A 12-Mb Complete Coverage BAC Contig Map in Human Chromosome 16p13.1–p11.2

We have constructed a complete coverage BAC contig map that spans a 12-Mb genomic segment in the human chromosome 16p13.1–p11.2 region. The map consists of 68 previously mapped STSs and 289 BAC clones, 51 of which—corresponding to a total of 7.721 Mb of genomic DNA—have been sequenced, and provides a high resolution physical map of the region. Contigs were initially built based mainly on the analysis of STS contents and restriction fingerprint patterns of the clones. To close the gaps, probes derived from BAC clone ends were used to screen deeper BAC libraries. Clone end sequence data obtained from chromosome 16-specific BACs, as well as from public databases, were used for the identification of BACs that overlap with fully sequenced BACs by means of sequence match. This approach allowed precise alignment of clone overlaps in addition to restriction fingerprint comparison. A freehand contig drawing software tool was developed and used to manage the map data graphically and generate a real scale physical map. The map we present here is ∼3.5 × deep and provides a minimal tiling path that covers the region in an array of contigous, overlapping BACs.

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Homology-Driven Assembly of a Sequence-Ready Mouse BAC Contig Map Spanning Regions Related to the 46-Mb Gene-Rich Euchromatic Segments of Human Chromosome 19

Genomics ◽

10.1006/geno.2001.6521 ◽

2001 ◽

Vol 74 (2) ◽

pp. 129-141 ◽

Cited By ~ 20

Author(s):

Joomyeong Kim ◽

Laurie Gordon ◽

Paramvir Dehal ◽

Hummy Badri ◽

Mari Christensen ◽

...

Keyword(s):

Human Chromosome ◽

Chromosome 19 ◽

Bac Contig ◽

Contig Map ◽

Human Chromosome 19

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A novel high-accuracy genome assembly method utilizing a high-throughput workflow

10.1101/2020.11.26.400507 ◽

2020 ◽

Author(s):

Qingdong Zeng ◽

Wenjin Cao ◽

Liping Xing ◽

Guowei Qin ◽

Jianhui Wu ◽

...

Keyword(s):

High Throughput ◽

Genome Assembly ◽

Large Scale ◽

Sequence Data ◽

Physical Map ◽

Bac Library ◽

High Accuracy ◽

Biological Research ◽

Bac Clone ◽

Assembly Method

AbstractAcross domains of biological research using genome sequence data, high-quality reference genome sequences are essential for characterizing genetic variation and understanding the genetic basis of phenotypes. However, the construction of genome assemblies for various species is often hampered by complexities of genome organization, especially repetitive and complex sequences, leading to mis-assembly and missing regions. Here, we describe a high-throughput gold standard genome assembly workflow using a large-scale bacterial artificial chromosome (BAC) library with a refined two-step pooling strategy and the Lamp assembler algorithm. This strategy minimizes the laborious processes of physical map construction and clone-by-clone sequencing, enabling inexpensive sequencing of several thousand BAC clones. By applying this strategy with a minimum tiling path BAC clone library for the short arm of chromosome 2D (2DS) of bread wheat, 98% of BAC sequences, covering 92.7% of the 2DS chromosome, were assembled correctly for this species with a highly complex and repetitive genome. We also identified 48 large mis-assemblies in the reference wheat genome assembly (IWGSC RefSeq v1.0) and corrected these large mis-assemblies in addition to filling 92.2% of the gaps in RefSeq v1.0. Our 2DS assembly represents a new benchmark for the assembly of complex genomes with both high accuracy and efficiency.

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Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17☆☆Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under Accession Nos. AY178785, AY178786, AY178787, AY178788, AY178789, AY178790, AY178791, and AY178792.

Genomics ◽

10.1016/s0888-7543(02)00028-9 ◽

2003 ◽

Vol 81 (2) ◽

pp. 138-148 ◽

Cited By ~ 10

Author(s):

D.J Sidjanin ◽

B Miller ◽

J Kijas ◽

J McElwee ◽

J Pillardy ◽

...

Keyword(s):

Human Chromosome ◽

Radiation Hybrid ◽

Genomic Sequence ◽

Sequence Data ◽

Physical Map ◽

Chromosome 17 ◽

Low Pass ◽

Radiation Hybrid Map ◽

Human Chromosome 17 ◽

Data Libraries

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

HortScience ◽

10.21273/hortsci.35.3.477e ◽

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.

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A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb

Genome Research ◽

10.1101/gr.7.7.673 ◽

1997 ◽

Vol 7 (7) ◽

pp. 673-692 ◽

Cited By ~ 55

Author(s):

Gerard G. Bouffard ◽

Jacquelyn R. Idol ◽

Valerie V. Braden ◽

Leslie M. Iyer ◽

Aimee F. Cunningham ◽

...

Keyword(s):

Human Chromosome ◽

Physical Map ◽

Chromosome 7 ◽

Yac Contig ◽

Human Chromosome 7 ◽

Contig Map

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A Sequence-Ready BAC Clone Contig of Human Chromosome 10p15 Spanning the Loss of Heterozygosity Region in Glioma

Genomics ◽

10.1006/geno.2000.6257 ◽

2000 ◽

Vol 67 (3) ◽

pp. 268-272 ◽

Cited By ~ 5

Author(s):

Kei Harada, ◽

Takafumi Nishizaki ◽

Kohei Maekawa ◽

Hisashi Kubota ◽

Katsumi Harada ◽

...

Keyword(s):

Human Chromosome ◽

Loss Of Heterozygosity ◽

Bac Clone ◽

Chromosome 10P15

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Comparative analysis of a BAC contig of porcine chromosome 13q31-q32 and human chromosome 3q21-q22

BMC Genomics ◽

10.1186/1471-2164-6-133 ◽

2005 ◽

Vol 6 (1) ◽

Cited By ~ 2

Author(s):

Mario Van Poucke ◽

David Bourry ◽

François Piumi ◽

Marc Mattheeuws ◽

Alex Van Zeveren ◽

...

Keyword(s):

Comparative Analysis ◽

Human Chromosome ◽

Porcine Chromosome ◽

Bac Contig

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High-Resolution Pachytene Chromosome Mapping of Bacterial Artificial Chromosomes Anchored by Genetic Markers Reveals the Centromere Location and the Distribution of Genetic Recombination Along Chromosome 10 of Rice

Genetics ◽

10.1093/genetics/157.4.1749 ◽

2001 ◽

Vol 157 (4) ◽

pp. 1749-1757 ◽

Cited By ~ 11

Author(s):

Zhukuan Cheng ◽

Gernot G Presting ◽

C Robin Buell ◽

Rod A Wing ◽

Jiming Jiang

Keyword(s):

Large Scale ◽

Genetic Recombination ◽

Physical Map ◽

Rice Chromosome ◽

Resolving Power ◽

Pachytene Chromosome ◽

Chromosome 10 ◽

Bac Clone ◽

Fish Mapping ◽

Artificial Chromosomes

AbstractLarge-scale physical mapping has been a major challenge for plant geneticists due to the lack of techniques that are widely affordable and can be applied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacterial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. This physical map is fully integrated with a genetic linkage map of rice chromosome 10 because each BAC clone is anchored by a genetically mapped restriction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metaphase chromosome-based methods. The telomere-centromere orientation of DNA clones separated by 40 kb can be resolved on early pachytene chromosomes. Genetic recombination is generally evenly distributed along rice chromosome 10. However, the highly heterochromatic short arm shows a lower recombination frequency than the largely euchromatic long arm. Suppression of recombination was found in the centromeric region, but the affected region is far smaller than those reported in wheat and barley. Our FISH mapping effort also revealed the precise genetic position of the centromere on chromosome 10.

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

Comparative and Functional Genomics ◽

10.1002/cfg.476 ◽

2005 ◽

Vol 6 (4) ◽

pp. 194-203 ◽

Cited By ~ 8

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.

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