scholarly journals Patterns of Genomic Differentiation in the Drosophila nasuta Species Complex

2019 ◽  
Vol 37 (1) ◽  
pp. 208-220 ◽  
Author(s):  
Dat Mai ◽  
Matthew J Nalley ◽  
Doris Bachtrog
Keyword(s):  
Single Molecule ◽  
Species Complex ◽  
Postzygotic Isolation ◽  
Additional Species ◽  
Single Molecule Sequencing ◽  
Phylogenetic Methods ◽  
Low Levels ◽  
Taxonomic Groups ◽  
Drosophila Nasuta ◽  
High Quality Genome

Abstract The Drosophila nasuta species complex contains over a dozen recently diverged species that are distributed widely across South-East Asia, and which shows varying degrees of pre- and postzygotic isolation. Here, we assemble a high-quality genome for D. albomicans using single-molecule sequencing and chromatin conformation capture, and draft genomes for 11 additional species and 67 individuals across the clade, to infer the species phylogeny and patterns of genetic diversity in this group. Our assembly recovers entire chromosomes, and we date the origin of this radiation ∼2 Ma. Despite low levels of overall differentiation, most species or subspecies show clear clustering into their designated taxonomic groups using population genetics and phylogenetic methods. Local evolutionary history is heterogeneous across the genome, and differs between the autosomes and the X chromosome for species in the sulfurigaster subgroup, likely due to autosomal introgression. Our study establishes the nasuta species complex as a promising model system to further characterize the evolution of pre- and postzygotic isolation in this clade.

scholarly journals GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing

2018 ◽  
Author(s):  
Danny E. Miller ◽  
Cynthia Staber ◽  
Julia Zeitlinger ◽  
R. Scott Hawley
Keyword(s):  
Single Molecule ◽  
Drosophila Species ◽  
High Quality ◽  
Additional Species ◽  
Oxford Nanopore ◽  
Wide Range ◽  
Long Read ◽  
Genome Assemblies ◽  
High Quality Genome ◽  
Reference Genomes

ABSTRACTThe Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present high-quality genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba), four additional species that had previously reported assemblies (biarmipes, bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close over 60% of the gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately $1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes.

scholarly journals Genome resource for Elsinoë batatas, the causal agent of stem and foliage scab disease of sweet potato

2021 ◽  
Author(s):  
Xinxin Zhang ◽  
Hongda Zou ◽  
Yiling Yang ◽  
Boping Fang ◽  
Lifei Huang
Keyword(s):  
Sweet Potato ◽  
Single Molecule ◽  
Reference Genome ◽  
Gc Content ◽  
Basic Research ◽  
Phytopathogenic Fungus ◽  
Sequencing Technology ◽  
High Quality ◽  
Single Molecule Sequencing ◽  
High Quality Genome

Elsinoë batatas is a phytopathogenic fungus causing stem and foliage scab disease of sweet potato. At present, there is no reference genome available for E. batatas, limiting basic research for the pathogen. The present study applied the nanopore single molecule sequencing technology to sequence the E. batatas genome. This study thus reports the first high-quality genome sequence of E. batatas, with a total contig size of 26.49 Mb, 50.8% GC content and an N50 of 2,546,814bp. The sequences obtained serve as a reference for analysis of E. batatas isolates and provide a resource to better understand the biology of stem and foliage scab disease of sweet potato.

scholarly journals Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

2021 ◽  
Author(s):  
Fei Ge ◽  
Jingtao Qu ◽  
Peng Liu ◽  
Lang Pan ◽  
Chaoying Zou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Inbred Line ◽  
Genome Mapping ◽  
Maize Inbred Line ◽  
Sequencing Data ◽  
Structural Variations ◽  
Single Molecule Sequencing ◽  
Maize Genetic ◽  
Induction Ratio ◽  
Phenotypic Variations

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ~30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.

scholarly journals Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference

2013 ◽  
Vol 280 (1771) ◽  
pp. 20131945 ◽  
Author(s):  
Joana Segura ◽  
Luca Ferretti ◽  
Sebastián Ramos-Onsins ◽  
Laia Capilla ◽  
Marta Farré ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mammalian Species ◽  
Evolutionary Change ◽  
Critical Importance ◽  
Recombination Rates ◽  
Allelic Variants ◽  
Crossover Interference ◽  
Chromosomal Segregation ◽  
Low Levels ◽  
Taxonomic Groups

Recombination allows faithful chromosomal segregation during meiosis and contributes to the production of new heritable allelic variants that are essential for the maintenance of genetic diversity. Therefore, an appreciation of how this variation is created and maintained is of critical importance to our understanding of biodiversity and evolutionary change. Here, we analysed the recombination features from species representing the major eutherian taxonomic groups Afrotheria, Rodentia, Primates and Carnivora to better understand the dynamics of mammalian recombination. Our results suggest a phylogenetic component in recombination rates (RRs), which appears to be directional, strongly punctuated and subject to selection. Species that diversified earlier in the evolutionary tree have lower RRs than those from more derived phylogenetic branches. Furthermore, chromosome-specific recombination maps in distantly related taxa show that crossover interference is especially weak in the species with highest RRs detected thus far, the tiger. This is the first example of a mammalian species exhibiting such low levels of crossover interference, highlighting the uniqueness of this species and its relevance for the study of the mechanisms controlling crossover formation, distribution and resolution.

2. How to read the book of life

2018 ◽  
pp. 12-27
Author(s):  
John Archibald
Keyword(s):  
Dna Sequencing ◽  
Human Genome ◽  
Single Molecule ◽  
Human Genome Project ◽  
Genome Project ◽  
Chain Termination ◽  
Single Molecule Sequencing ◽  
Semiconductor Sequencing ◽  
The Cost ◽  
The Human Genome Project

For all its biological importance, DNA is a fragile molecule so extracting it is a difficult process. ‘How to read the book of life’ explains the techniques required to sequence DNA. It begins by explaining the techniques developed for protein and RNA sequencing by Frederick Sanger, Robert Holley, and Carl Woese that were then developed further for DNA sequencing. Following the success of the Human Genome Project, the next generation of DNA sequencing was developed in the mid-2000s. Pyrosequencing was capable of generating orders of magnitude more data at a fraction of the cost, but was superceded within a decade by semiconductor sequencing, reversible chain-termination sequencing, and single-molecule sequencing.

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