scholarly journals Insights into the Structural and Functional Evolution of Plant Genomes Afforded by the Nucleotide Sequences of Chromosomes 2 and 4 of Arabidopsis thaliana

Yeast ◽  
2000 ◽  
Vol 1 (1) ◽  
pp. 1-5
Author(s):  
Ian Bancroft
Keyword(s):  
Arabidopsis Thaliana ◽  
Sequence Data ◽  
Plant Genome ◽  
Gene Products ◽  
Duplicated Genes ◽  
Genetic Redundancy ◽  
Macro Scale ◽  
Genome Content ◽  
High Level ◽  
Plant Genome Evolution

The rapidly accumulating genome sequence data from the plant Arabidopsis thaliana allows more detailed analysis of genome content and organisation than ever bafore possible in plants. The genome shows a surprisingly high level of genetic redundancy, with as many as 75% of gene products showing signficant homology to another protien of A. thaliana. Many duplicated genes occur in arrays of conserved order and indicate that A. thaliana is likely to have had a tetraploid ancestor. Analysis of the divergence of duplicated genome segments leads to the prediction of two major modes of plant genome evolution: macro-scale duplication and rearrangement of chromosomes and micro-scale translocation, duplication and loss of individual genes or small groups of genes.

scholarly journals Insights into the Structural and Functional Evolution of Plant Genomes Afforded by the Nucleotide Sequences of Chromosomes 2 and 4 ofArabidopsis thaliana

Yeast ◽  
2000 ◽  
Vol 1 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Ian Bancroft
Keyword(s):  
Sequence Data ◽  
Plant Genome ◽  
Gene Products ◽  
Duplicated Genes ◽  
Genetic Redundancy ◽  
Ofarabidopsis Thaliana ◽  
Macro Scale ◽  
Genome Content ◽  
High Level ◽  
Plant Genome Evolution

The rapidly accumulating genome sequence data from the plantArabidopsis thalianaallows more detailed analysis of genome content and organisation than ever bafore possible in plants. The genome shows a surprisingly high level of genetic redundancy, with as many as 75% of gene products showing signficant homology to another protien ofA. thaliana.Many duplicated genes occur in arrays of conserved order and indicate thatA. thalianais likely to have had a tetraploid ancestor. Analysis of the divergence of duplicated genome segments leads to the prediction of two major modes of plant genome evolution: macro-scale duplication and rearrangement of chromosomes and micro-scale translocation, duplication and loss of individual genes or small groups of genes.

Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 887-892 ◽  
Author(s):  
Anne-Marie van Dodeweerd ◽  
Caroline R Hall ◽  
Elisabeth G Bent ◽  
Samantha J Johnson ◽  
Michael W Bevan ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Genome Structure ◽  
Plant Genome ◽  
Fine Scale ◽  
Plant Genomics ◽  
Homologous Genes ◽  
Conserved Genes ◽  
Plant Genome Evolution

Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.Key words: plant genomics, comparative mapping.

scholarly journals High level expression of transgenes by use of 5^|^#8242;-untranslated region of the Arabidopsis thaliana arabinogalactan-protein 21 gene in dicotyledons

2012 ◽  
Vol 29 (3) ◽  
pp. 319-322 ◽  
Author(s):  
Takeshi Matsui ◽  
Hideyuki Matsuura ◽  
Kazutoshi Sawada ◽  
Eiji Takita ◽  
Satoko Kinjo ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Untranslated Region ◽  
Arabinogalactan Protein ◽  
High Level Expression ◽  
High Level

Leveraging a Pharmacogenomics Knowledgebase to Formulate a Drug Response Phenotype Terminology for Genomic Medicine (Preprint)

2021 ◽  
Author(s):  
Yiqing Zhao ◽  
Matthew Brush ◽  
Chen Wang ◽  
Hongfang Liu ◽  
Robert R Freimuth
Keyword(s):  
Drug Response ◽  
Genomic Medicine ◽  
Genetic Mutations ◽  
Gene Products ◽  
Knowledge Model ◽  
Knowledge Models ◽  
Response Phenotype ◽  
Structured Knowledge ◽  
High Level ◽  
Clinical Systems

BACKGROUND Despite the increasing evidence of utility of genomic medicine in clinical practice, systematically integrating genomic medicine information and knowledge into clinical systems with a high-level of consistency, scalability, and computability remains challenging. A comprehensive terminology is required for relevant concepts and the associated knowledge model for representing relationships. OBJECTIVE Our study aims to propose a drug response phenotype terminology to represent relationships between genetic variants and drugs in existing knowledge models. METHODS In this study, we leveraged PharmGKB, a comprehensive pharmacogenomics (PGx) knowledgebase, to formulate a terminology for drug response phenotypes that can represent relationships between genetic mutations and treatments. We evaluated coverage of the terminology through manual review of a randomly selected subset of 200 sentences extracted from genetic reports that contained concepts for “Genes and Gene Products” and “Treatments”. RESULTS Results showed that our proposed drug response phenotype terminology could cover 96% of the drug response phenotypes in genetic reports. Among 18,653 sentences that contained both “Genes and Gene Products” and “Treatments”, 3,011 sentences were able to be mapped to a drug response phenotype in our proposed terminology, among which the most discussed drug response phenotypes were response (994), sensitivity (829), and survival (332). In addition, we were able to re-analyze genetic report context incorporating the proposed terminology and enrich our previously proposed PGx knowledge model to reveal relationships between genetic mutations and treatments. CONCLUSIONS In conclusion, we proposed a drug response phenotype terminology that enhanced structured knowledge representation of genomic medicine.

Regulation of the junB gene by v-src

1992 ◽  
Vol 12 (8) ◽  
pp. 3356-3364
Author(s):  
I Apel ◽  
C L Yu ◽  
T Wang ◽  
C Dobry ◽  
M E Van Antwerp ◽  
...  
Keyword(s):  
Kinase Activity ◽  
Gene Products ◽  
3T3 Cells ◽  
Tyrosine Kinase Activity ◽  
Basal Expression ◽  
High Level ◽  
Transformed Cell Lines ◽  
Point Mutagenesis ◽  
Nih 3T3 ◽  
Nucleotide Region

The proteins encoded by cellular and viral src genes are believed to be involved in the transmission of mitogenic signals, the nuclear recipients of which are largely unknown. In this work, we report that four different v-src-transformed cell lines from three different species possess elevated levels of junB transcripts. Transient expression of junB promoter-chloramphenicol acetyltransferase constructs in NIH 3T3 cells was used to demonstrate that the increase in junB transcripts was specifically associated with v-src expression and could not be recapitulated with a c-src, v-H-ras, or v-raf expression vector. Deletion mutants were used to localize the v-src-responsive region in the junB promoter to a 121-nucleotide region encompassing the CCAAT and TATAA elements. This region is distinct from one in the 5' untranslated region of the junB gene which is required to maintain its high-level basal expression. Point mutagenesis of the junB TATAA box completely abolished v-src responsiveness, suggesting that proteins which bind to this element are modified by src transformation. Several v-src and c-src mutants were used to demonstrate that elevated tyrosine kinase activity of src proteins is required for the observed effects on junB expression. Finally, homology between the TATAA box regions of junB and the unrelated but src-responsive gene 9E3/CEF-4 suggests that modulation of gene activity through proteins which bind to this region may be a recurrent, although not exclusive, theme in src transforming action. Our results suggest that src proteins may modulate some nuclear effectors through pathways not involving cellular ras or raf gene products.

Isolation of Listeria monocytogenes mutants with high-level in vitro expression of host cytosol-induced gene products

2003 ◽  
Vol 48 (6) ◽  
pp. 1537-1551 ◽  
Author(s):  
Lynne M. Shetron-Rama ◽  
Kimberly Mueller ◽  
Juan M. Bravo ◽  
H. G. Archie Bouwer ◽  
Sing Sing Way ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Gene Products ◽  
In Vitro Expression ◽  
High Level

Two new genera and twelve new species of Graphidaceae from Puerto Rico: a case for higher endemism of lichenized fungi in islands of the Caribbean?

Phytotaxa ◽  
2014 ◽  
Vol 189 (1) ◽  
pp. 186 ◽  
Author(s):  
JOEL A. MERCADO-DÍAZ ◽  
ROBERT LÜCKING ◽  
SITTIPORN PARNMEN
Keyword(s):  
Puerto Rico ◽  
New Species ◽  
Sequence Data ◽  
New Combination ◽  
New Genera ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Biodiversity Knowledge ◽  
Three New Species ◽  
High Level

Two new genera and twelve new species of Graphidaceae are described from Puerto Rico. The two new genera, Borinquenotrema and Paratopeliopsis, are based on a combination of molecular sequence data and phenotype characters. Borinquenotrema, with the single new species B. soredicarpum, features rounded ascomata developing beneath and persistently covered with soralia and with an internal anatomy reminescent of Carbacanthographis; it is close to the  tribe Ocellularieae. Paratopeliopsis, including the single new species P. caraibica, resembles a miniature Topeliopsis but differs in the distinctly farinose thallus and the small, brown ascospores; it is not closely related to the latter genus but belongs in tribe Thelotremateae. The other ten new species belong in the genera Acanthotrema, Clandestinotrema, Compositrema, Fissurina, Ocellularia, and Thalloloma. Acanthotrema alboisidiatum is closely related to A. brasilianum but differs in the short, white isidia resembling insect eggs. Clandestinotrema portoricense has a unique ascospore type with a longitudinal septum only in the proximal cell. Compositrema borinquense resembles a species of Stegobolus but belongs in Compositrema based on sequence data, and is characterized by ascomata with a unique columella composed of thick, irregularly radiating strands. The second new species in this genus, C. isidiofarinosum, differs by its ecorticate, farinose thallus with scattered, corticate isidia and by its small ascomata with inconspicuous columella. The three new species of Fissurina all have 3-septate ascospores and are otherwise characterized by an isidiate thallus and stellate, orange-yellow lirellae (F. aurantiacostellata), a verrucose thallus strongly encrusted with calcium oxalate crystals and white, irregularly branched lirellae (F. crystallifera), and myriotremoid ascomata arranged in short lines (F. monilifera). Ocellularia portoricensis belongs in the core group of Ocellularia and differs from O. cavata in the white medulla and the larger ascospores becoming brown, whereas O. vulcanisorediata produces prominent soralia and immersed ascomata with apically carbonized excipulum and columella and small, transversely septate, hyaline ascospores; it is closely related to O. conformalis. Finally, Thalloloma rubromarginatum resembles T. haemographum in the brownish lirellae with bright red margin but differs from that and other species in the corticate thallus and the norstictic acid chemistry. The new combination Ampliotrema rimosum (Hale) Mercado-Díaz, Lücking & Parnmen is also proposed. Considering the current biodiversity knowledge on this family, the high level of endemism observed in other groups of organisms in the island, and the relatively high number of Graphidaceae described, it is highly likely that at least some of these new taxa are endemic to the island. This view is further supported by the unique features of several of the new species, representing novel characters in the corresponding genera.

Isolation of a cDNA corresponding to a developmentally regulated transcript in rat intestine

1988 ◽  
Vol 8 (10) ◽  
pp. 4243-4249
Author(s):  
J Filmus ◽  
J G Church ◽  
R N Buick
Keyword(s):  
Cell Line ◽  
Sequence Data ◽  
Human Colon ◽  
Intestinal Cell ◽  
Homologous Gene ◽  
Rat Intestine ◽  
Human Colon Carcinoma Cell ◽  
Reading Frame ◽  
Intestinal Cell Line ◽  
High Level

We report the isolation of a cDNA clone corresponding to a transcript that is accumulated differentially in rat intestine during development. Clone OCI-5 was selected from the rat intestinal cell line IEC-18, which represents primitive intestinal epithelial crypt cells. Expression was high in rat fetal intestine between 15 and 19 days of development and thereafter was progressively down regulated, becoming undetectable after weaning. Clone OCI-5 detected homologous sequences in human and murine cells. In particular, a high level of expression was detected in CaCo-2, a human colon carcinoma cell line, which is known to express molecules characteristic of fetal small intestinal cells. Expression of a homologous gene was also detected in F9 murine teratocarcinoma cells when they were induced to differentiate into parietal or visceral endodermlike cells. When IEC-18 cells were transformed by activated H-ras or v-src genes, expression of clone OCI-5 was suppressed; the degree of down-regulation correlated with the extent of morphological change induced in the transformed IEC-18 cells. The sequence of clone OCI-5 showed an open reading frame that was capable of encoding a protein of 597 amino acids, but no strong homology was found with any of the proteins registered in the protein sequence data base.

scholarly journals Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana

2020 ◽  
Vol 21 (19) ◽  
pp. 7404
Author(s):  
Yanqiao Zhu ◽  
Oliver Berkowitz ◽  
Jennifer Selinski ◽  
Andreas Hartmann ◽  
Reena Narsai ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Hordeum Vulgare ◽  
Mitochondrial Biogenesis ◽  
Expression Patterns ◽  
Tca Cycle ◽  
Transcript Abundance ◽  
Pentatricopeptide Repeat ◽  
Orthologous Genes ◽  
Regulatory Processes ◽  
High Level

Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.

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