scholarly journals A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

2011 ◽  
Vol 12 (5) ◽  
pp. R48 ◽  
Author(s):  
Andrea Zuccolo ◽  
John E Bowers ◽  
James C Estill ◽  
Zhiyong Xiong ◽  
Meizhong Luo ◽  
...  
Keyword(s):  
Physical Map ◽  
Genome Structure ◽  
Angiosperm Genome

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

2007 ◽  
Vol 58 (6) ◽  
pp. 470 ◽  
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.

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.

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 Computational Tools forBrassica–ArabidopsisComparative Genomics

2005 ◽  
Vol 6 (3) ◽  
pp. 147-152 ◽  
Author(s):  
Paul Beckett ◽  
Ian Bancroft ◽  
Martin Trick
Keyword(s):  
Genome Sequence ◽  
In Silico ◽  
Physical Map ◽  
Genome Structure ◽  
Genome Project ◽  
Genome Survey ◽  
Physical Maps ◽  
Alignment Tool ◽  
Wide Range ◽  
Survey Sequence

Recent advances, such as the availability of extensive genome survey sequence (GSS) data and draft physical maps, are radically transforming the means by which we can dissectBrassicagenome structure and systematically relate it to theArabidopsismodel. Hitherto, our view of the co-linearities between these closely related genomes had been largely inferred from comparative RFLP data, necessitating substantial interpolation and expert interpretation. Sequencing of theBrassica rapagenome by the MultinationalBrassicaGenome Project will, however, enable an entirely computational approach to this problem. Meanwhile we have been developing databases and bioinformatics tools to support our work inBrassicacomparative genomics, including a recently completed draft physical map ofB. rapaintegrated with anchor probes derived from theArabidopsisgenome sequence. We are also exploring new ways to display the emergingBrassica–Arabidopsissequence homology data. We have mapped all publicly available Brassica sequencesin silicoto theArabidopsisTIGR v5 genome sequence and published this in the ATIDB database that uses Generic Genome Browser (GBrowse). Thisin silicoapproach potentially identifies all paralogous sequences and so we colour-code the significance of the mappings and offer an integrated, real-time multiple alignment tool to partition them into paralogous groups. The MySQL database driving GBrowse can also be directly interrogated, using the powerful API offered by the Perl Bio∷DB∷GFF methods, facilitating a wide range of data-mining possibilities.

Comparison off genetic distance and order off DNA markers in five populations of rice

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 946-956 ◽  
Author(s):  
B. A. Antonio ◽  
T. Inoue ◽  
H. Kajiya ◽  
Y. Nagamura ◽  
N. Kurata ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Linkage Map ◽  
Gene Order ◽  
Dna Markers ◽  
Physical Map ◽  
Recombinant Inbred Lines ◽  
Genome Structure ◽  
High Density ◽  
Backcross Population ◽  
Mapping Populations

A group of about 300 evenly distributed DNA markers from a high density RFLP linkage map of rice constructed using an F2 population derived from a japonica variety, Nipponbare, and an indica variety, Kasalath, were used to evaluate gene order and genetic distance in four other rice mapping populations. The purpose of this study was to determine the degree to which information gained from the high density linkage map could be applied to other mapping populations, particularly with regard to its utility in bridging quantitative traits and molecular and physical mapping information. The mapping populations consisted of two F2 populations derived from Dao Ren Qiao/Fl-1084 and Kinandangputi/Fl-1007, recombinant inbred lines from Asominori/IR24, and a backcross population from Sasanishiki/Habataki//Sasanishiki. All DNA markers commonly mapped in the four populations showed the same linkage groups as in the Nipponbare/Kasalath linkage map with conserved linkage order. The genetic distance between markers among the different populations did not vary to a significant level in any of the 12 chromosomes. The differences in some markers could be attributed to the size of the population used in the construction of the linkage maps. Furthermore, the conservation of linkage order found in the distal region of chromosomes 11 and 12 was also confirmed in the RFLP maps based on the four populations of rice. These suggest that any major genetic information from the Nipponbare/Kasalath map can be expected to be approximately the same in other crosses or populations. This high density RFLP linkage map, which is being utilized in constructing a physical map of rice, can be very useful in interpreting genome structure with great accuracy in other populations. Key words : linkage map, japonica, indica, gene order, genetic distance.

Dysregulation of HOX as a Potential Therapeutic Target in Breast Cancer

2020 ◽  
Vol 27 ◽  
Author(s):  
Ji-Yeon Lee ◽  
Myoung Hee Kim
Keyword(s):  
Breast Cancer ◽  
Hox Genes ◽  
Therapeutic Potential ◽  
Expression Patterns ◽  
Genome Structure ◽  
Control Cell ◽  
Three Dimensional ◽  
Cellular Processes ◽  
Hox Protein

: HOX genes belong to the highly conserved homeobox superfamily, responsible for the regulation of various cellular processes that control cell homeostasis, from embryogenesis to carcinogenesis. The abnormal expression of HOX genes is observed in various cancers, including breast cancer; they act as oncogenes or as suppressors of cancer, according to context. In this review, we analyze HOX gene expression patterns in breast cancer and examine their relationship, based on the three-dimensional genome structure of the HOX locus. The presence of non-coding RNAs, embedded within the HOX cluster, and the role of these molecules in breast cancer have been reviewed. We further evaluate the characteristic activity of HOX protein in breast cancer and its therapeutic potential.

Targeting IDH Mutations in AML: Wielding the Double-edged Sword of Differentiation

2020 ◽  
Vol 20 (7) ◽  
pp. 490-500 ◽  
Author(s):  
Justin S. Becker ◽  
Amir T. Fathi
Keyword(s):  
Genome Structure ◽  
Cellular Metabolism ◽  
Standard Of Care ◽  
Competitive Inhibitor ◽  
Driver Mutations ◽  
New Class ◽  
Regulatory Enzymes ◽  
Idh Mutations ◽  
Genomic Characterization

The genomic characterization of acute myeloid leukemia (AML) by DNA sequencing has illuminated subclasses of the disease, with distinct driver mutations, that might be responsive to targeted therapies. Approximately 15-23% of AML genomes harbor mutations in one of two isoforms of isocitrate dehydrogenase (IDH1 or IDH2). These enzymes are constitutive mediators of basic cellular metabolism, but their mutated forms in cancer synthesize an abnormal metabolite, 2- hydroxyglutarate, that in turn acts as a competitive inhibitor of multiple gene regulatory enzymes. As a result, leukemic IDH mutations cause changes in genome structure and gene activity, culminating in an arrest of normal myeloid differentiation. These discoveries have motivated the development of a new class of selective small molecules with the ability to inhibit the mutant IDH enzymes while sparing normal cellular metabolism. These agents have shown promising anti-leukemic activity in animal models and early clinical trials, and are now entering Phase 3 study. This review will focus on the growing preclinical and clinical data evaluating IDH inhibitors for the treatment of IDH-mutated AML. These data suggest that inducing cellular differentiation is central to the mechanism of clinical efficacy for IDH inhibitors, while also mediating toxicity for patients who experience IDH Differentiation Syndrome. Ongoing trials are studying the efficacy of IDH inhibitors in combination with other AML therapies, both to evaluate potential synergistic combinations as well as to identify the appropriate place for IDH inhibitors within existing standard-of-care regimens.

Coronavirus: history, genome structure and pathogenesis

Coronaviruses ◽  
2020 ◽  
Vol 01 ◽  
Author(s):  
Poonam B ◽  
Prabhjot Kaur Gill
Keyword(s):  
Genome Structure ◽  
Public Health Research ◽  
Replication Process ◽  
Virus Family ◽  
Enveloped Virus ◽  
Target Organs ◽  
Transcription Process ◽  
Recent Emergence ◽  
The Family ◽  
Discontinuous Transcription

Background: The positive sense and inordinate large RNA genome are enclosed by helical nuceocapsids along with an outermost layer belongs to the family Coronaviridae. The phylogenetic tree of this family has been quartered into Class1 as alpha, Class 2 as beta, Class 3 as gamma and Class 4 as delta CoV. The mammalian respiratory and gastrointestinal tracts are the main target organs of this enveloped virus with misperceived mechanisms. The relevance of this virus family has considerably increased by the dint of recent emergence of the Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), which are caused by viruses belonging to the beta-CoV group. Aim: Aforesaid illustrations of emergence of coronavirus diseases over the past two decades, SARS (2002 and 2003) and MERS (2012 to present) - the ongoing COVID-19 outbreak has pressurized the WHO to take innovative measures for public health, research and medical communities. The aim of the present review is to have proficiency in coronavirus replication and transcription process which is still in its infancy. Conclusion: An outcome of epidemics, it is being recognized as one of the most advancing viruses by the virtue of high genomic nucleotide substitution rates and recombination. The hallmark of coronavirus replication is discontinuous transcription resulting in the production of multiple subgenomic mRNAs having sequences complementary to both ends of the genome. Therefore, complete genome sequence of coronavirus will be used as frame of reference for knowing this classical phenomenon of RNA replication process. Finally, research on the pathogenesis of coronaviruses and the host immunopathological response will aid in designing vaccines and minimizing mortality rate.

Sign in / Sign up

Export Citation Format

Share Document