scholarly journals A4Mb High Resolution BAC Contig on Bovine Chromosome1q12and Comparative Analysis With Human Chromosome21q22

2005 ◽  
Vol 6 (4) ◽  
pp. 194-203 ◽  
Author(s):  
Cord Drögemüller ◽  
Anne Wöhlke ◽  
Tosso Leeb ◽  
Ottmar Distl
Keyword(s):  
Positional Cloning ◽  
Physical Map ◽  
Dominant Gene ◽  
Bac Library ◽  
Exact Order ◽  
Bac Contig ◽  
Nucleotide Sequence Data ◽  
New Genes ◽  
Human Genes ◽  
First Time

The bovine RPCI-42 BAC library was screened to construct a sequence-ready ~4 Mb single contig of 92 BAC clones on BTA 1q12. The contig covers the region between the genesKRTAP8P1andCLIC6. This genomic segment in cattle is of special interest as it contains the dominant gene responsible for the hornless or polled phenotype in cattle. The construction of the BAC contig was initiated by screening the bovine BAC library with heterologous cDNA probes derived from 12 human genes of the syntenic region on HSA 21q22. Contig building was facilitated by BAC end sequencing and chromosome walking. During the construction of the contig, 165 BAC end sequences and 109 single-copy STS markers were generated. For comparative mapping of 25 HSA 21q22 genes, genomic PCR primers were designed from bovine EST sequences and the gene-associated STSs mapped on the contig. Furthermore, bovine BAC end sequence comparisons against the human genome sequence revealed significant matches to HSA 21q22 and allowed thein silicomapping of two new genes in cattle. In total, 31 orthologues of human genes located on HSA 21q22 were directly mapped within the bovine BAC contig, of which 16 genes have been cloned and mapped for the first time in cattle. In contrast to the existing comparative bovine–human RH maps of this region, these results provide a better alignment and reveal a completely conserved gene order in this 4 Mb segment between cattle, human and mouse. The mapping of known polled linked BTA 1q12 microsatellite markers allowed the integration of the physical contig map with existing linkage maps of this region and also determined the exact order of these markers for the first time. Our physical map and transcript map may be useful for positional cloning of the putative polled gene in cattle. The nucleotide sequence data reported in this paper have been submitted to EMBL and have been assigned Accession Numbers AJ698510–AJ698674.

scholarly journals Assembly, Annotation, and Integration of UNIGENE Clusters into the Human Genome Draft

2001 ◽  
Vol 11 (5) ◽  
pp. 904-918
Author(s):  
Degen Zhuo ◽  
Wei D. Zhao ◽  
Fred A. Wright ◽  
Hee-Yung Yang ◽  
Jian-Ping Wang ◽  
...  
Keyword(s):  
Human Genome ◽  
Positional Cloning ◽  
Physical Map ◽  
Sequence Contigs ◽  
New Genes ◽  
Human Genes ◽  
Individual Transcript ◽  
Genome Draft ◽  
Human Transcript ◽  
The Individual

The recent release of the first draft of the human genome provides an unprecedented opportunity to integrate human genes and their functions in a complete positional context. However, at least three significant technical hurdles remain: first, to assemble a complete and nonredundant human transcript index; second, to accurately place the individual transcript indices on the human genome; and third, to functionally annotate all human genes. Here, we report the extension of the UNIGENE database through the assembly of its sequence clusters into nonredundant sequence contigs. Each resulting consensus was aligned to the human genome draft. A unique location for each transcript within the human genome was determined by the integration of the restriction fingerprint, assembled genomic contig, and radiation hybrid (RH) maps. A total of 59,500 UNIGENE clusters were mapped on the basis of at least three independent criteria as compared with the 30,000 human genes/ESTs currently mapped in Genemap'99. Finally, the extension of the human transcript consensus in this study enabled a greater number of putative functional assignments than the 11,000 annotated entries in UNIGENE. This study reports a draft physical map with annotations for a majority of the human transcripts, called the Human Index of Nonredundant Transcripts (HINT). Such information can be immediately applied to the discovery of new genes and the identification of candidate genes for positional cloning.

scholarly journals Development of a sequence-based reference physical map of pea (Pisum sativum L.)

2019 ◽  
Author(s):  
Krishna Kishore Gali ◽  
Bunyamin Tar’an ◽  
Mohammed-Amin Madoui ◽  
Edwin van der Vossen ◽  
Jan van Oeveren ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Positional Cloning ◽  
Physical Map ◽  
Repetitive Sequences ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Bac Clones ◽  
Pooled Dna ◽  
Mapping Technology ◽  
Generation Sequencing

AbstractWhole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (~4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.

scholarly journals A Bacterial Artificial Chromosome Contig Spanning the Major Domestication Locus Q in Wheat and Identification of a Candidate Gene

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 311-321 ◽  
Author(s):  
Justin D Faris ◽  
John P Fellers ◽  
Steven A Brooks ◽  
Bikram S Gill
Keyword(s):  
Physical Map ◽  
Bac Library ◽  
Wheat Chromosome ◽  
Artificial Chromosome ◽  
Physical Distance ◽  
Bac Contig ◽  
Complete Sequencing ◽  
Bacterial Artificial Chromosome Contig ◽  
Q Gene ◽  
Similarity Searches

Abstract The Q locus played a major role in the domestication of wheat because it confers the free-threshing character and influences many other agronomically important traits. We constructed a physical contig spanning the Q locus using a Triticum monococcum BAC library. Three chromosome walking steps were performed by complete sequencing of BACs and identification of low-copy markers through similarity searches of database sequences. The BAC contig spans a physical distance of ∼300 kb corresponding to a genetic distance of 0.9 cM. The physical map of T. monococcum had perfect colinearity with the genetic map of wheat chromosome arm 5AL. Recombination data in conjunction with analysis of fast neutron deletions confirmed that the contig spanned the Q locus. The Q gene was narrowed to a 100-kb segment, which contains an APETALA2 (AP2)-like gene that cosegregates with Q. AP2 is known to play a major role in controlling floral homeotic gene expression and thus is an excellent candidate for Q.

scholarly journals Genetic and Physical Mapping of Avr1a in Phytophthora sojae

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 949-959 ◽  
Author(s):  
Terry MacGregor ◽  
Madan Bhattacharyya ◽  
Brett Tyler ◽  
Ravindra Bhat ◽  
August F Schmitthenner ◽  
...  
Keyword(s):  
Positional Cloning ◽  
Dna Marker ◽  
Physical Map ◽  
Phytophthora Sojae ◽  
Distance Ratio ◽  
Bac Contig ◽  
F2 Population ◽  
Genetic Linkage Maps ◽  
F2 Progeny ◽  
Avr Genes

Abstract The interaction between soybean and the phytopathogenic oomycete Phytophthora sojae is controlled by host resistance (Rps) genes and pathogen avirulence (Avr) genes. We have mapped the Avr1a locus in F2 populations derived from four different P. sojae races. Four RAPD and nine AFLP markers linked to Avr1a were initially identified. Nine markers were used to compare genetic linkage maps of the Avr1a locus in two distinct F2 populations. Distorted segregation ratios favoring homozygous genotypes were noted in both crosses. Segregation analysis of all the markers in one F2 population of 90 progeny generated a map of 113.2 cM encompassing Avr1a, with one marker cosegregating with the gene. The cosegregating DNA marker was used to isolate P. sojae BAC clones and construct a physical map covering 170 kb, from which additional DNA markers were developed. Three markers occurring within the BAC contig were mapped in an enlarged population of 486 F2 progeny. Avr1a was localized to a 114-kb interval, and an average physical to genetic distance ratio of 391 kb/cM was calculated for this region. This work provides a basis for the positional cloning of Avr1a.

scholarly journals 484 Constructing the BAC Contig for the Evergreen Gene Region in Peach [Prunus persica (L.) Batsch]

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 477E-478
Author(s):  
Ying Wang ◽  
Laura L. George ◽  
Gregory L. Reighard ◽  
Ralph Scorza ◽  
Albert G. Abbott
Keyword(s):  
Prunus Persica ◽  
Physical Map ◽  
Single Gene ◽  
Bac Library ◽  
Gene Region ◽  
Average Insert Size ◽  
Insert Size ◽  
Bac Clone ◽  
Bac Contig ◽  
Peach Genome

Evergreen genotypes of peach [Prunus persica (L.) Batsch] have been identified in Mexico, where terminal growth on evergreen trees is continuous under favorable environmental conditions. This evergreen trait in peach is controlled by one single gene (evg), and this evergreen condition is homozygous recessive. Four dominant AFLP markers, EAT/MCAC, ETT/MCCA2, EAT/MCTA, and ETT/MACC, were found to be tightly linked to the evg locus at 1 cM, 4.6 cM, 5.8 cM, and 11 cM, respectively. All four markers were sequenced and identified. A peach BAC library was constructed by using the pBeloBAC11 vector for building the physical map for the evg gene. This library represents four times the coverage of the peach genome with the average insert size of 50 to 70 kb. The EAT/MCAC AFLP marker fragment was used for screening the peach BAC library. A single BAC clone, 18F12, was confirmed to contain this fragment. The final BAC contig for this evg gene region and the potential homology between peach and Arabidopsis thaliana will be presented and discussed.

scholarly journals Saturation Mapping of a Gene-Rich Recombination Hot Spot Region in Wheat

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 823-835 ◽  
Author(s):  
Justin D Faris ◽  
Karri M Haen ◽  
Bikram S Gill
Keyword(s):  
Positional Cloning ◽  
Physical Map ◽  
Hot Spot ◽  
Chromosome Breakage ◽  
Small Chromosome ◽  
Gene Density ◽  
Chromosome 5B ◽  
High Gene ◽  
The Many ◽  
Recombination Hot Spots

AbstractPhysical mapping of wheat chromosomes has revealed small chromosome segments of high gene density and frequent recombination interspersed with relatively large regions of low gene density and infrequent recombination. We constructed a detailed genetic and physical map of one highly recombinant region on the long arm of chromosome 5B. This distally located region accounts for 4% of the physical size of the long arm and at least 30% of the recombination along the entire chromosome. Multiple crossovers occurred within this region, and the degree of recombination is at least 11-fold greater than the genomic average. Characteristics of the region such as gene order and frequency of recombination appear to be conserved throughout the evolution of the Triticeae. The region is more prone to chromosome breakage by gametocidal gene action than gene-poor regions, and evidence for genomic instability was implied by loss of gene collinearity for six loci among the homeologous regions. These data suggest that a unique level of chromatin organization exists within gene-rich recombination hot spots. The many agronomically important genes in this region should be accessible by positional cloning.

Genetic and contig map of a 2200-kb region encompassing 5.5 cM on chromosome 1 of Arabidopsis thaliana

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1086-1092 ◽  
Author(s):  
Christian S. Hardtke ◽  
Thomas Berleth
Keyword(s):  
Arabidopsis Thaliana ◽  
Positional Cloning ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Primary Root ◽  
Artificial Chromosome ◽  
Chromosome 1 ◽  
Rflp Markers ◽  
Caps Markers ◽  
Yac Contig

In the course of the isolation of the MONOPTEROS (MP) gene, required for primary root formation in Arabidopsis thaliana, a yeast artificial chromosome (YAC) contig encompassing approximately 2200 kilobases corresponding to 5.5 cM on the top arm of chromosome 1 was established. Forty-six YAC clones were characterized and 12 new restriction fragment length polymorphism (RFLP) markers are presented. Three new codominant amplified polymorphic sequence (CAPS) markers were generated that enabled high resolution genetic mapping and correlation of physical and genetic distances along the contig. The map contributes to the completion of a physical map of the Arabidopsis genome and should facilitate positional cloning of other genes in the region as well as studies on genome organization. We also present another set of 11 physically linked probes, as well as mapping data for additional RFLP markers within a broader interval of 10.4 cM. Key words : Arabidopsis, CAPS markers, MONOPTEROS gene, physical map, RFLP markers, YAC contig.

scholarly journals Characterization of the OmyY1 Region on the Rainbow Trout Y Chromosome

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Ruth B. Phillips ◽  
Jenefer J. DeKoning ◽  
Joseph P. Brunelli ◽  
Joshua J. Faber-Hammond ◽  
John D. Hansen ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Candidate Genes ◽  
Y Chromosome ◽  
X Chromosome ◽  
Bac Library ◽  
Single Copy ◽  
Bac Contig ◽  
Protein Coding ◽  
Additional Signal ◽  
Male Specific

We characterized the male-specific region on the Y chromosome of rainbow trout, which contains both sdY (the sex-determining gene) and the male-specific genetic marker, OmyY1. Several clones containing the OmyY1 marker were screened from a BAC library from a YY clonal line and found to be part of an 800 kb BAC contig. Using fluorescencein situhybridization (FISH), these clones were localized to the end of the short arm of the Y chromosome in rainbow trout, with an additional signal on the end of the X chromosome in many cells. We sequenced a minimum tiling path of these clones using Illumina and 454 pyrosequencing. The region is rich in transposons and rDNA, but also appears to contain several single-copy protein-coding genes. Most of these genes are also found on the X chromosome; and in several cases sex-specific SNPs in these genes were identified between the male (YY) and female (XX) homozygous clonal lines. Additional genes were identified by hybridization of the BACs to the cGRASP salmonid 4x44K oligo microarray. By BLASTn evaluations using hypothetical transcripts of OmyY1-linked candidate genes as query against several EST databases, we conclude at least 12 of these candidate genes are likely functional, and expressed.

scholarly journals A physical map of the human regulator of complement activation gene cluster linking the complement genes CR1, CR2, DAF, and C4BP.

1988 ◽  
Vol 167 (2) ◽  
pp. 664-669 ◽  
Author(s):  
J Rey-Campos ◽  
P Rubinstein ◽  
S Rodriguez de Cordoba
Keyword(s):  
Gene Cluster ◽  
Complement Activation ◽  
Gel Electrophoresis ◽  
Physical Map ◽  
Pulsed Field Gel Electrophoresis ◽  
Complement Components ◽  
Pulsed Field ◽  
Human Genes ◽  
Tight Linkage ◽  
Genes Encoding

We report the organization of the human genes encoding the complement components C4-binding protein (C4BP), C3b/C4b receptor (CR1), decay accelerating factor (DAF), and C3dg receptor (CR2) within the regulator of complement activation (RCA) gene cluster. Using pulsed field gel electrophoresis analysis these genes have been physically linked and aligned as CR1-CR2-DAF-C4BP in an 800-kb DNA segment. The very tight linkage between the CR1 and the C4BP loci, contrasted with the relative long DNA distance between these genes, suggests the existence of mechanisms interfering with recombination within the RCA gene cluster.

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