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

2004 ◽  
Vol 41 (7) ◽  
pp. 657-666 ◽  
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

scholarly journals Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

2011 ◽  
Vol 3 ◽  
pp. 219-229 ◽  
Author(s):  
Maud I. Tenaillon ◽  
Matthew B. Hufford ◽  
Brandon S. Gaut ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Element ◽  
Genome Size ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Element Content ◽  
Zea Luxurians

scholarly journals Physical Map and Organization of Chromosome 7 in the Rice Blast Fungus, Magnaporthe grisea

1999 ◽  
Vol 9 (8) ◽  
pp. 739-750 ◽  
Author(s):  
Heng Zhu ◽  
Barbara P. Blackmon ◽  
Maciek Sasinowski ◽  
Ralph A. Dean
Keyword(s):  
Rice Blast ◽  
Magnaporthe Grisea ◽  
Physical Map ◽  
Rice Blast Fungus ◽  
Chromosome 7 ◽  
Rflp Markers ◽  
Plant Interactions ◽  
Bac Clones ◽  
Blast Fungus ◽  
Biological Studies

The rice blast fungus Magnaporthe grisea is a highly destructive plant pathogen and one of the most important for studying various aspects of host-plant interactions. It has been widely adopted as a model organism because it is ideally suited for genetic and biological studies. To facilitate map-based cloning, chromosome walking, and genome organization studies of M. grisea, a complete physical map of chromosome 7 was constructed using a large-insert (130 kb) bacterial artificial chromosome (BAC) library. Using 147 chromosome 7-specific single-copy BAC clones and 20 RFLP markers on chromosome 7, 625 BAC clones were identified by hybridization. BAC clones were digested with HindIII, and fragments were size separated on analytical agarose gels to create DNA fingerprints. Hybridization contigs were constructed using a random cost algorithm, whereas fingerprinting contigs were constructed using the software package FPC. Results from both methods were generally in agreement, but numerous anomalies were observed. The combined data produced five robust anchored contigs after gap closure by chromosomal walking. The genetic and physical maps agreed closely. The final physical map was estimated to cover >95% of the 4.2 Mb of chromosome 7. Based on the contig maps, a minimum BAC tile containing 42 BAC clones was created, and organization of repetitive elements and expressed genes of the chromosome was investigated.

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

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 572-581 ◽  
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.

Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content

2012 ◽  
pp. 41-58 ◽  
Author(s):  
Concepcion Muñoz-Diez ◽  
Clémentine Vitte ◽  
Jeffrey Ross-Ibarra ◽  
Brandon S. Gaut ◽  
Maud I. Tenaillon
Keyword(s):  
Transposable Element ◽  
Genome Size ◽  
Size Variation ◽  
Element Content ◽  
Genome Size Variation ◽  
Nextgen Sequencing

scholarly journals Soybean Genomics: Developments through the Use of Cultivar “Forrest”

2008 ◽  
Vol 2008 ◽  
pp. 1-22 ◽  
Author(s):  
David A. Lightfoot
Keyword(s):  
Crop Production ◽  
Physical Map ◽  
Genomic Analysis ◽  
Transcript Abundance ◽  
Gene Pools ◽  
The North ◽  
Mutant Isolation ◽  
End Sequences ◽  
Genomic Locations ◽  
Soybean Nodulation

Legume crops are particularly important due to their ability to support symbiotic nitrogen fixation, a key to sustainable crop production and reduced carbon emissions. Soybean (Glycine max) has a special position as a major source of increased protein and oil production in the common grass-legume rotation. The cultivar “Forrest” has saved US growers billions of dollars in crop losses due to resistances programmed into the genome. Moreover, since Forrest grows well in the north-south transition zone, breeders have used this cultivar as a bridge between the southern and northern US gene pools. Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96>n>975), (iii) ~200 NILs, (iv) 115,220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25,123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2,408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes. The SoyGD portal provides access to the data. To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance. This review summarizes the resources and their uses.

Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps

Genome ◽  
2008 ◽  
Vol 51 (4) ◽  
pp. 294-302 ◽  
Author(s):  
Randy C. Shoemaker ◽  
David Grant ◽  
Terry Olson ◽  
Wesley C. Warren ◽  
Rod Wing ◽  
...  
Keyword(s):  
Genetic Map ◽  
Physical Map ◽  
Genetic Maps ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Dinucleotide Repeats ◽  
Length Polymorphisms ◽  
Glycine Max L ◽  
Physical And Genetic Map ◽  
End Sequences

Whole-genome sequencing of the soybean ( Glycine max (L.) Merr. ‘Williams 82’) has made it important to integrate its physical and genetic maps. To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the ‘Williams 82’ physical map. SSRs were screened against 3 mapping populations. We found the AAT and ACT motifs produced the greatest frequency of length polymorphisms, ranging from 17.2% to 32.3% and from 11.8% to 33.3%, respectively. Other useful motifs include the dinucleotide repeats AG, AT, and AG, with frequency of length polymorphisms ranging from 11.2% to 18.4% (AT), 12.4% to 20.6% (AG), and 11.3% to 16.4% (GT). Repeat lengths less than 16 bp were generally less useful than repeat lengths of 40–60 bp. Two hundred and sixty-five SSRs were genetically mapped in at least one population. Of the 265 mapped SSRs, 60 came from BAC singletons not yet placed into contigs of the physical map. One hundred and ten originated in BACs located in contigs for which no genetic map location was previously known. Ninety-five SSRs came from BACs within contigs for which one or more other BACs had already been mapped. For these fingerprinted contigs (FPC) a high percentage of the mapped markers showed inconsistent map locations. A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4× assembly of the whole genome sequence of soybean.

scholarly journals Variation in piRNA and Transposable Element Content in Strains of Drosophila melanogaster

2014 ◽  
Vol 6 (10) ◽  
pp. 2786-2798 ◽  
Author(s):  
Jimin Song ◽  
Jixia Liu ◽  
Sandra L. Schnakenberg ◽  
Hongseok Ha ◽  
Jinchuan Xing ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Element Content

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

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Erika Asamizu ◽  
Kenta Shirasawa ◽  
Hideki Hirakawa ◽  
Shusei Sato ◽  
Satoshi Tabata ◽  
...  
Keyword(s):  
Physical Map ◽  
Repetitive Sequences ◽  
Genome Rearrangements ◽  
Chromosome 2 ◽  
Tomato Genome ◽  
Bac Contig ◽  
Entire Genome ◽  
End Sequences ◽  
Standard Cultivar ◽  
Bac Contigs

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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