A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

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Standard

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. / Wang, Chao; Wallerman, Ola; Arendt, Maja Louise; Sundström, Elisabeth; Karlsson, Åsa; Nordin, Jessika; Mäkeläinen, Suvi; Pielberg, Gerli Rosengren; Hanson, Jeanette; Ohlsson, Åsa; Saellström, Sara; Rönnberg, Henrik; Ljungvall, Ingrid; Häggström, Jens; Bergström, Tomas F.; Hedhammar, Åke; Meadows, Jennifer R.S.; Lindblad-Toh, Kerstin.

I: Communications Biology , Bind 4, 185, 2021.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Wang, C, Wallerman, O, Arendt, ML, Sundström, E, Karlsson, Å, Nordin, J, Mäkeläinen, S, Pielberg, GR, Hanson, J, Ohlsson, Å, Saellström, S, Rönnberg, H, Ljungvall, I, Häggström, J, Bergström, TF, Hedhammar, Å, Meadows, JRS & Lindblad-Toh, K 2021, 'A novel canine reference genome resolves genomic architecture and uncovers transcript complexity', Communications Biology , bind 4, 185. https://doi.org/10.1038/s42003-021-01698-x

APA

Wang, C., Wallerman, O., Arendt, M. L., Sundström, E., Karlsson, Å., Nordin, J., Mäkeläinen, S., Pielberg, G. R., Hanson, J., Ohlsson, Å., Saellström, S., Rönnberg, H., Ljungvall, I., Häggström, J., Bergström, T. F., Hedhammar, Å., Meadows, J. R. S., & Lindblad-Toh, K. (2021). A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Communications Biology , 4, [185]. https://doi.org/10.1038/s42003-021-01698-x

Vancouver

Wang C, Wallerman O, Arendt ML, Sundström E, Karlsson Å, Nordin J o.a. A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Communications Biology . 2021;4. 185. https://doi.org/10.1038/s42003-021-01698-x

Author

Wang, Chao ; Wallerman, Ola ; Arendt, Maja Louise ; Sundström, Elisabeth ; Karlsson, Åsa ; Nordin, Jessika ; Mäkeläinen, Suvi ; Pielberg, Gerli Rosengren ; Hanson, Jeanette ; Ohlsson, Åsa ; Saellström, Sara ; Rönnberg, Henrik ; Ljungvall, Ingrid ; Häggström, Jens ; Bergström, Tomas F. ; Hedhammar, Åke ; Meadows, Jennifer R.S. ; Lindblad-Toh, Kerstin. / A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. I: Communications Biology . 2021 ; Bind 4.

Bibtex

@article{1876aeb890114187a62050570cac9d10,
title = "A novel canine reference genome resolves genomic architecture and uncovers transcript complexity",
abstract = "We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.",
author = "Chao Wang and Ola Wallerman and Arendt, {Maja Louise} and Elisabeth Sundstr{\"o}m and {\AA}sa Karlsson and Jessika Nordin and Suvi M{\"a}kel{\"a}inen and Pielberg, {Gerli Rosengren} and Jeanette Hanson and {\AA}sa Ohlsson and Sara Saellstr{\"o}m and Henrik R{\"o}nnberg and Ingrid Ljungvall and Jens H{\"a}ggstr{\"o}m and Bergstr{\"o}m, {Tomas F.} and {\AA}ke Hedhammar and Meadows, {Jennifer R.S.} and Kerstin Lindblad-Toh",
year = "2021",
doi = "10.1038/s42003-021-01698-x",
language = "English",
volume = "4",
journal = "Communications Biology",
issn = "2399-3642",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

AU - Wang, Chao

AU - Wallerman, Ola

AU - Arendt, Maja Louise

AU - Sundström, Elisabeth

AU - Karlsson, Åsa

AU - Nordin, Jessika

AU - Mäkeläinen, Suvi

AU - Pielberg, Gerli Rosengren

AU - Hanson, Jeanette

AU - Ohlsson, Åsa

AU - Saellström, Sara

AU - Rönnberg, Henrik

AU - Ljungvall, Ingrid

AU - Häggström, Jens

AU - Bergström, Tomas F.

AU - Hedhammar, Åke

AU - Meadows, Jennifer R.S.

AU - Lindblad-Toh, Kerstin

PY - 2021

Y1 - 2021

N2 - We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.

AB - We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.

U2 - 10.1038/s42003-021-01698-x

DO - 10.1038/s42003-021-01698-x

M3 - Journal article

C2 - 33568770

AN - SCOPUS:85100970715

VL - 4

JO - Communications Biology

JF - Communications Biology

SN - 2399-3642

M1 - 185

ER -

ID: 257969715