons
Alexandra Cerqueira de Araujo, Benjamin Noël, Anthony Bretaudeau

et al.

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: Jan. 21, 2025

Language: Английский

Citations

3
The origin of the odorant receptor gene family in insects DOI Creative Commons
Philipp Brand, Hugh M. Robertson, Wei‐Hung Lin

et al.

eLife, Journal Year: 2018, Volume and Issue: 7

Published: July 31, 2018

The origin of the insect odorant receptor (OR) gene family has been hypothesized to have coincided with evolution terrestriality in insects. Missbach et al. (2014) suggested that ORs instead evolved an ancestral OR co-receptor (Orco) after and OR/Orco system is adaptation winged flight We investigated genomes Collembola, Diplura, Archaeognatha, Zygentoma, Odonata, Ephemeroptera, find present all but absent from lineages predating Orco only ancestrally wingless lineage Archaeognatha. Our new genome sequence zygentoman firebrat Thermobia domestica reveals a full system. conclude before flight, perhaps as terrestriality, representing key evolutionary novelty ancestor insects, hence molecular synapomorphy for Class Insecta.

Language: Английский

Citations

144
Drosophilasensory receptors—a set of molecular Swiss Army Knives DOI Open Access
Craig Montell

Genetics, Journal Year: 2021, Volume and Issue: 217(1), P. 1 - 34

Published: Jan. 1, 2021

Genetic approaches in the fruit fly, Drosophila melanogaster, have led to a major triumph field of sensory biology-the discovery multiple large families receptors and channels. Some these families, such as transient receptor potential channels, are conserved from animals ranging worms humans, while others, "gustatory receptors," "olfactory "ionotropic restricted invertebrates. Prior identification flies, it was widely assumed that proteins function just one modality vision, smell, taste, hearing, somatosensation, which includes thermosensation, light, noxious mechanical touch. By employing vast combination genetic, behavioral, electrophysiological, other concept emerge is many multitaskers. The earliest example this idea individual channels senses. It now clear multitasking exhibited by including gustatory receptors, ionotropic epithelial Na+ (also referred Pickpockets), even opsins, were formerly thought exclusively light sensors. characterizations neurons express them also reveal mechanisms through flies can accurately differentiate between different stimuli when they activate same receptor, well adaptation, amplification, integration. insights gleaned studies been highly influential directing investigations animal models.

Language: Английский

Citations

106