scholarly journals Comparative DNA Sequence Analysis of Wheat and Rice Genomes

2003 ◽  
Vol 13 (8) ◽  
pp. 1818-1827 ◽  
Author(s):  
Mark E. Sorrells ◽  
Mauricio La Rota ◽  
Catherine E. Bermudez-Kandianis ◽  
Robert A. Greene ◽  
Ramesh Kantety ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Chromosomal Rearrangements ◽  
Crop Improvement ◽  
Rice Genome ◽  
Wheat Chromosome ◽  
Comparative Sequence Analysis ◽  
Crop Species ◽  
Transfer Of Information

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to crop species has revolutionized molecular genetics and crop improvement strategies. This study compared 4485 expressed sequence tags (ESTs) that were physically mapped in wheat chromosome bins, to the public rice genome sequence data from 2251 ordered BAC/PAC clones using BLAST. A rice genome view of homologous wheat genome locations based on comparative sequence analysis revealed numerous chromosomal rearrangements that will significantly complicate the use of rice as a model for cross-species transfer of information in nonconserved regions.

DNA

1995 ◽  
Author(s):  
Peter M. Rice ◽  
Keith EHiston
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Software Package ◽  
Sequence Data ◽  
Sequence Assembly ◽  
Analysis Software ◽  
Considerable Time ◽  
Laboratory Computer ◽  
Software Packages ◽  
Common Laboratory

Software packages are available for all common laboratory computer systems. The packages for personal computers (PC or Macintosh) are able assemble and correct the sequence, those for the larger systems (VAX or Unix) are generally able to analyze the sequence in greater detail. Most laboratories will be able to use sequence assembly programs in their favorite sequence analysis software package. In general, the stages of sequence assembly are gel entry, overlap detection, editing, and reporting. The available programs differ in the ways they handle each of these tasks. No single package is ideal, though all should be adequate for a smaller project such as a single cDNA. Particular attention should be given to the quality and features of the editor, as this is where most time will be spent, and to the possibilities of extending the software to cope with problems that may arise. Good status reports and a choice of methods for overlap detection can save considerable time in resolving ambiguities and correcting errors later. Figure 1 lists some of the commonly used sequence assembly programs. The prices vary widely depending on the features of the package and the options for academic or commercial licenses. Originally, each package used its own “special” codes to represent ambiguous bases and gaps in sequences. Mostpackages now use the standard IUB-IUPAC codes (Figure 2) for the nucleotides, though the program documentation should be checked before starting the project. The task of sequence reading depends on the sequencing protocol used. In many laboratories the sequence is generated on an autoradiograph (Figure 3) from which the sequence is read. Although automated gel readers are on the market, most sequence data is read manually with the aid of a digitizer. Most sequence assembly programs accept DNA sequence read by a sonic digitizer. An example of a device which is supported by most of the available programs is the GrafBar GP-7 [Science Accessories Corporation, Southport, CT, US A and P.M.S. (Instruments) Ltd., Waldeck House, Reform Road, Maidenhead, Berks, SL6 8BX, UK]. Sonic digitizers have a stylus to point to locations on an autoradiograph, which is illuminated from below by a light box.

scholarly journals DNA Sequence Analysis of dtxR Gene (Partial) of Corynebacterium diphtheriae Causing Diphtheria in Jawa and Kalimantan Islands, Indonesia

2017 ◽  
Vol 9 (2) ◽  
pp. 91
Author(s):  
Sunarno Sunarno ◽  
Yuanita Mulyastuti ◽  
Nelly Puspandari ◽  
Kambang Sariadji
Keyword(s):  
Sequence Analysis ◽  
Multiplex Pcr ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Clinical Specimen ◽  
Corynebacterium Diphtheriae ◽  
Dna Sequence Analysis ◽  
Local Alignment ◽  
Pcr Products

BACKGROUND: dtxR gene is a global regulator that can be used as a marker for detection of Corynebacterium diphtheriae (C. diphtheriae) and it is also a representative tool for mapping purpose (molecular typing) of this bacteria. The aim of this study was to analyze the DNA sequences of partial dtxR gene of C. diphtheriae causing diphtheria in some region of Indonesia. DNA sequence analysis was used to verify the accuracy of the in-house multiplex polymerase chain reaction (PCR) method that used for detection of C. diphtheriae in the clinical specimen as well as a preliminary study to determine the strain diversity of C. diphtheriae circulating in Indonesia.METHODS:Ten PCR products targeting the dtxR gene that have been detected as positive C. diphtheriae previously by in-house multiplex PCR used as samples in this study. The DNA sequencing carried out by Sanger method and the sequence data was analyzed by Bioedit software offline and basic local alignment sequence typing (BLAST) online.RESULTS: All of DNA sequence analyzed in this study were similar or identical to the dtxR gene sequence data of C. diphtheriae registered in GenBank. Within the 162 nucleotides (base 150-311) of dtxR gene that analyzed, at least 2 clonals were found among 10 samples. Substitutions of 2 nucleotides (base 225 and 273) was detected, both were silent mutation.CONCLUSION:Ten partial DNA sequences of dtxR genes in this study verify the accuracy of in-house multiplex PCR which used to identify the bacteria causing diphtheria in the clinical specimen. The DNA sequences also represent the existing diversity of the bacteria causing diphtheria circulating in Indonesia.KEYWORDS: dtxR, C. diphtheriae, diphtheria, Indonesia

scholarly journals Information Theory and Multivariate Techniques for Analyzing DNA Sequence Data: An Example from Tomato Genes

1970 ◽  
Vol 1 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Bal K Joshi ◽  
Dilip R Panthee
Keyword(s):  
Information Theory ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Crop Improvement ◽  
Principal Component ◽  
Amino Acid Sequences ◽  
Multivariate Techniques ◽  
Sequence Complexity ◽  
Diversity Assessment

DNA and amino acid sequences are alphabetic symbols having no underlying metric. Use of information theory is one of the solutions for sequence metric problems. The reflection of DNA sequence complexity in phenotype stability might be useful for crop improvement. Shannon-Weaver index (Shannon Entropy, H') and mutual information (MI) index were estimated from DNA sequences of 22 genes, consisted of two gene families of tomato, namely disease resistance and fruit quality. Main objective was use of information theory and multivariate techniques to understand diversity among genes and relate the sequence complexity with phenotypes. The normalized H' value ranged from 0.429 to 0.461. The highest diversity was observed in the gene Crtr-B (beta carotene hydroxylase). Two principal components which accounted for 36.65% variation placed these genes into four groups. Groupings of these genes by both principal component and cluster analyses showed clearly the similarity at phenotypes levels within cluster. Sequences similarity among genes was observed within a family. Diversity assessment of genes applying information theory should link to understand the sequences complexity with respect to gene stability for example stability of resistance gene.Key words: Diversity analysis; DNA sequences; principal component analysis; tomato genesNepal Journal of Biotechnology, 2011, Vol. 1, No. 1 pp.1-9

scholarly journals Comparative Sequence Analysis of Human Minisatellites Showing Meiotic Repeat Instability

1999 ◽  
Vol 9 (2) ◽  
pp. 130-136 ◽  
Author(s):  
John Murray ◽  
Jérôme Buard ◽  
David L. Neil ◽  
Edouard Yeramian ◽  
Keiji Tamaki ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Sequence Data ◽  
Comparative Sequence Analysis ◽  
Gene Promoters ◽  
Repeat Instability ◽  
Repeat Array ◽  
Comparative Sequence ◽  
Link Type ◽  
Genomic Environment ◽  
Data Library

The highly variable human minisatellites MS32 (D1S8), MS31A (D7S21), and CEB1 (D2S90) all show recombination-based repeat instability restricted to the germline. Mutation usually results in polar interallelic conversion or occasionally in crossovers, which, at MS32 at least, extend into DNA flanking the repeat array, defining a localized recombination hotspot and suggesting that cis-acting elements in flanking DNA can influence repeat instability. Therefore, comparative sequence analysis was performed to search for common flanking elements associated with these unstable loci. All three minisatellites are located in GC-rich DNA abundant in dispersed and tandem repetitive elements. There were no significant sequence similarities between different loci upstream of the unstable end of the repeat array. Only one of the three loci showed clear evidence for putative coding sequences near the minisatellite. No consistent patterns of thermal stability or DNA secondary structure were shared by DNA flanking these loci. This work extends previous data on the genomic environment of minisatellites. In addition, this work suggests that recombinational activity is not controlled by primary or secondary characteristics of the DNA sequence flanking the repeat array and is not obviously associated with gene promoters as seen in yeast.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF048727(CEB1), AF048728 (MS31A), and AF048729 (MS32).]

scholarly journals Development of Genomic Tools for Cucumber, Cucumis sativus L.

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 774C-774
Author(s):  
Rebecca Grumet* ◽  
Xiaofeng Wang ◽  
Mohamed Tawfik ◽  
Mitch McGrath
Keyword(s):  
Cucumis Sativus ◽  
Genomic Library ◽  
Sequence Data ◽  
Crop Improvement ◽  
Limited Attention ◽  
Yeast Two Hybrid ◽  
High Quality ◽  
Crop Species ◽  
Genomic Tools ◽  
Two Hybrid

Genomics tools have become increasingly varied and valuable for crop improvement. While several species have been targeted for concerted genomic efforts, the majority of horticultural species have received limited attention. Despite the wide variety of important cucurbit crop species, the Cucurbitaceae family has had minimal effort. We have initiated projects to develop genomic tools for cucumber, Cucumis sativus L. Efforts include production of cDNA, yeast two-hybrid, and genomic libraries, and development of an EST database and website for cucumber genomics. Sequences of cucumber leaf ESTs so far indicate that the cDNA library is of high quality and has modest redundancy. Distribution of sequences, as nominally predicted from GeneBank BLAST analysis, indicates that expressed genes fall in the following general categories: photosynthesis (21%), DNA/RNA/protein synthesis (20%), metabolism (15%), signaling (5%), other (16%), and unknown proteins (23%). Cucumber sequence data have been deposited into GenBank and are available on the Michigan State Univ. website (http://genomics.msu.edu/cucumberdb). The yeast two-hybrid library has been successfully used to identify and characterize several genes based on interaction with key proteins of interest, including genes interacting with viral replicases and poly(A) binding protein. The genomic library has been verified to be of high quality and has been used to identify clones of interest.

Sequence analysis of cloned human satellite DNAs reveals nonrandom variations

Genome ◽  
1993 ◽  
Vol 36 (2) ◽  
pp. 334-342
Author(s):  
Katia Sol ◽  
Michael S. DuBow
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Hela Cells ◽  
Comparative Sequence Analysis ◽  
Satellite Dnas ◽  
Repetitive Dnas ◽  
Comparative Sequence ◽  
Mutational Hotspots ◽  
Rapid Amplification ◽  
High Degree

We have cloned, from the genome of HeLa cells, related 1.8-kb highly repetitive EcoRI satellite II (and III) DNA family members that displayed a high degree of TaqI and HinfI variations. Comparative sequence analysis of these cloned DNAs suggests that highly repetitive satellite DNAs may have evolved and diversified from the rapid amplification of a pentameric unit (5′ TTCCA 3′), by processes including random and non-random mutations. Base conservation, as well as mutational hotspots, were found associated with these related satellite II and III DNAs. The accumulation of C to G transversions within the pentamers, generating TaqI and HinfI sites, as well as C to T transitions at CpN dinucleotides, appear to be responsible for much of the microheterogeneity observed between related satellite II and III DNA family members.Key words: repetitive DNAs, heterochromatin, satellite DNAs, DNA sequence.

scholarly journals Epigenetics for Crop Improvement in Times of Global Change

Biology ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 766
Author(s):  
Ioanna Kakoulidou ◽  
Evangelia V. Avramidou ◽  
Miroslav Baránek ◽  
Sophie Brunel-Muguet ◽  
Sara Farrona ◽  
...  
Keyword(s):  
Climate Change ◽  
Gene Expression ◽  
Dna Sequence ◽  
Crop Production ◽  
In Vitro Regeneration ◽  
Crop Improvement ◽  
Research Field ◽  
Plant Performance ◽  
Crop Species

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity—naturally, genetically, chemically, or environmentally induced—can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.

scholarly journals IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae

2019 ◽  
Author(s):  
Daniel S. Carvalho ◽  
James C. Schnable
Keyword(s):  
Wild Species ◽  
Sequence Data ◽  
Transcriptome Assembly ◽  
Crop Improvement ◽  
Grass Species ◽  
Crop Species ◽  
Long Read ◽  
Syntenic Gene ◽  
Panicoid Grass ◽  
Reference Genomes

AbstractThe number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses – Poaceae – have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here we used long read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on alignments to the sorghum genome we estimate that assembled consensus transcripts from each species capture between 54.2 and 65.7% of the conserved syntenic gene space in grasses. Genes co-opted into C4 were also well represented in this dataset, despite concerns that, because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript-based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long read sequences from these wild species was consistent with previously published phylogenies. It is hoped that this data, targeting under represented classes of species within the PACMAD grasses – wild species and species utilizing C3 photosynthesis – will aid in futurue studies of domestication and C4 evolution by decreasing the evolutionary distance between C4 and C3 species within this clade, enabling more accurate comparisons associated with evolution of the C4 pathway.

Sign in / Sign up

Export Citation Format

Share Document