Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats

2006 ◽  
Vol 33 (8) ◽  
pp. 765 ◽  
Author(s):  
Andrew Nunberg ◽  
Joseph A. Bedell ◽  
Mohammad A. Budiman ◽  
Robert W. Citek ◽  
Sandra W. Clifton ◽  
...  
Keyword(s):  
Genome Structure ◽  
Artificial Chromosome ◽  
Repeat Sequence ◽  
Soybean Genome ◽  
Dna Repeats ◽  
Gene Enrichment ◽  
Dna Repeat ◽  
Glycine Max L ◽  
Soybean Gene ◽  
End Sequences

In order to expand our knowledge of the soybean genome and to create a useful DNA repeat sequence database, over 24 000 DNA fragments from a soybean [Glycine max (L.) Merr.] cv. Williams 82 genomic shotgun library were sequenced. Additional sequences came from over 29 000 bacterial artificial chromosome (BAC) end sequences derived from a BstI library of the cv. Williams 82 genome. Analysis of these sequences identified 348 different DNA repeats, many of which appear to be novel. To extend the utility of the work, a pilot study was also conducted using methylation filtration to estimate the hypomethylated, soybean gene space. A comparison between 8366 sequences obtained from a filtered library and 23 788 from an unfiltered library indicate a gene-enrichment of ~3.2-fold in the hypomethylated sequences. Given the 1.1-Gb soybean genome, our analysis predicts a ~343-Mb hypomethylated, gene-rich space.

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.

scholarly journals Structure of the Chromosome VII Centromere Region in Neurospora crassa: Degenerate Transposons and Simple Repeats

1998 ◽  
Vol 18 (9) ◽  
pp. 5465-5477 ◽  
Author(s):  
Edward B. Cambareri ◽  
Rafael Aisner ◽  
John Carbon
Keyword(s):  
Neurospora Crassa ◽  
Yeast Artificial Chromosome ◽  
Fragment Length Polymorphism ◽  
Artificial Chromosome ◽  
Polymorphism Analysis ◽  
Dna Repeats ◽  
Centromere Region ◽  
Simple Repeats ◽  
Restriction Fragment Length ◽  
Repeat Induced Point Mutation

ABSTRACT DNA from the centromere region of linkage group (LG) VII ofNeurospora crassa was cloned previously from a yeast artificial chromosome library and was found to be atypical ofNeurospora DNA in both composition (AT rich) and complexity (repetitive). We have determined the DNA sequence of a small portion (∼16.1 kb) of this region and have identified a cluster of three new retrotransposon-like elements as well as degenerate fragments from the 3′ end of Tad, a previously identified LINE-like retrotransposon. This region contains a novel full-length but nonmobilecopia-like element, designated Tcen, that is only associated with centromere regions. Adjacent DNA contains portions of a gypsy-like element designated Tgl1. A third new element, Tgl2, shows similarity to theTy3 transposon of Saccharomyces cerevisiae. All three of these elements appear to be degenerate, containing predominantly transition mutations suggestive of the repeat-induced point mutation (RIP) process. Three new simple DNA repeats have also been identified in the LG VII centromere region. While Tcenelements map exclusively to centromere regions by restriction fragment length polymorphism analysis, the defective Tad elements appear to occur most frequently within centromeres but are also found at other loci including telomeres. The characteristics and arrangement of these elements are similar to those seen in theDrosophila centromere, but the relative abundance of each class of repeats, as well as the sequence degeneracy of the transposon-like elements, is unique to Neurospora. These results suggest that the Neurospora centromere is heterochromatic and regional in character, more similar to centromeres of Drosophila than to those of most single-cell yeasts.

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 32-37 ◽  
Author(s):  
Shoko Saji ◽  
Yosuke Umehara ◽  
Baltazar A Antonio ◽  
Hiroko Yamane ◽  
Hiroshi Tanoue ◽  
...  
Keyword(s):  
Genetic Map ◽  
Dna Markers ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Genome Structure ◽  
Rice Genome ◽  
Artificial Chromosome ◽  
Physical Length ◽  
Rice Chromosomes ◽  
Yac Contig

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

scholarly journals Chromosome Evolution in the Thermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences

2006 ◽  
Vol 188 (7) ◽  
pp. 2364-2374 ◽  
Author(s):  
Robert T. DeBoy ◽  
Emmanuel F. Mongodin ◽  
Joanne B. Emerson ◽  
Karen E. Nelson
Keyword(s):  
Sequence Analysis ◽  
Large Scale ◽  
Thermotoga Maritima ◽  
Chromosomal Rearrangements ◽  
Pcr Amplification ◽  
Trna Genes ◽  
Thermotoga Neapolitana ◽  
Dna Repeats ◽  
Dna Rearrangements ◽  
Dna Repeat

ABSTRACT In the present study, the chromosomes of two members of the Thermotogales were compared. A whole-genome alignment of Thermotoga maritima MSB8 and Thermotoga neapolitana NS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same replichore, i.e., the same replicating half of the chromosome (delimited by the replication origin and terminus). Based on cumulative GC skew analysis, both the T. maritima and T. neapolitana lineages contain one or two major inverted DNA segments. Also, based on PCR amplification and sequence analysis of the DNA joints that are associated with the major rearrangements, the overall chromosome architecture was found to be conserved at most DNA joints for other strains of T. neapolitana. Taken together, the results from this analysis suggest that the observed chromosomal rearrangements in the Thermotogales likely occurred by successive inversions after their divergence from a common ancestor and before strain diversification. Finally, sequence analysis shows that size polymorphisms in the DNA joints associated with CRISPRs can be explained by expansion and possibly contraction of the DNA repeat and spacer unit, providing a tool for discerning the relatedness of strains from different geographic locations.

Distribution of a Secale cereale DNA repeat sequence among 25 Hordeum species

Genome ◽  
1989 ◽  
Vol 32 (3) ◽  
pp. 383-388 ◽  
Author(s):  
P. K. Gupta ◽  
G. Fedak ◽  
S. J. Molnar ◽  
Roger Wheatcroft
Keyword(s):  
Dna Sequences ◽  
Secale Cereale ◽  
Dna Hybridization ◽  
Interspecific Variation ◽  
Repeat Sequence ◽  
Species Variation ◽  
Repeated Dna ◽  
Repeat Units ◽  
Dna Repeat ◽  
Hordeum Species

DNA of 61 accessions representing 25 Hordeum species was tested for homology to a highly repeated 120-bp sequence from Secale cereale (rye). Homology to the probe (pSC119) was detected in dot blots of all species except H. vulgare (cultivated barley) and its related species, H. agriocrithon and H. spontaneum. Hybridization patterns of Southern blots of restriction fragments demonstrated both intraspecific and interspecific variation in the organization of complex units of DNA having homology to the probe. For eight species, digestion of the DNA with BamHI gave ladder patterns characteristic of tandem arrays of 120-bp repeat units. For EcoRI, HindIII, and SacI digests, the hybridization patterns appeared to be highly conserved in the section Hordeum, except those for H. bulbosum, which were unique. A further set of patterns for these three enzymes was common among the remaining species of the genus. Thus, DNA hybridization with pSC119 generally gave patterns consistent with the current taxonomy of Hordeum species, except that H. bulbosum and H. vulgare were not shown to be closely related.Key words: Hordeum, repeated DNA sequences, pSC119, species variation.

scholarly journals Survey of genomic repeat sequence-PCRs that detect differences between inbred mouse strains

1995 ◽  
Vol 65 (2) ◽  
pp. 151-155 ◽  
Author(s):  
Philip A. Wood ◽  
Doug A. Hamm
Keyword(s):  
Genomic Dna ◽  
Inbred Mouse ◽  
Pcr Amplification ◽  
Repeat Sequence ◽  
Mouse Strains ◽  
Repeat Sequences ◽  
Dna Repeat ◽  
Polymerase Chain ◽  
Dna Repeat Sequences ◽  
Congenic Mouse Strains

SummaryWe have developed molecular markers that distinguish between several inbred and congenic mouse strains using polymerase chain reaction (PCR) amplification of genomic DNA repeat sequences. Mouse genomic DNA, digested with four base recognition site-restriction endonucleases, was amplified by PCR using primers for the following repeat sequences: Bl (Alu homolog), LINE, LLR3, IAP, human Alu and myoglobin. Amplification products analysed by agarose gel electrophoresis and stained with ethidium bromide produced unique DNA fragments, some of which are specific for each of 12 strains tested. This method can be used for molecular analysis of the mouse genome, including genetic monitoring.

Physical mapping of resistant and susceptible soybean genomes near the soybean cyst nematode resistance gene Rhg4

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 1057-1064 ◽  
Author(s):  
K S Lewers ◽  
S D Nilmalgoda ◽  
A L Warner ◽  
H T Knap ◽  
B F Matthews
Keyword(s):  
Resistance Gene ◽  
Soybean Cyst Nematode ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Nematode Resistance ◽  
Physical Distance ◽  
Cyst Nematode ◽  
Nematode Resistance Gene ◽  
Glycine Max L ◽  
Soybean Cyst Nematode Resistance

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is the foremost pest of soybean (Glycine max L. Merr.). The rhg1 allele on linkage group (LG) G and the Rhg4 allele on LG A2 are important in conditioning resistance. Markers closely linked to the Rhg4 locus were used previously to screen a library of bacterial artificial chromosome (BAC) clones from susceptible 'Williams 82' and identified a single 150-kb BAC, Gm_ISb001_056_G02 (56G2). End-sequenced subclones positioned onto a restriction map provided landmarks for identifying the corresponding region from a BAC library from accession PI 437654 with broad resistance to SCN. Seventy-three PI 437654 BACs were assigned to contigs based upon HindIII restriction fragment profiles. Four contigs represented the PI 437654 counterpart of the 'Williams 82' BAC, with PCR assays connecting these contigs. Some of the markers on the PI 437654 contigs are separated by a greater physical distance than in the 'Williams 82' BAC and some primers amplify bands from BACs in the mid-portion of the connected PI 437654 BAC contigs that are not amplified from the 'Williams 82' BAC. These observations suggest that there is an insertion in the PI 437654 genome relative to the 'Williams 82' genome in the Rhg4 region.Key words: BAC, deletion, insertion, resistance gene, soybean cyst nematode.

scholarly journals A Dual-Targeted Soybean Protein Is Involved in Bradyrhizobium japonicum Infection of Soybean Root Hair and Cortical Cells

2011 ◽  
Vol 24 (9) ◽  
pp. 1051-1060 ◽  
Author(s):  
Marc Libault ◽  
Manjula Govindarajulu ◽  
R. Howard Berg ◽  
Yee Tsuey Ong ◽  
Kari Puricelli ◽  
...  
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Soybean Protein ◽  
Carbon Utilization ◽  
Plant Host ◽  
Cortical Cells ◽  
Symbiotic Interaction ◽  
Carbon Supply ◽  
Glycine Max L ◽  
Soybean Gene

The symbiotic interaction between legumes and soil bacteria (e.g., soybean [Glycine max L.] and Bradyrhizobium japonicum]) leads to the development of a new root organ, the nodule, where bacteria differentiate into bacteroids that fix atmospheric nitrogen for assimilation by the plant host. In exchange, the host plant provides a steady carbon supply to the bacteroids. This carbon can be stored within the bacteroids in the form of poly-3-hydroxybutyrate granules. The formation of this symbiosis requires communication between both partners to regulate the balance between nitrogen fixation and carbon utilization. In the present study, we describe the soybean gene GmNMNa that is specifically expressed during the infection of soybean cells by B. japonicum. GmNMNa encodes a protein of unknown function. The GmNMNa protein was localized to the nucleolus and also to the mitochondria. Silencing of GmNMNa expression resulted in reduced nodulation, a reduction in the number of bacteroids per infected cell in the nodule, and a clear reduction in the accumulation of poly-3-hydroxybutyrate in the bacteroids. Our results highlight the role of the soybean GmNMNa gene in regulating symbiotic bacterial infection, potentially through the regulation of the accumulation of carbon reserves.

scholarly journals Construction, Characterization, and Preliminary BAC-End Sequence Analysis of a Bacterial Artificial Chromosome Library of the Tea Plant (Camellia sinensis)

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Jinke Lin ◽  
Dave Kudrna ◽  
Rod A. Wing
Keyword(s):  
Camellia Sinensis ◽  
Bac Library ◽  
Gc Content ◽  
Artificial Chromosome ◽  
Tea Plant ◽  
Average Insert Size ◽  
Plant Genomics ◽  
Insert Size ◽  
Sequence Class ◽  
End Sequences

We describe the construction and characterization of a publicly available BAC library for the tea plant,Camellia sinensis. Using modified methods, the library was constructed with the aim of developing public molecular resources to advance tea plant genomics research. The library consists of a total of 401,280 clones with an average insert size of 135 kb, providing an approximate coverage of 13.5 haploid genome equivalents. No empty vector clones were observed in a random sampling of 576 BAC clones. Further analysis of 182 BAC-end sequences from randomly selected clones revealed a GC content of 40.35% and low chloroplast and mitochondrial contamination. Repetitive sequence analyses indicated that LTR retrotransposons were the most predominant sequence class (86.93%–87.24%), followed by DNA retrotransposons (11.16%–11.69%). Additionally, we found 25 simple sequence repeats (SSRs) that could potentially be used as genetic markers.

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