A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)

Bernhard F. Benkel; Amanda Smith; Knud Christensen; Razvan Marian Anistoroaei; Ye Zhang; Christoph W. Sensen; Hossain Farid; Lyn Paterson; Ronald M. Teather

doi:10.1007/s13258-011-0160-8

A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)

Bernhard F. Benkel, Amanda Smith, Knud Christensen, Razvan Marian Anistoroaei, Ye Zhang, Christoph W. Sensen, Hossain Farid, Lyn Paterson, Ronald M. Teather

4 Citationer (Scopus)

Abstract

In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000th of the mink genome, suggests that simple sequence repeats (SSRs) are less common in the mink than in the human genome, whereas the average GC content of the mink genome is slightly higher than that of its human counterpart. The 2.7 Mb mink genomic dataset also contained 2,416 repeat elements (retroids and DNA transposons) occupying almost 31% of the sequence space. Among repeat elements, LINEs were over-represented and endogenous viruses (aka LTRs) under-represented in comparison to the human genome. Finally, we present a virtual map of the mink genome constructed with reference to the human and canine genome assemblies using a comparative genomics approach and incorporating over 200 mink BESs with unique hits to the human genome.

Originalsprog	Engelsk
Tidsskrift	Genes and Genomics
Vol/bind	34
Udgave nummer	1
Sider (fra-til)	83-91
Antal sider	9
ISSN	1976-9571
DOI	https://doi.org/10.1007/s13258-011-0160-8
Status	Udgivet - feb. 2012

Emneord

Det tidligere LIFE
American mink
BAC end sequencing
Comparatve mapping
Structural genomics

Adgang til dokumentet

10.1007/s13258-011-0160-8

Citationsformater

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title = "A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)",

abstract = "In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000th of the mink genome, suggests that simple sequence repeats (SSRs) are less common in the mink than in the human genome, whereas the average GC content of the mink genome is slightly higher than that of its human counterpart. The 2.7 Mb mink genomic dataset also contained 2,416 repeat elements (retroids and DNA transposons) occupying almost 31% of the sequence space. Among repeat elements, LINEs were over-represented and endogenous viruses (aka LTRs) under-represented in comparison to the human genome. Finally, we present a virtual map of the mink genome constructed with reference to the human and canine genome assemblies using a comparative genomics approach and incorporating over 200 mink BESs with unique hits to the human genome. ",

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T1 - A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)

AU - Benkel, Bernhard F.

AU - Smith, Amanda

AU - Christensen, Knud

AU - Anistoroaei, Razvan Marian

AU - Zhang, Ye

AU - Sensen, Christoph W.

AU - Farid, Hossain

AU - Paterson, Lyn

AU - Teather, Ronald M.

PY - 2012/2

Y1 - 2012/2

N2 - In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000th of the mink genome, suggests that simple sequence repeats (SSRs) are less common in the mink than in the human genome, whereas the average GC content of the mink genome is slightly higher than that of its human counterpart. The 2.7 Mb mink genomic dataset also contained 2,416 repeat elements (retroids and DNA transposons) occupying almost 31% of the sequence space. Among repeat elements, LINEs were over-represented and endogenous viruses (aka LTRs) under-represented in comparison to the human genome. Finally, we present a virtual map of the mink genome constructed with reference to the human and canine genome assemblies using a comparative genomics approach and incorporating over 200 mink BESs with unique hits to the human genome.

AB - In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000th of the mink genome, suggests that simple sequence repeats (SSRs) are less common in the mink than in the human genome, whereas the average GC content of the mink genome is slightly higher than that of its human counterpart. The 2.7 Mb mink genomic dataset also contained 2,416 repeat elements (retroids and DNA transposons) occupying almost 31% of the sequence space. Among repeat elements, LINEs were over-represented and endogenous viruses (aka LTRs) under-represented in comparison to the human genome. Finally, we present a virtual map of the mink genome constructed with reference to the human and canine genome assemblies using a comparative genomics approach and incorporating over 200 mink BESs with unique hits to the human genome.

KW - Former LIFE faculty

KW - American mink

KW - BAC end sequencing

KW - Comparatve mapping

KW - Structural genomics

U2 - 10.1007/s13258-011-0160-8

DO - 10.1007/s13258-011-0160-8

M3 - Journal article

SN - 1976-9571

VL - 34

SP - 83

EP - 91

JO - Genes and Genomics

JF - Genes and Genomics

IS - 1

ER -