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101. Additional file 3: Figure S2. of De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Author

Carruthers, Madeleine, Yurchenko, Andrey, Augley, Julian, Adams, Colin, Herzyk, Pawel, and Elmer, Kathryn

Subjects
14. Life underwater
Abstract

Comparison of orthogroup size distribution between the current de novo assembly for Atlantic salmon, at each stage of filtering, relative to Atlantic salmon reference genome proteins (GCF_000233375.4). (PDF 57Â kb)

102. Additional file 4: Table S3. of De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Author

Carruthers, Madeleine, Yurchenko, Andrey, Augley, Julian, Adams, Colin, Herzyk, Pawel, and Elmer, Kathryn

Subjects
14. Life underwater
Abstract

Distribution of orthologs in the current Atlantic salmon de novo assembly compared to the distribution of orthologs in the NCBI Atlantic salmon RefSeq protein dataset (GCF_000233375.1). OrthoFinder results were filtered to retain only OrthoGroups with at least one RefSeq salmon protein present. (PDF 228Â kb)

106. Additional file 4: Table S3. of De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Author

Carruthers, Madeleine, Yurchenko, Andrey, Augley, Julian, Adams, Colin, Herzyk, Pawel, and Elmer, Kathryn

Subjects
14. Life underwater
Abstract

Distribution of orthologs in the current Atlantic salmon de novo assembly compared to the distribution of orthologs in the NCBI Atlantic salmon RefSeq protein dataset (GCF_000233375.1). OrthoFinder results were filtered to retain only OrthoGroups with at least one RefSeq salmon protein present. (PDF 228Â kb)

107. Additional file 3: Figure S2. of De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Author

Carruthers, Madeleine, Yurchenko, Andrey, Augley, Julian, Adams, Colin, Herzyk, Pawel, and Elmer, Kathryn

Subjects
14. Life underwater
Abstract

Comparison of orthogroup size distribution between the current de novo assembly for Atlantic salmon, at each stage of filtering, relative to Atlantic salmon reference genome proteins (GCF_000233375.4). (PDF 57Â kb)

108. Additional file 5: Figure S1. of De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Author

Carruthers, Madeleine, Yurchenko, Andrey, Augley, Julian, Adams, Colin, Herzyk, Pawel, and Elmer, Kathryn

Subjects
14. Life underwater
Abstract

Comparison of full-length transcript reconstruction between the four current assemblies and three previously published transcriptomes; Magnanou et al.â s Arctic charr assembly [34], and the PhyloFish DB brown trout and European whitefish assemblies [35]. Cumulative number of unique matching proteins that aligned to the NCBI protein database for Atlantic salmon (GCF_000233375.1) at a given coverage: Atlantic salmon (yellow), brown trout (green), Arctic charr (blue), European whitefish (red), Magnanou et al. Arctic charr transcriptome (black), PhyloFish brown trout (dark grey), and PhyloFish European whitefish (light grey). (PDF 35Â kb)

111. Additional file 5: Figure S1. of De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Author

Carruthers, Madeleine, Yurchenko, Andrey, Augley, Julian, Adams, Colin, Herzyk, Pawel, and Elmer, Kathryn

Subjects
14. Life underwater
Abstract

Comparison of full-length transcript reconstruction between the four current assemblies and three previously published transcriptomes; Magnanou et al.â s Arctic charr assembly [34], and the PhyloFish DB brown trout and European whitefish assemblies [35]. Cumulative number of unique matching proteins that aligned to the NCBI protein database for Atlantic salmon (GCF_000233375.1) at a given coverage: Atlantic salmon (yellow), brown trout (green), Arctic charr (blue), European whitefish (red), Magnanou et al. Arctic charr transcriptome (black), PhyloFish brown trout (dark grey), and PhyloFish European whitefish (light grey). (PDF 35Â kb)

113. Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations.

Author

Koepfli, Klaus-Peter, Tamazian, Gaik, Wildt, David, Dobrynin, Pavel, Changhoon Kim, Frandsen, Paul B., Godinho, Raquel, Yurchenko, Andrey A., Komissarov, Aleksey, Krasheninnikova, Ksenia, Kliver, Sergei, Kolchanova, Sofia, Gonçalves, Margarida, Carneiro, Miguel, Pinto, Pedro Vaz, Ferrand, Nuno, Maldonado, Jesús E., Ferrie, Gina M., Chemnick, Leona, and Ryder, Oliver A.

Subjects
*ANTELOPES, *NUCLEOTIDE sequencing, *WILDLIFE conservation, *ENDANGERED species, *BOVIDAE, *INBREEDING, *BIRD populations
Abstract

Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive (ex situ) and wild (in situ) populations of threatened species. The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is a species that is being managed ex situ in both public (zoo) and private (ranch) collections in the United States. Our objective was to develop whole genome sequence resources that will serve as a foundation for characterizing the genetic status of ex situ populations of sable antelope relative to populations in the wild. Here we report the draft genome assembly of a male sable antelope, a member of the subfamily Hippotraginae (Bovidae, Cetartiodactyla, Mammalia). The 2.596 Gb draft genome consists of 136,528 contigs with an N50 of 45.5 Kbp and 16,927 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 18,828 protein-coding genes and repetitive sequences encompassing 46.97% of the genome. The discovery of single nucleotide variants (SNVs) was assisted by the re-sequencing of seven additional captive and wild individuals, representing two different subspecies, leading to the identification of 1,987,710 bi-allelic SNVs. Assembly of the mitochondrial genomes revealed that each individual was defined by a unique haplotype and these data were used to infer the mitochondrial gene tree relative to other hippotragine species. The sable antelope genome constitutes a valuable resource for assessing genome-wide diversity and evolutionary potential, thereby facilitating long-term conservation of this charismatic species. [ABSTRACT FROM AUTHOR]

Published
2019
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