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

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

doi:10.1016/j.ygeno.2006.03.002

Cited by 52 publications

(39 citation statements)

References 18 publications

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“…whole genome sequence for the horse, projecting it to be ϳ 2700 Mb in size, i.e., ϳ 13% smaller than the human genome (size: ϳ 3100 Mb; Build 36.1). Similar observations were recently reported in horses (Leeb et al, 2006). Sequence data is presently available for the chimpanzee (PTR), dog (CFA), cattle (BTA), mouse (MMU), rat (RNO), opossum (MDO), and chicken (GGA) genomes and size estimates can be obtained for the region corresponding to the contig in these species.…”

Section: Comparative Size Of the Contig Across Speciessupporting

confidence: 81%

A BAC contig map over the proximal ∼3.3 Mb region of horse chromosome 21

Brinkmeyer-Langford

Raudsepp²,

Gustafson-Seabury³

et al. 2008

Cytogenet Genome Res

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A total of 207 BAC clones containing 155 loci were isolated and arranged into a map of linearly ordered overlapping clones over the proximal part of horse chromosome 21 (ECA21), which corresponds to the proximal half of the short arm of human chromosome 19 (HSA19p) and part of HSA5. The clones form two contigs – each corresponding to the respective human chromosomes – that are estimated to be separated by a gap of ∼200 kb. Of the 155 markers present in the two contigs, 141 (33 genes and 108 STS) were generated and mapped in this study. The BACs provide a 4–5× coverage of the region and span an estimated length of ∼3.3 Mb. The region presently contains one mapped marker per 22 kb on average, which represents a major improvement over the previous resolution of one marker per 380 kb obtained through the generation of a dense RH map for this segment. Dual color fluorescence in situ hybridization on metaphase and interphase chromosomes verified the relative order of some of the BACs and helped to orient them accurately in the contigs. Despite having similar gene order and content, the equine region covered by the contigs appears to be distinctly smaller than the corresponding region in human (3.3 Mb vs. 5.5–6 Mb) because the latter harbors a host of repetitive elements and gene families unique to humans/primates. Considering limited representation of the region in the latest version of the horse whole genome sequence EquCab2, the dense map developed in this study will prove useful for the assembly and annotation of the sequence data on ECA21 and will be instrumental in rapid search and isolation of candidate genes for traits mapped to this region.

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Section: Comparative Size Of the Contig Across Speciessupporting

confidence: 81%

A BAC contig map over the proximal ∼3.3 Mb region of horse chromosome 21

Brinkmeyer-Langford

Raudsepp²,

Gustafson-Seabury³

et al. 2008

Cytogenet Genome Res

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“…Several single-gene disorders in quarter horses, such as polysaccharide storage myopathy (McCue et al, 2008;Tryon et al, 2009), hyperkalemic periodic paralysis, glycogen branching enzyme deficiency (Rudolph et al,1992), and hereditary equine regional dermal asthenia (Ward et al, 2004;Finno et al, 2009) has been reported due to wholegenome sequencing of an individual American quarter horse mare. A high-quality draft assembly was constructed and additional sequence were provided by the inclusion of bacterial artificial chromosome end sequences from a related male thorough bred horse (Leeb et al, 2006). Kinoshita et al, (2014) reported the genera Bacteroides and Prevotella especially B. fragilis and P. heparinolytica are dominant anaerobes in lower respiratory tract infection in horses.…”

Section: Sequence Analysis Studymentioning

confidence: 99%

Biotechnological tools for diagnosis of equine infectious diseases

Prasad¹,

Brar²,

Ikbal³

et al. 2016

JEBAS

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Rapid diagnosis of infectious diseases and appropriate treatment with in time are important steps that promote optimal clinical outcomes and general public health. Today there is large number of new technologies such as nanotechnology, biosensors, and microarray techniques, are being developed and used as diagnostic tools for equine infectious diseases. Nucleic acid based techniques such as polymerase chain reaction (PCR) have become conventional tools in veterinary research and plays an important role in specific typing determinations as well as for rapid screening of ample numbers of samples at the time of equine disease outbreaks. Other biotechnological techniques are populous to be used in the coming times as they can enhance diagnostic efficacy in less time and cost as compared to conventional techniques. This review focuses on biotechnological tools available for equine diseases diagnosis and its applications hold great promise for improving the speed and accuracy of diagnostics for equine infectious diseases.

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“…The homologous human genome position of the end sequences for BAC '558', shown in FISH experiments to contain the distal breakpoint of the inversion, were determined by searching the database available at the Horse Genome Project web site (Leeb et al, 2006). Within these endpoints regions of high conservation approximately 3-5 kb apart were selected based on the conservation track of the UCSC Genome Browser (Kent, 2002).…”

Section: Primer Design For Breakpoint Screeningmentioning

confidence: 99%

A chromosome inversion near the <i>KIT</i> gene and the Tobiano spotting pattern in horses

Brooks

Lear²,

Adelson³

et al. 2007

Cytogenet Genome Res

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Tobiano is a white spotting pattern in horses caused by a dominant gene, Tobiano(TO). Here, we report TO associated with a large paracentric chromosome inversion on horse chromosome 3. DNA sequences flanking the inversion were identified and a PCR test was developed to detect the inversion. The inversion was only found in horses with the tobiano pattern, including horses with diverse genetic backgrounds, which indicated a common genetic origin thousands of years ago. The inversion does not interrupt any annotated genes, but begins approximately 100 kb downstream of the KIT gene. This inversion may disrupt regulatory sequences for the KIT gene and cause the white spotting pattern. This manuscript is accompanied by supplemental figures S1, S2 and S3, as well as supplemental Tables S1 and S2 (www.karger.com/doi/10.1159/000112065). The DNA sequence generated in this work has been submitted to GenBank under the following accession number: EF442014.

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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 Show more

Cited by 52 publications

References 18 publications

A BAC contig map over the proximal ∼3.3 Mb region of horse chromosome 21

A BAC contig map over the proximal ∼3.3 Mb region of horse chromosome 21

Biotechnological tools for diagnosis of equine infectious diseases

A chromosome inversion near the <i>KIT</i> gene and the Tobiano spotting pattern in horses

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