scholarly journals Extensive horizontal exchange of transposable elements in the Drosophila pseudoobscura group

2018 ◽  
Author(s):  
Tom Hill ◽  
Andrea J. Betancourt
Keyword(s):  
Horizontal Transfer ◽  
Species Group ◽  
Data Availability ◽  
Drosophila Pseudoobscura ◽  
Chromosome Size ◽  
Short Read ◽  
Short Read Archive ◽  
Ncbi Short Read Archive ◽  
Mobile Component ◽  
Different Levels

AbstractWhile the horizontal transfer of a parasitic element can be a potentially catastrophic, it is increasingly recognized as a common occurrence. The horizontal exchange, or lack of exchange, of TE content between species results in different levels of divergence among a species group in the mobile component of their genomes. Here, we examine differences in the TE content of the Drosophila pseudoobscura species group. We identify several putative horizontal transfer events, and examine the role that horizontal transfer plays in the spread of TE families to new species and the homogenization of TE content in these species. Despite rampant exchange of TE families between species, we find that both TE content differs hugely across the group, likely due to differing activity of each TE family and differing suppression of TEs due to divergence in Y chromosome size, and its resulting effects of TE regulation. Overall, we show that TE content is highly dynamic in this species group, and that it plays a large role in shaping the differences seen between species.Data availabilityAll data used in this study (summarized in table S1) is freely available online through the NCBI short read archive (NCBI SRA: ERR127385, SRR330416, SRR330418, SRR1925723, SRR330426, SRR330420, SRR330423, SRR617430-74). All genomes used are either available through flybase.org or popoolation.at.

scholarly journals Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2644 ◽  
Author(s):  
William P. Gilks ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Matthew T. Webster ◽  
Edward H. Morrow
Keyword(s):  
Drosophila Melanogaster ◽  
Complex Traits ◽  
Population Sample ◽  
Genomic Variation ◽  
Genotype Data ◽  
Whole Genome ◽  
Unique Haplotype ◽  
Short Read ◽  
Short Read Archive ◽  
Ncbi Short Read Archive

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics (https://zenodo.org/communities/sussex_drosophila_sequencing/).

scholarly journals Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2644 ◽  
Author(s):  
William P. Gilks ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Matthew T. Webster ◽  
Edward H. Morrow
Keyword(s):  
Drosophila Melanogaster ◽  
Complex Traits ◽  
High Throughput Sequencing ◽  
Population Sample ◽  
Genomic Variation ◽  
Genotype Data ◽  
Whole Genome ◽  
Short Read ◽  
Short Read Archive ◽  
Ncbi Short Read Archive

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics (https://zenodo.org/communities/sussex_drosophila_sequencing/).

scholarly journals Whole genome resequencing of a laboratory-adapted Drosophila melanogaster

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2644
Author(s):  
William P. Gilks ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Matthew T. Webster ◽  
Edward H. Morrow
Keyword(s):  
Drosophila Melanogaster ◽  
Complex Traits ◽  
High Throughput Sequencing ◽  
Genomic Variation ◽  
Genotype Data ◽  
Whole Genome ◽  
Unique Haplotype ◽  
Short Read ◽  
Short Read Archive ◽  
Ncbi Short Read Archive

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics (https://zenodo.org/communities/sussex_drosophila_sequencing/).

scholarly journals The complete genome sequences of two species of seventeen-year cicadas: Magicicada septendecim and Magicicada septendecula

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 215
Author(s):  
Harold B. White ◽  
Stacy Pirro
Keyword(s):  
North America ◽  
Related Species ◽  
De Novo ◽  
Eastern North America ◽  
Whole Genome ◽  
Genome Sequences ◽  
Short Read ◽  
Short Read Archive ◽  
Periodical Cicadas ◽  
Ncbi Short Read Archive

The genus Magicicada (Hemiptera: Cicadidae) includes the periodical cicadas of Eastern North America. Spending the majority of their long lives underground, the adult cicadas emerge every 13 or 17 years to spend 4-6 weeks as adult to mate. We present the whole genome sequences of two species of 17-year cicadas, Magicicada septendecim and Magicicada septendecula. The reads were assembled by a de novo method followed by alignments to related species. Annotation was performed by GeneMark-ES. The raw and assembled data is available via NCBI Short Read Archive and Assembly databases.

scholarly journals Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

2016 ◽  
Author(s):  
William P. Gilks ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Matthew T. Webster ◽  
Edward H. Morrow
Keyword(s):  
Drosophila Melanogaster ◽  
Complex Traits ◽  
Population Sample ◽  
Genomic Variation ◽  
Reference Line ◽  
Genotype Data ◽  
Whole Genome ◽  
Short Read ◽  
Short Read Archive ◽  
Ncbi Short Read Archive

AbstractAs part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 2 females from the Berkeley reference line (BDGP6/dm6), and 220 hemiclonal females that were heterozygous for the same reference line genome, and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (BioProject PRJNA282591). Haplotype Caller discovered and genotyped 1,726,931 genetic variants (SNPs and indels, <200bp). Additionally, we used GenomeStrip/2.0 to discover and genotype 167 large structural variants (1-100Kb in size). Sequence data and quality-filtered genotype data are publicly-available at NCBI (Short Read Archive, dbSNP and dbVar). We have also released the unfiltered genotype data, and the code and logs for data processing, summary statistics, and graphs, via the research data repository, Zenodo, (https://zenodo.org/, ’Sussex Drosophila Sequencing’ community).

scholarly journals Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO

2019 ◽  
Author(s):  
Alexander H. Wilcox ◽  
Eric Delwart ◽  
Samuel L. Díaz Muñoz
Keyword(s):  
Next Generation Sequencing ◽  
Limit Of Detection ◽  
Genetic Material ◽  
Dsrna Virus ◽  
Next Generation ◽  
Short Read ◽  
Double Stranded Rna ◽  
Ncbi Short Read Archive ◽  
Dmso Treatment ◽  
Generation Sequencing

AbstractDouble stranded RNA (dsRNA) is the genetic material of important viruses and a key component of RNA interference-based immunity in eukaryotes. Previous studies have noted difficulties in determining the sequence of dsRNA molecules that have affected studies of immune function and estimates of viral diversity in nature. Dimethyl sulfoxide (DMSO) has been used to denature dsRNA prior to the reverse transcription stage to improve RT-PCR and Sanger sequencing. We systematically tested the utility of DMSO to improve sequencing yield of a dsRNA virus (Φ6) in a short-read next generation sequencing platform. DMSO treatment improved sequencing read recovery by over two orders of magnitude, even when RNA and cDNA concentrations were below the limit of detection. We also tested the effects of DMSO on a mock eukaryotic viral community and found that dsRNA virus reads increased with DMSO treatment. Furthermore, we provide evidence that DMSO treatment does not adversely affect recovery of reads from a single-stranded RNA viral genome (Influenza A/California/07/2009). We suggest that up to 50% DMSO treatment be used prior to cDNA synthesis when samples of interest are composed of or may contain dsRNA.Data SummarySequence data was deposited in the NCBI Short Read Archive (accession numbers: PRJNA527100, PRJNA527101, PRJNA527098). Data and code for analysis is available on GitHub (https://github.com/awilcox83/dsRNA-sequencing/, doi:10.5281/zenodo.1453423). Protocol for dsRNA sequencing is posted on protocols.io (doi:10.17504/protocols.io.ugnetve).

scholarly journals An Improved Genome Assembly of Azadirachta indica A. Juss.

2015 ◽  
Author(s):  
Neeraja M Krishnan ◽  
Prachi Jain ◽  
Saurabh Gupta ◽  
Arun K Hariharan ◽  
Binay Panda
Keyword(s):  
Azadirachta Indica ◽  
Genome Assembly ◽  
Draft Genome ◽  
Fold Increase ◽  
Sequencing Data ◽  
Short Read ◽  
Short Reads ◽  
Short Read Sequencing ◽  
Long Reads ◽  
Ncbi Short Read Archive

Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of the plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additional short reads from Illumina and long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error corrected long reads using Platanus, an assembler designed to perform well for heterozygous genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the percentage repeat, over the earlier assembly (v1.0). The current assembly also maps better to the genes known to be involved in the terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. indica genome. The raw data described in this manuscript are submitted to the NCBI Short Read Archive under the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 (SRP013453).

scholarly journals Nucleotide Sequence of the Adh Gene Region of Drosophila pseudoobscura: Evolutionary Change and Evidence for an Ancient Gene Duplication

Genetics ◽  
1987 ◽  
Vol 117 (1) ◽  
pp. 61-73
Author(s):  
Stephen W Schaeffer ◽  
Charles F Aquadro
Keyword(s):  
Amino Acid ◽  
Species Group ◽  
Drosophila Pseudoobscura ◽  
Protein Coding ◽  
The Third ◽  
Adh Gene ◽  
Nad Oxidoreductase ◽  
Nucleotide Divergence ◽  
Ancient Gene Duplication ◽  
Silent Substitutions

ABSTRACT The alcohol dehydrogenase (Adh) locus (ADH; alcohol: NAD+ oxidoreductase, EC 1.1.1.1) of Drosophila pseudoobscura was cloned and sequenced. Forty-five percent of the "effectively silent sites" have changed between Adh in D. pseudoobscura of the obscura species group and the homologous DNA sequence in D. mauritiana, the latter representing the melanogaster species group. The untranslated leader sequence of the adult transcript of D. pseudoobscura has two deletions relative to the D. mauritiana message. The ADH protein sequences of D. pseudoobscura is missing the third and fourth amino acids at the N-terminus relative to the D. mauritiana enzyme. Of the remaining 254 amino acid positions, 27 (10.64%) differ between the two species. Amino acid replacements are randomly distributed into hydrophilic and hydrophobic domains of ADH. However, replacement substitutions are distributed nonrandomly across the three exons among D. pseudoobscura and members of the melanogaster subgroup, suggesting that functional constraints across the exons are different. Surprisingly, silent substitutions are also nonrandomly distributed with the third exon being the most divergent. This pattern suggests possible selective constraints on supposedly neutral silent substitutions and/or variation in underlying mutation rates across the gene. The presence of transcriptional and translational signals at the beginning and end of conserved sequences 3′ to Adh implies the existence of a previously undescribed gene. Codon usage and patterns of nucleotide divergence are consistent with a protein coding function for this gene. In addition, conservation of nucleotide and amino acid sequence and similarity in hydropathy plots suggests that the gene 3′ to Adh represents an ancient duplication of the Adh gene.

Assessing Physical Climate Risks for the European Bank for Reconstruction and Development's Power Generation Project Investment Portfolio

2021 ◽  
Author(s):  
Tianyi Luo ◽  
Lihuan Zhou ◽  
James Falzon ◽  
Yan Cheng ◽  
Giulia Christianson ◽  
...  
Keyword(s):  
Power Generation ◽  
Recurrent Neural Networks ◽  
Data Availability ◽  
Machine Learning Techniques ◽  
Investment Portfolio ◽  
Project Investment ◽  
Climate Risks ◽  
European Bank ◽  
Learning Techniques ◽  
Different Levels

This paper introduces a new method to quantify physical climate risks for power generation projects at the portfolio level. Co-developed by WRI and the European Bank for Reconstruction and Development (EBRD), the approach is designed to be flexible enough to work with portfolios with different levels of data availability, leverage the latest science in climate and hydrology, and use machine-learning techniques such as recurrent neural networks.

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