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Authors = Steven Bilobram

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6 pages, 623 KiB  
Communication
De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries
by Daniel Berner, Marius Roesti, Steven Bilobram, Simon K. Chan, Heather Kirk, Pawan Pandoh, Gregory A. Taylor, Yongjun Zhao, Steven J. M. Jones and Jacquelin DeFaveri
Genes 2019, 10(6), 426; https://doi.org/10.3390/genes10060426 - 3 Jun 2019
Cited by 10 | Viewed by 4372
Abstract
The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the [...] Read more.
The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7). Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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7 pages, 930 KiB  
Article
The Genome of the Beluga Whale (Delphinapterus leucas)
by Steven J. M. Jones, Gregory A. Taylor, Simon Chan, René L. Warren, S. Austin Hammond, Steven Bilobram, Gideon Mordecai, Curtis A. Suttle, Kristina M. Miller, Angela Schulze, Amy M. Chan, Samantha J. Jones, Kane Tse, Irene Li, Dorothy Cheung, Karen L. Mungall, Caleb Choo, Adrian Ally, Noreen Dhalla, Angela K. Y. Tam, Armelle Troussard, Heather Kirk, Pawan Pandoh, Daniel Paulino, Robin J. N. Coope, Andrew J. Mungall, Richard Moore, Yongjun Zhao, Inanc Birol, Yussanne Ma, Marco Marra and Martin Haulenaadd Show full author list remove Hide full author list
Genes 2017, 8(12), 378; https://doi.org/10.3390/genes8120378 - 11 Dec 2017
Cited by 31 | Viewed by 18342
Abstract
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned [...] Read more.
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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6 pages, 757 KiB  
Article
The Genome of the Northern Sea Otter (Enhydra lutris kenyoni)
by Samantha J. Jones, Martin Haulena, Gregory A. Taylor, Simon Chan, Steven Bilobram, René L. Warren, S. Austin Hammond, Karen L. Mungall, Caleb Choo, Heather Kirk, Pawan Pandoh, Adrian Ally, Noreen Dhalla, Angela K. Y. Tam, Armelle Troussard, Daniel Paulino, Robin J. N. Coope, Andrew J. Mungall, Richard Moore, Yongjun Zhao, Inanc Birol, Yussanne Ma, Marco Marra and Steven J. M. Jonesadd Show full author list remove Hide full author list
Genes 2017, 8(12), 379; https://doi.org/10.3390/genes8120379 - 11 Dec 2017
Cited by 17 | Viewed by 12310
Abstract
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly [...] Read more.
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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