A human-horse comparative map based on equine BAC end sequences

Tosso Leeb; Claus Vogl; Baoli Zhu; Pieter J. de Jong; Matthew M. Binns; Bhanu P. Chowdhary; Maren Scharfe; Michael Jarek; Gabriele Nordsiek; Frank Schrader; Helmut Blöcker

doi:10.1016/j.ygeno.2006.03.002

A human-horse comparative map based on equine BAC end sequences

Tosso Leeb, Claus Vogl, Baoli Zhu, Pieter J. de Jong, Matthew M. Binns, Bhanu P. Chowdhary, Maren Scharfe, Michael Jarek, Gabriele Nordsiek, Frank Schrader, Helmut Blöcker

Research output: Contribution to journal › Article › peer-review

50 Citations (Scopus)

Abstract

In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E ≤ 10^-5) in the human genome that provide useful markers for the human-horse comparative map. The 4036 BLASTN hits allowed the anchoring of 3079 BAC clones to the human genome, on average one corresponding equine BAC clone per megabase of human DNA. We used the BLASTN anchored BESs for an in silico prediction of the gene content and chromosome assignment of comparatively mapped equine BAC clones. As a first verification of our in silico mapping strategy we placed 19 equine BESs with matches to HSA6 onto the RH map. All markers were assigned to the predicted localizations on ECA10, ECA20, and ECA31, respectively.

Original language	English
Pages (from-to)	772-776
Number of pages	5
Journal	Genomics
Volume	87
Issue number	6
DOIs	https://doi.org/10.1016/j.ygeno.2006.03.002
Publication status	Published - Jun 2006
Externally published	Yes

Keywords

BES
BLASTN
Comparative map
Database
Horse
Physical map
RH map

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2006.03.002

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title = "A human-horse comparative map based on equine BAC end sequences",

abstract = "In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E ≤ 10-5) in the human genome that provide useful markers for the human-horse comparative map. The 4036 BLASTN hits allowed the anchoring of 3079 BAC clones to the human genome, on average one corresponding equine BAC clone per megabase of human DNA. We used the BLASTN anchored BESs for an in silico prediction of the gene content and chromosome assignment of comparatively mapped equine BAC clones. As a first verification of our in silico mapping strategy we placed 19 equine BESs with matches to HSA6 onto the RH map. All markers were assigned to the predicted localizations on ECA10, ECA20, and ECA31, respectively.",

keywords = "BES, BLASTN, Comparative map, Database, Horse, Physical map, RH map",

author = "Tosso Leeb and Claus Vogl and Baoli Zhu and {de Jong}, {Pieter J.} and Binns, {Matthew M.} and Chowdhary, {Bhanu P.} and Maren Scharfe and Michael Jarek and Gabriele Nordsiek and Frank Schrader and Helmut Bl{\"o}cker",

note = "Funding Information: We thank J. Kanter, H. Klippert-Hasberg, D. Seinige, T. Unger, C. Berg, A. Conrad, T.-H. L{\"o}hnert, S. Severitt, C. Schindewolf, and S. Thies for expert technical assistance. Technical advice from B.W. Plumb (Sanger Institute, UK) is gratefully acknowledged. This study was supported by a grant from the German Research Council (DFG LE1032/20-1). ",

year = "2006",

month = jun,

doi = "10.1016/j.ygeno.2006.03.002",

language = "English",

volume = "87",

pages = "772--776",

journal = "Genomics",

issn = "0888-7543",

publisher = "Academic Press Inc.",

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T1 - A human-horse comparative map based on equine BAC end sequences

AU - Leeb, Tosso

AU - Vogl, Claus

AU - Zhu, Baoli

AU - de Jong, Pieter J.

AU - Binns, Matthew M.

AU - Chowdhary, Bhanu P.

AU - Scharfe, Maren

AU - Jarek, Michael

AU - Nordsiek, Gabriele

AU - Schrader, Frank

AU - Blöcker, Helmut

N1 - Funding Information: We thank J. Kanter, H. Klippert-Hasberg, D. Seinige, T. Unger, C. Berg, A. Conrad, T.-H. Löhnert, S. Severitt, C. Schindewolf, and S. Thies for expert technical assistance. Technical advice from B.W. Plumb (Sanger Institute, UK) is gratefully acknowledged. This study was supported by a grant from the German Research Council (DFG LE1032/20-1).

PY - 2006/6

Y1 - 2006/6

N2 - In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E ≤ 10-5) in the human genome that provide useful markers for the human-horse comparative map. The 4036 BLASTN hits allowed the anchoring of 3079 BAC clones to the human genome, on average one corresponding equine BAC clone per megabase of human DNA. We used the BLASTN anchored BESs for an in silico prediction of the gene content and chromosome assignment of comparatively mapped equine BAC clones. As a first verification of our in silico mapping strategy we placed 19 equine BESs with matches to HSA6 onto the RH map. All markers were assigned to the predicted localizations on ECA10, ECA20, and ECA31, respectively.

AB - In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E ≤ 10-5) in the human genome that provide useful markers for the human-horse comparative map. The 4036 BLASTN hits allowed the anchoring of 3079 BAC clones to the human genome, on average one corresponding equine BAC clone per megabase of human DNA. We used the BLASTN anchored BESs for an in silico prediction of the gene content and chromosome assignment of comparatively mapped equine BAC clones. As a first verification of our in silico mapping strategy we placed 19 equine BESs with matches to HSA6 onto the RH map. All markers were assigned to the predicted localizations on ECA10, ECA20, and ECA31, respectively.

KW - BES

KW - BLASTN

KW - Comparative map

KW - Database

KW - Horse

KW - Physical map

KW - RH map

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ER -

A human-horse comparative map based on equine BAC end sequences

Abstract

Keywords

ASJC Scopus subject areas

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