scholarly journals Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster

2019 ◽  
Vol 48 (1) ◽  
pp. 290-303 ◽  
Author(s):  
Christopher E Ellison ◽  
Weihuan Cao
Keyword(s):  
Drosophila Melanogaster ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Population Level ◽  
Chromosome Length ◽  
Nanopore Sequencing ◽  
Long Reads ◽  
Wild Strains ◽  
Genome Assemblies ◽  
Insight Into

Abstract Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which has provided important insight into the population dynamics of TEs. However, such approaches are not able to identify insertions of uncharacterized TEs, nor can they assemble the full sequence of inserted elements. Here, we use nanopore sequencing and Hi-C scaffolding to produce de novo genome assemblies for two wild strains of Drosophila melanogaster from the Drosophila Genetic Reference Panel (DGRP). Ovarian piRNA populations and Illumina split-read TE insertion profiles have been previously produced for both strains. We find that nanopore sequencing with Hi-C scaffolding produces highly contiguous, chromosome-length scaffolds, and we identify hundreds of TE insertions that were missed by Illumina-based methods, including a novel micropia-like element that has recently invaded the DGRP population. We also find hundreds of piRNA-producing loci that are specific to each strain. Some of these loci are created by strain-specific TE insertions, while others appear to be epigenetically controlled. Our results suggest that Illumina approaches reveal only a portion of the repetitive sequence landscape of eukaryotic genomes and that population-level resequencing using long reads is likely to provide novel insight into the evolutionary dynamics of repetitive elements.

scholarly journals Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

2016 ◽  
Author(s):  
Derek M. Bickhart ◽  
Benjamin D. Rosen ◽  
Sergey Koren ◽  
Brian L. Sayre ◽  
Alex R. Hastie ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Chromosome Length ◽  
Chromatin Interaction ◽  
Capra Hircus ◽  
Immune Gene ◽  
Ruminant Species ◽  
Long Reads ◽  
Assembly Algorithms ◽  
Genome Assemblies

AbstractThe decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a >250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.

scholarly journals Multiple mechanisms drive genomic adaptation to extreme O2 levels in Drosophila melanogaster

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Arya Iranmehr ◽  
Tsering Stobdan ◽  
Dan Zhou ◽  
Huiwen Zhao ◽  
Sergey Kryazhimskiy ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
De Novo Mutations ◽  
Multiple Alleles ◽  
Adaptive Mechanisms ◽  
Genomic Adaptation ◽  
Soft Selective Sweeps ◽  
Analyze Time Series ◽  
Insight Into

AbstractTo detect the genomic mechanisms underlying evolutionary dynamics of adaptation in sexually reproducing organisms, we analyze multigenerational whole genome sequences of Drosophila melanogaster adapting to extreme O2 conditions over an experiment conducted for nearly two decades. We develop methods to analyze time-series genomics data and predict adaptive mechanisms. Here, we report a remarkable level of synchronicity in both hard and soft selective sweeps in replicate populations as well as the arrival of favorable de novo mutations that constitute a few asynchronized sweeps. We additionally make direct experimental observations of rare recombination events that combine multiple alleles on to a single, better-adapted haplotype. Based on the analyses of the genes in genomic intervals, we provide a deeper insight into the mechanisms of genome adaptation that allow complex organisms to survive harsh environments.

scholarly journals Donkey genome and insight into the imprinting of fast karyotype evolution

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Jinlong Huang ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Wunierfu Shiraigol ◽  
Bei Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Karyotype Evolution ◽  
De Novo ◽  
Cycle Phase ◽  
Satellite Sequences ◽  
Chromatid Segregation ◽  
Karyotypic Instability ◽  
Wild Ass ◽  
Genome Assemblies ◽  
Insight Into

Abstract The donkey, like the horse, is a promising model for exploring karyotypic instability. We report the de novo whole-genome assemblies of the donkey and the Asiatic wild ass. Our results reflect the distinct characteristics of donkeys, including more effective energy metabolism and better immunity than horses. The donkey shows a steady demographic trajectory. We detected abundant satellite sequences in some inactive centromere regions but not in neocentromere regions, while ribosomal RNAs frequently emerged in neocentromere regions but not in the obsolete centromere regions. Expanded miRNA families and five newly discovered miRNA target genes involved in meiosis may be associated with fast karyotype evolution. APC/C, controlling sister chromatid segregation, cytokinesis and the establishment of the G1 cell cycle phase were identified by analysis of miRNA targets and rapidly evolving genes.

scholarly journals De novo Genome Assembly of the indica Rice Variety IR64 Using Linked-Read Sequencing and Nanopore Sequencing

2020 ◽  
Vol 10 (5) ◽  
pp. 1495-1501 ◽  
Author(s):  
Tsuyoshi Tanaka ◽  
Ryo Nishijima ◽  
Shota Teramoto ◽  
Yuka Kitomi ◽  
Takeshi Hayashi ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Genome Assembly ◽  
De Novo ◽  
Rice Variety ◽  
Rice Genome ◽  
High Yield ◽  
Nanopore Sequencing ◽  
Long Reads ◽  
A Genome ◽  
Modern Varieties

IR64 is a rice variety with high-yield that has been widely cultivated around the world. IR64 has been replaced by modern varieties in most growing areas. Given that modern varieties are mostly progenies or relatives of IR64, genetic analysis of IR64 is valuable for rice functional genomics. However, chromosome-level genome sequences of IR64 have not been available previously. Here, we sequenced the IR64 genome using synthetic long reads obtained by linked-read sequencing and ultra-long reads obtained by nanopore sequencing. We integrated these data and generated the de novo assembly of the IR64 genome of 367 Mb, equivalent to 99% of the estimated size. Continuity of the IR64 genome assembly was improved compared with that of a publicly available IR64 genome assembly generated by short reads only. We annotated 41,458 protein-coding genes, including 657 IR64-specific genes, that are missing in other high-quality rice genome assemblies IRGSP-1.0 of japonica cultivar Nipponbare or R498 of indica cultivar Shuhui498. The IR64 genome assembly will serve as a genome resource for rice functional genomics as well as genomics-driven and/or molecular breeding.

scholarly journals Contrasting genome dynamics between domesticated and wild yeasts

2016 ◽  
Author(s):  
Jia-Xing Yue ◽  
Jing Li ◽  
Louise Aigrain ◽  
Johan Hallin ◽  
Karl Persson ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Accumulation Rate ◽  
Population Level ◽  
Structural Rearrangements ◽  
Chromosome Partitioning ◽  
Long Read ◽  
Definition Of ◽  
Genome Assemblies ◽  
Reference Genomes

AbstractStructural rearrangements have long been recognized as an important source of genetic variation with implications in phenotypic diversity and disease, yet their evolutionary dynamics are difficult to characterize with short-read sequencing. Here, we report long-read sequencing for 12 strains representing major subpopulations of the partially domesticated yeastSaccharomyces cerevisiaeand its wild relativeSaccharomyces paradoxus. Complete genome assemblies and annotations generate population-level reference genomes and allow for the first explicit definition of chromosome partitioning into cores, subtelomeres and chromosome-ends. High-resolution view of structural dynamics uncovers that, in chromosomal cores,S. paradoxusexhibits higher accumulation rate of balanced structural rearrangements (inversions, translocations and transpositions) whereasS. cerevisiaeaccumulates unbalanced rearrangements (large insertions, deletions and duplications) more rapidly. In subtelomeres, recurrent interchromosomal reshuffling was found in both species, with higher rate inS. cerevisiae. Such striking contrasts between wild and domesticated yeasts reveal the influence of human activities on structural genome evolution.

scholarly journals Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Caroline Belser ◽  
Franc-Christophe Baurens ◽  
Benjamin Noel ◽  
Guillaume Martin ◽  
Corinne Cruaud ◽  
...  
Keyword(s):  
Musa Acuminata ◽  
Genetic Maps ◽  
Nanopore Sequencing ◽  
Genome Coverage ◽  
Long Reads ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read ◽  
Genome Assemblies ◽  
First Time

AbstractLong-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes.

scholarly journals Contrasting evolutionary genome dynamics between domesticated and wild yeasts

2017 ◽  
Vol 49 (6) ◽  
pp. 913-924 ◽  
Author(s):  
Jia-Xing Yue ◽  
Jing Li ◽  
Louise Aigrain ◽  
Johan Hallin ◽  
Karl Persson ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Population Level ◽  
Structural Rearrangements ◽  
Reciprocal Translocations ◽  
Genome Dynamics ◽  
Long Read ◽  
Wild Yeasts ◽  
Definition Of ◽  
Genome Assemblies

Abstract Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.

scholarly journals Long-reads are revolutionizing 20 years of insect genome sequencing

2021 ◽  
Author(s):  
Scott Hotaling ◽  
John S. Sproul ◽  
Jacqueline Heckenhauer ◽  
Ashlyn Powell ◽  
Amanda M. Larracuente ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Nuclear Genome ◽  
Sequencing Technology ◽  
Assembly Quality ◽  
Insect Genome ◽  
Long Reads ◽  
Long Read ◽  
Field Perspective ◽  
Genome Assemblies ◽  
The Impact

The first insect genome (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 different insects representing 20 orders. Here, we analyzed the best assembly for each insect and provide a “state of the field” perspective, emphasizing taxonomic representation, assembly quality, gene completeness, and sequencing technology. We show that while genomic efforts have been biased towards specific groups (e.g., Diptera), assemblies are generally contiguous with gene regions intact. Most notable, however, has been the impact of long-read sequencing; assemblies that incorporate long-reads are ∼48x more contiguous than those that do not.

scholarly journals LongStitch: High-quality genome assembly correction and scaffolding using long reads

2021 ◽  
Author(s):  
Lauren Coombe ◽  
Janet X Li ◽  
Theodora Lo ◽  
Johnathan Wong ◽  
Vladimir Nikolic ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Model Organisms ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Long Reads ◽  
Long Read ◽  
Genomic Regions ◽  
Genome Assemblies

Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 2.0-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently runs in under five hours using less than 23GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.

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