scholarly journals Homology-Dependent Silencing by an Exogenous Sequence in theDrosophilaGermline

2012 ◽  
Vol 2 (3) ◽  
pp. 331-338 ◽  
Author(s):  
Maria Pöyhönen ◽  
Augustin de Vanssay ◽  
Valérie Delmarre ◽  
Catherine Hermant ◽  
Anne Laure Todeschini ◽  
...  
Keyword(s):  
Exogenous Sequence

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2017 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A. Dolby ◽  
Melissa Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2018 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A Dolby ◽  
Melissa A Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 kb, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2018 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A Dolby ◽  
Melissa A Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 kb, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2017 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A. Dolby ◽  
Melissa Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Heritable endogenization of an RNA virus in a mammalian species

2020 ◽  
Author(s):  
Atsuo Iida ◽  
Ronald Tarigan ◽  
Hiroshi Shimoda ◽  
Kanako Endo ◽  
Masaya Furuta ◽  
...  
Keyword(s):  
Driving Forces ◽  
Rna Virus ◽  
Mammalian Species ◽  
Reverse Transcriptase Activity ◽  
Encephalomyocarditis Virus ◽  
Laboratory Mice ◽  
Germline Transmission ◽  
Exogenous Sequence ◽  
The Impact ◽  
Borna Disease

AbstractViruses are considered one of the driving forces for genome rearrangements via infection and endogenization into the host genome (Kazazian, 2004; Maksakova et al., 2006). In 2010, Horie and colleagues demonstrated that a non-retroviral RNA virus, Borna disease virus (BDV), could integrate into the genome in cultured somatic cells (Horie et al., 2010). However, germline transmission of viral-derived sequences using animal models is yet to be experimentally demonstrated. In this study, we reported a case of heritable endogenization using the encephalomyocarditis virus (EMCV) and laboratory mice. The EMCV is a small non-enveloped single-strand RNA virus without its own reverse transcriptase activity (Carocci et al., 2012). Here, we demonstrated that the EMCV genomic RNA was reverse transcribed into DNA fragments in the murine testes. The DNA sequence originated from the RNA genome of EMCV was also detected in the liver and earlobes of the offspring generated from the EMCV-infected father. This suggests that the exogenous sequence derived from the EMCV is transmitted into the host germline and inherited across subsequent generations. This first experimental demonstration of viral endogenization proposes reconsideration about the impact of viruses as a driving force for genome modification.

scholarly journals A Mouse Mammary Tumor Virus env-Like Exogenous Sequence Is Strictly Related to Progression of Human Sporadic Breast Carcinoma

2011 ◽  
Vol 179 (4) ◽  
pp. 2083-2090 ◽  
Author(s):  
Chiara Maria Mazzanti ◽  
Mohammad Al Hamad ◽  
Giovanni Fanelli ◽  
Cristian Scatena ◽  
Francesca Zammarchi ◽  
...  
Keyword(s):  
Breast Carcinoma ◽  
Mammary Tumor ◽  
Mouse Mammary Tumor Virus ◽  
Mammary Tumor Virus ◽  
Mouse Mammary Tumor ◽  
Sporadic Breast Carcinoma ◽  
Tumor Virus ◽  
Exogenous Sequence

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2017 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A. Dolby ◽  
Melissa Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals VAECGAN: a generating framework for long-term prediction in multivariate time series

Cybersecurity ◽  
2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xiang Yin ◽  
Yanni Han ◽  
Zhen Xu ◽  
Jie Liu
Keyword(s):  
Empirical Studies ◽  
Multivariate Time Series ◽  
Difficult Problem ◽  
Data Generation ◽  
Generative Adversarial Network ◽  
Term Prediction ◽  
Exogenous Sequence ◽  
Real World Datasets ◽  
Long Term Prediction

AbstractLong-term prediction is still a difficult problem in data mining. People usually use various kinds of methods of Recurrent Neural Network to predict. However, with the increase of the prediction step, the accuracy of prediction decreases rapidly. In order to improve the accuracy of long-term prediction,we propose a framework Variational Auto-Encoder Conditional Generative Adversarial Network(VAECGAN). Our model is divided into three parts. The first part is the encoder net, which can encode the exogenous sequence into latent space vectors and fully save the information carried by the exogenous sequence. The second part is the generator net which is responsible for generating prediction data. In the third part, the discriminator net is used to classify and feedback, adjust data generation and improve prediction accuracy. Finally, extensive empirical studies tested with five real-world datasets (NASDAQ, SML, Energy, EEG,KDDCUP)demonstrate the effectiveness and robustness of our proposed approach.

scholarly journals CRISPR/Cas-9 mediated knock-in by homology dependent repair in the West Nile Virus vector Culex quinquefasciatus Say

2021 ◽  
Author(s):  
Deepak-Kumar Purusothaman ◽  
Lewis Shackleford ◽  
Michelle A. E. Anderson ◽  
Tim Harvey-Samuel ◽  
Luke Alphey
Keyword(s):  
West Nile Virus ◽  
Culex Quinquefasciatus ◽  
Fluorescent Protein ◽  
Mosquito Species ◽  
Marker Gene ◽  
Transformation Rate ◽  
West Nile ◽  
Gene Encoding ◽  
Exogenous Sequence ◽  
Species Specific

AbstractCulex quinquefasciatus Say is a brown, medium sized mosquito distributed widely in both tropical and subtropical regions of the world. It is a night-active, opportunistic blood-feeder and is responsible for vectoring many animal and human diseases, including West Nile Virus and avian malaria. Current vector control methods (e.g. physical / chemical) are increasingly ineffective; use of insecticides also imposes some hazards to both human and ecosystem health. Recent advances in genome editing have allowed the development of genetic methods of insect control, which is species-specific and, theoretically, highly effective. CRISPR/Cas9 is a bacteria-derived programmable gene editing tool that has been shown to be functional in a range of species. We demonstrate here, the first successful germline gene knock-in by homology dependent repair in C. quinquefasciatus. Using CRISPR/Cas9, we integrated exogenous sequence comprising a sgRNA expression cassette and marker gene encoding a fluorescent protein fluorophore (Hr5/IE1-DsRed, Cq7SK-sgRNA) into the kynurenine 3-monooxygenase (kmo) gene. We achieved a minimum transformation rate of 2.8% similar to rates achieved in other mosquito species. Precise knock-in at the intended locus was confirmed by sequencing. Insertion homozygotes displayed a white eye phenotype in early-mid stage larvae and a recessive lethal phenotype by pupation. This work shows an alternative and efficient method for genetic engineering of C. quinquefasciatus, providing a new tool for researchers interested in developing genetic control tools for this vector.

Sign in / Sign up

Export Citation Format

Share Document