Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database.

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Soybean genomic survey: BAC-end sequences near RFLP and SSR markers

Genome ◽

10.1139/g01-052 ◽

2001 ◽

Vol 44 (4) ◽

pp. 572-581 ◽

Cited By ~ 39

Author(s):

Laura Fredrick Marek ◽

Joann Mudge ◽

Laura Darnielle ◽

David Grant ◽

Nadja Hanson ◽

...

Keyword(s):

Physical Map ◽

Repetitive Sequences ◽

Genome Structure ◽

Soybean Genome ◽

Bacterial Artificial Chromosomes ◽

University Of Minnesota ◽

Artificial Chromosomes ◽

Metabolic Functions ◽

Wide Range ◽

End Sequences

We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs (bacterial artificial chromosomes) from two soybean BAC libraries. The libraries were prepared from two genotypes, each digested with a different restriction enzyme. The BACs identified by each marker were grouped into contigs. We have obtained BAC-end sequence from BACs within each contig. The sequences were analyzed by the University of Minnesota Center for Computational Genomics and Bioinformatics using BLAST algorithms to search nucleotide and protein databases. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was due to a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs that was offset in part, however, by a somewhat larger proportion of RFLP-identified significant hits with similarity to experimentally defined genes and soybean ESTs (expressed sequence tags). These genes represented a wide range of metabolic functions. In these analyses, only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC-end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. This map-based approach to genome sampling provides a means of assaying soybean genome structure and organization.Key words: Glycine max, sequencing, physical map, contig.

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High Frequency Recombination During the Sexual Cycle of Dictyostelium discoideum

Genetics ◽

10.1093/genetics/148.4.1829 ◽

1998 ◽

Vol 148 (4) ◽

pp. 1829-1832 ◽

Cited By ~ 1

Author(s):

David Francis

Keyword(s):

Dictyostelium Discoideum ◽

Genetic Map ◽

High Frequency ◽

Cell Biology ◽

Physical Map ◽

Genetic System ◽

Sexual Cycle ◽

Chromosome 2 ◽

New Combinations ◽

Restriction Sites

Abstract Analysis of Dictyostelium development and cell biology has suffered from the lack of an ordinary genetic system whereby genes can be arranged in new combinations. Genetic exchange between two long ignored strains, A2Cycr and WS205 is here reexamined. Alleles which differ in size or restriction sites between these two strains were found for seven genes. Six of these are in two clusters on chromosome 2. Frequencies of recombinant progeny indicate that the genetic map of the two mating strains is colinear with the physical map recently worked out for the standard nonsexual strain, NC4. The rate of recombination is high, about 0.1% per kilobase in three different regions of chromosome 2. This value is comparable to rates found in yeast, and will permit fine dissection of the genome.

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Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana

Genome ◽

10.1139/g03-106 ◽

2004 ◽

Vol 47 (1) ◽

pp. 141-155 ◽

Cited By ~ 38

Author(s):

H H Yan ◽

J Mudge ◽

D-J Kim ◽

R C Shoemaker ◽

D R Cook ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Glycine Max ◽

Medicago Truncatula ◽

Physical Mapping ◽

Large Scale ◽

Sequence Similarity ◽

Artificial Chromosome ◽

Bac Contig ◽

Cross Hybridization ◽

Bac Contigs

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.Key words: Glycine max, Medicago truncatula, Arabidopsis thaliana, conserved microsynteny, genome duplication.

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Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium

Australian Journal of Agricultural Research ◽

10.1071/ar06155 ◽

2007 ◽

Vol 58 (6) ◽

pp. 470 ◽

Cited By ~ 11

Author(s):

P. Moolhuijzen ◽

D. S. Dunn ◽

M. Bellgard ◽

M. Carter ◽

J. Jia ◽

...

Keyword(s):

Genome Sequencing ◽

Physical Map ◽

Genome Structure ◽

Genetic Research ◽

Structure And Function ◽

Wheat Genome ◽

D Genome ◽

Genome Sequencing Consortium ◽

And Function ◽

Bac Contigs

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.

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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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Isolation and structural analysis of a 1.2-megabase N-myc amplicon from a human neuroblastoma

Molecular and Cellular Biology ◽

10.1128/mcb.12.12.5563-5570.1992 ◽

1992 ◽

Vol 12 (12) ◽

pp. 5563-5570

Author(s):

S S Schneider ◽

J L Hiemstra ◽

B A Zehnbauer ◽

P Taillon-Miller ◽

D L Le Paslier ◽

...

Keyword(s):

Cell Line ◽

Gene Amplification ◽

De Novo ◽

Physical Map ◽

Neuroblastoma Cell ◽

Neuroblastoma Cell Line ◽

Chromosome 2 ◽

Human Neuroblastoma ◽

Artificial Chromosomes ◽

Yeast Artificial Chromosomes

Oncogene amplification is observed frequently in human cancers, but little is known about the mechanism of gene amplification or the structure of amplified DNA in tumor cells. We have studied the N-myc amplified domain from a representative neuroblastoma cell line, SMS-KAN, and compared the map of the amplicon in this cell line with that seen in normal DNA. The SMS-KAN cell line DNA was cloned into yeast artificial chromosomes (YACs), and clones were identified by screening the YAC library with amplified DNA probes that were obtained previously (B. Zehnbauer, D. Small, G. M. Brodeur, R. Seeger, and B. Vogelstein, Mol. Cell. Biol. 8:522-530, 1988). In addition, YAC clones corresponding to the normal N-myc locus on chromosome 2 were obtained by screening two normal human YAC libraries with these probes, and the restriction maps of the two sets of overlapping YACs were compared. Our results suggest that the amplified domain in this cell line is a approximately 1.2-Mb circular molecule with a head-to-tail configuration, and the physical map of the normal N-myc locus generally is conserved in the amplicon. These results provide a physical map of the amplified domain of a neuroblastoma cell line that has de novo amplification of an oncogene. The head-to-tail organization, the general conservation of the normal physical map in the amplicon, and the extrachromosomal location of the amplified DNA are most consistent with the episome formation-plus-segregation mechanism of gene amplification in these tumors.

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BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea

Fungal Genetics and Biology ◽

10.1016/j.fgb.2004.02.003 ◽

2004 ◽

Vol 41 (7) ◽

pp. 657-666 ◽

Cited By ~ 17

Author(s):

Michael R. Thon ◽

Stanton L. Martin ◽

Stephen Goff ◽

Rod A. Wing ◽

Ralph A. Dean

Keyword(s):

Transposable Element ◽

Magnaporthe Grisea ◽

Physical Map ◽

Element Content ◽

End Sequences ◽

Clustering Patterns

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Microdissection of and microcloning from the short arm of human chromosome 2.

Molecular and Cellular Biology ◽

10.1128/mcb.6.11.3826 ◽

1986 ◽

Vol 6 (11) ◽

pp. 3826-3830 ◽

Cited By ~ 38

Author(s):

G P Bates ◽

B J Wainwright ◽

R Williamson ◽

S D Brown

Keyword(s):

Human Chromosome ◽

Dna Sequences ◽

Chromosomal Location ◽

Genetic Diseases ◽

Repetitive Sequences ◽

Single Copy ◽

Chromosome 2 ◽

Insert Size ◽

Base Pairs ◽

The Mean

A bank of cloned DNA sequences from the distal half of the short arm of human chromosome 2 was generated by using microdissection and microcloning techniques. DNA was purified from 106 chromosomal fragments, manually dissected from peripheral lymphocytes in metaphase, and cloned into the EcoRI site of lambda gt10. A total of 257 putative recombinants were recovered, of which 41% were found to contain human inserts. The mean insert size was 380 base pairs (median size, 83 base pairs), and fewer than 10% of the clones contained highly repetitive sequences. All single-copy sequences examined were shown to map to the short arm of chromosome 2 by using hybrid panels. This technique provides a rapid method of isolating probes specific to a human subchromosomal region to generate linked markers to genetic diseases for which the chromosomal location is known.

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

10.1101/518563 ◽

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.

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Progress towards a reference genome for sunflower

Botany ◽

10.1139/b11-032 ◽

2011 ◽

Vol 89 (7) ◽

pp. 429-437 ◽

Cited By ~ 60

Author(s):

N.C. Kane ◽

N. Gill ◽

M.G. King ◽

J.E. Bowers ◽

H. Berges ◽

...

Keyword(s):

Reference Genome ◽

Physical Map ◽

Repetitive Sequences ◽

Whole Genome Shotgun ◽

Whole Genome ◽

Horticultural Crops ◽

Physical Maps ◽

Linear Assembly ◽

Sequencing Strategy ◽

Sunflower Genome

The Compositae is one of the largest and most economically important families of flowering plants and includes a diverse array of food crops, horticultural crops, medicinals, and noxious weeds. Despite its size and economic importance, there is no reference genome sequence for the Compositae, which impedes research and improvement efforts. We report on progress toward sequencing the 3.5 Gb genome of cultivated sunflower ( Helianthus annuus ), the most important crop in the family. Our sequencing strategy combines whole-genome shotgun sequencing using the Solexa and 454 platforms with the generation of high-density genetic and physical maps that serve as scaffolds for the linear assembly of whole-genome shotgun sequences. The performance of this approach is enhanced by the construction of a sequence-based physical map, which provides unique sequence-based tags every 5–6 kb across the genome. Thus far, our physical map covers ∼85% of the sunflower genome, and we have generated ∼80× genome coverage with Solexa reads and 15.5× with 454 reads. Preliminary analyses indicated that ∼78% of the sunflower genome consists of repetitive sequences. Nonetheless, ∼76% of contigs >5 kb in size can be assigned to either the physical or genetic map or to both, suggesting that our approach is likely to deliver a highly accurate and contiguous reference genome for sunflower.

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