The Experts below are selected from a list of 11634 Experts worldwide ranked by ideXlab platform

Edward S Rice - One of the best experts on this subject based on the ideXlab platform.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    BMC Genomics, 2021
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    bioRxiv, 2020
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background: Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits make understanding their genome structure relative to more modern Dog Breeds of great interest. Here, we report the de novo assemblies of two Basenji: a female, China, and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). We then align representative whole genome sequences from 58 Dog Breeds and show the importance of genome reference when assessing variation among Dog Breeds. Results: Here we present two high quality Basenji genome assemblies, CanFam_Bas (China) and Wags. CanFam_Bas is superior to CanFam v3,1 is terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Further, we generate a conservative list of structural variant calls using a consensus of both Pacific Bioscience and Oxford Nanopore long reads to identify large structural breed differences. Collectively this work highlights the importance the choice of reference genome makes in canid variation studies. Conclusions: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, as is increasingly being employed in other model organisms, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach.

Olga Dudchenko - One of the best experts on this subject based on the ideXlab platform.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    BMC Genomics, 2021
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    bioRxiv, 2020
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background: Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits make understanding their genome structure relative to more modern Dog Breeds of great interest. Here, we report the de novo assemblies of two Basenji: a female, China, and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). We then align representative whole genome sequences from 58 Dog Breeds and show the importance of genome reference when assessing variation among Dog Breeds. Results: Here we present two high quality Basenji genome assemblies, CanFam_Bas (China) and Wags. CanFam_Bas is superior to CanFam v3,1 is terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Further, we generate a conservative list of structural variant calls using a consensus of both Pacific Bioscience and Oxford Nanopore long reads to identify large structural breed differences. Collectively this work highlights the importance the choice of reference genome makes in canid variation studies. Conclusions: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, as is increasingly being employed in other model organisms, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach.

Matthew A Field - One of the best experts on this subject based on the ideXlab platform.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    BMC Genomics, 2021
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    bioRxiv, 2020
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background: Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits make understanding their genome structure relative to more modern Dog Breeds of great interest. Here, we report the de novo assemblies of two Basenji: a female, China, and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). We then align representative whole genome sequences from 58 Dog Breeds and show the importance of genome reference when assessing variation among Dog Breeds. Results: Here we present two high quality Basenji genome assemblies, CanFam_Bas (China) and Wags. CanFam_Bas is superior to CanFam v3,1 is terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Further, we generate a conservative list of structural variant calls using a consensus of both Pacific Bioscience and Oxford Nanopore long reads to identify large structural breed differences. Collectively this work highlights the importance the choice of reference genome makes in canid variation studies. Conclusions: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, as is increasingly being employed in other model organisms, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach.

Richard J Edwards - One of the best experts on this subject based on the ideXlab platform.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    BMC Genomics, 2021
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    bioRxiv, 2020
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background: Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits make understanding their genome structure relative to more modern Dog Breeds of great interest. Here, we report the de novo assemblies of two Basenji: a female, China, and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). We then align representative whole genome sequences from 58 Dog Breeds and show the importance of genome reference when assessing variation among Dog Breeds. Results: Here we present two high quality Basenji genome assemblies, CanFam_Bas (China) and Wags. CanFam_Bas is superior to CanFam v3,1 is terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Further, we generate a conservative list of structural variant calls using a consensus of both Pacific Bioscience and Oxford Nanopore long reads to identify large structural breed differences. Collectively this work highlights the importance the choice of reference genome makes in canid variation studies. Conclusions: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, as is increasingly being employed in other model organisms, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach.

Gary S Johnson - One of the best experts on this subject based on the ideXlab platform.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    BMC Genomics, 2021
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

  • chromosome length genome assembly and structural variations of the primal basenji Dog canis lupus familiaris genome
    bioRxiv, 2020
    Co-Authors: Richard J Edwards, Gary S Johnson, Matthew A Field, James M Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D Rosen, Edward S Rice
    Abstract:

    Background: Basenjis are considered an ancient Dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless Dog, Basenjis possess unique phylogeny, geographical origins and traits make understanding their genome structure relative to more modern Dog Breeds of great interest. Here, we report the de novo assemblies of two Basenji: a female, China, and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three Dog Breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). We then align representative whole genome sequences from 58 Dog Breeds and show the importance of genome reference when assessing variation among Dog Breeds. Results: Here we present two high quality Basenji genome assemblies, CanFam_Bas (China) and Wags. CanFam_Bas is superior to CanFam v3,1 is terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. By aligning short read data from 58 representative Dog Breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Further, we generate a conservative list of structural variant calls using a consensus of both Pacific Bioscience and Oxford Nanopore long reads to identify large structural breed differences. Collectively this work highlights the importance the choice of reference genome makes in canid variation studies. Conclusions: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific Dog Breeds. However, as is increasingly being employed in other model organisms, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach.

  • genetic structure of the purebred domestic Dog
    Science, 2004
    Co-Authors: Heidi G Parker, Gary S Johnson, Lisa V Kim, Nathan B Sutter, Scott M Carlson, Travis D Lorentzen, Tiffany B Malek, Hawkins B Defrance
    Abstract:

    We used molecular markers to study genetic relationships in a diverse collection of 85 domestic Dog Breeds. Differences among Breeds accounted for approximately 30% of genetic variation. Microsatellite genotypes were used to correctly assign 99% of individual Dogs to Breeds. Phylogenetic analysis separated several Breeds with ancient origins from the remaining Breeds with modern European origins. We identified four genetic clusters, which predominantly contained Breeds with similar geographic origin, morphology, or role in human activities. These results provide a genetic classification of Dog Breeds and will aid studies of the genetics of phenotypic breed differences.