scholarly journals Analysis of Expressed Sequence Tags from Uromyces appendiculatus Hyphae and Haustoria and Their Comparison to Sequences from Other Rust Fungi

2008 ◽  
Vol 98 (10) ◽  
pp. 1126-1135 ◽  
Author(s):  
D. P. Puthoff ◽  
A. Neelam ◽  
M. L. Ehrenfried ◽  
B. E. Scheffler ◽  
L. Ballard ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Sequence Data ◽  
Cellular Function ◽  
Rust Fungi ◽  
Open Reading Frames ◽  
Uromyces Appendiculatus ◽  
Data Set ◽  
Uromyces Fabae ◽  
Expressed Sequence ◽  
Reading Frames

Hyphae, 2 to 8 days postinoculation (dpi), and haustoria, 5 dpi, were isolated from Uromyces appendiculatus infected bean leaves (Phaseolus vulgaris cv. Pinto 111) and a separate cDNA library prepared for each fungal preparation. Approximately 10,000 hyphae and 2,700 haustoria clones were sequenced from both the 5′ and 3′ ends. Assembly of all of the fungal sequences yielded 3,359 contigs and 927 singletons. The U. appendiculatus sequences were compared with sequence data for other rust fungi, Phakopsora pachyrhizi, Uromyces fabae, and Puccinia graminis. The U. appendiculatus haustoria library included a large number of genes with unknown cellular function; however, summation of sequences of known cellular function suggested that haustoria at 5 dpi had fewer transcripts linked to protein synthesis in favor of energy metabolism and nutrient uptake. In addition, open reading frames in the U. appendiculatus data set with an N-terminal signal peptide were identified and compared with other proteins putatively secreted from rust fungi. In this regard, a small family of putatively secreted RTP1-like proteins was identified in U. appendiculatus and P. graminis.

scholarly journals Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni

2004 ◽  
Vol 78 (6) ◽  
pp. 2967-2978 ◽  
Author(s):  
Ricardo DeMarco ◽  
Andre T. Kowaltowski ◽  
Abimael A. Machado ◽  
M. Bento Soares ◽  
Cybele Gargioni ◽  
...  
Keyword(s):  
Schistosoma Mansoni ◽  
Sequence Data ◽  
Open Reading Frames ◽  
Expression Library ◽  
Data Set ◽  
Human Parasite ◽  
Gene Transcripts ◽  
Different Populations ◽  
Expressed Sequence ◽  
Lower Copy

ABSTRACT Using the data set of 180,000 expressed sequence tags (ESTs) of the blood fluke Schistosoma mansoni generated recently by our group, we identified three novel long-terminal-repeat (LTR)- and one novel non-LTR-expressed retrotransposon, named Saci-1, -2, and -3 and Perere, respectively. Full-length sequences were reconstructed from ESTs and have deduced open reading frames (ORFs) with several uncorrupted features, characterizing them as possible active retrotransposons of different known transposon families. Alignment of reconstructed sequences to available preliminary genome sequence data confirmed the overall structure of the transposons. The frequency of sequenced transposon transcripts in cercariae was 14% of all transcripts from that stage, twofold higher than that in schistosomula and three- to fourfold higher than that in adults, eggs, miracidia, and germ balls. We show by Southern blot analysis, by EST annotation and tallying, and by counting transposon tags from a Social Analysis of Gene Expression library, that the four novel retrotransposons exhibit a 10- to 30-fold lower copy number in the genome and a 4- to 200-fold-higher transcriptional rate per copy than the four previously described S. mansoni retrotransposons. Such differences lead us to hypothesize that there are two different populations of retrotransposons in S. mansoni genome, occupying different niches in its ecology. Examples of retrotransposon fragment inserts were found into the 5′ and 3′ untranslated regions of four different S. mansoni target gene transcripts. The data presented here suggest a role for these elements in the dynamics of this complex human parasite genome.

scholarly journals Identification, Characterization, and Mapping of Expressed Sequence Tags from an Embryonic Zebrafish Heart cDNA Library

2000 ◽  
Vol 10 (12) ◽  
pp. 1915-1927
Author(s):  
Christopher Ton ◽  
David M. Hwang ◽  
Adam A. Dempsey ◽  
Hong-Chang Tang ◽  
Jennifer Yoon ◽  
...  
Keyword(s):  
Cdna Library ◽  
Expressed Sequence Tags ◽  
Sequence Data ◽  
Cell Structure ◽  
Expression Patterns ◽  
Data Set ◽  
Link Type ◽  
Chromosome Segments ◽  
Expressed Sequence ◽  
Zebrafish Heart

The generation of expressed sequence tags (ESTs) has proven to be a rapid and economical approach by which to identify and characterize expressed genes. We generated 5102 ESTs from a 3-d-old embryonic zebrafish heart cDNA library. Of these, 57.6% matched to known genes, 14.2% matched only to other ESTs, and 27.8% showed no match to any ESTs or known genes. Clustering of all ESTs identified 359 unique clusters comprising 1771 ESTs, whereas the remaining 3331 ESTs did not cluster. This estimates the number of unique genes identified in the data set to be approximately 3690. A total of 1242 unique known genes were used to analyze the gene expression patterns in the zebrafish embryonic heart. These were categorized into seven categories on the basis of gene function. The largest class of genes represented those involved in gene/protein expression (25.9% of known transcripts). This class was followed by genes involved in metabolism (18.7%), cell structure/motility (16.4%), cell signaling and communication (9.6%), cell/organism defense (7.1%), and cell division (4.4%). Unclassified genes constituted the remaining 17.91%. Radiation hybrid mapping was performed for 102 ESTs and comparison of map positions between zebrafish and human identified new synteny groups. Continued comparative analysis will be useful in defining the boundaries of conserved chromosome segments between zebrafish and humans, which will facilitate the transfer of genetic information between the two organisms and improve our understanding of vertebrate evolution.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.BE693120–BE693210 and BE704450.]

scholarly journals Nitrogen or Sulfur Starvation Differentially Affects Phycobilisome Degradation and Expression of the nblA Gene in Synechocystis Strain PCC 6803

2001 ◽  
Vol 183 (10) ◽  
pp. 2989-2994 ◽  
Author(s):  
Catherine Richaud ◽  
Gérald Zabulon ◽  
Annette Joder ◽  
Jean-Claude Thomas
Keyword(s):  
Sequence Data ◽  
Open Reading Frames ◽  
Northern Hybridization ◽  
Sulfur Starvation ◽  
P Limitation ◽  
Kanamycin Cassette ◽  
N Starvation ◽  
Pcc 7942 ◽  
Reading Frames ◽  
Pcc 6803

ABSTRACT Nitrogen (N) limitation in cyanobacteria is well documented: a reduced growth rate is observed, accompanied by a cessation of phycobiliprotein synthesis and an ordered degradation of phycobilisomes (PBS). This leads to a dramatic bleaching phenomenon known as chlorosis. In Synechococcus strain PCC 7942, bleaching due to PBS degradation is also observed under sulfur (S) or phosphorus (P) limitation, and all three are under the control of the nblAgene product, a 59-amino-acid polypeptide which is overexpressed under N, S, and P starvation (J. L. Collier, and A. R. Grossman, EMBO J. 13:1039–1047, 1994). Cyanobase sequence data forSynechocystis strain PCC 6803 indicate the presence of two tandem open reading frames (sll0452 and sll0453) homologous tonblA. We cloned the two genes, identified a unique 5′ mRNA end suggestive of a single transcription start site, and studiednblA expression under conditions of N or S starvation by Northern hybridization: transcripts were detected only under N starvation (no signal is detected in replete medium or with S starvation), whether nblA1 or nblA2 was used as a probe. Mutations in nblA1 and nblA2 were constructed by insertion of a kanamycin cassette; both mutations were nonbleaching under N starvation. Synechocystis strain PCC 6803 does not bleach under S starvation, consistent with the absence ofnblA induction in these conditions. These results were confirmed by analysis of the PBS components: sequential degradation of phycocyanin and associated linkers was observed only under conditions of N starvation. This indicates differences betweenSynechocystis strain PCC 6803 and Synechococcusstrain PCC 7942 in their regulatory and signaling pathways leading to N- and S-starved phenotypes.

scholarly journals Cloning and Genetic Analyses of the Bacteriocin 41 Determinant Encoded on the Enterococcus faecalis Pheromone-Responsive Conjugative Plasmid pYI14: a Novel Bacteriocin Complemented by Two Extracellular Components (Lysin and Activator)

2008 ◽  
Vol 190 (6) ◽  
pp. 2075-2085 ◽  
Author(s):  
Haruyoshi Tomita ◽  
Elizabeth Kamei ◽  
Yasuyoshi Ike
Keyword(s):  
Enterococcus Faecalis ◽  
Sequence Data ◽  
Open Reading Frames ◽  
Conjugative Plasmid ◽  
Cell Surface Receptor ◽  
Bacteriocin Activity ◽  
Lytic Enzymes ◽  
Repeat Structure ◽  
Surface Receptor ◽  
Reading Frames

ABSTRACT The conjugative plasmid pYI14 (61 kbp) was isolated from Enterococcus faecalis YI714, a clinical isolate. pYI14 conferred a pheromone response on its host and encoded bacteriocin 41 (bac41). Bacteriocin 41 (Bac41) only showed activity against E. faecalis. Physical mapping of pYI14 showed that it consisted of EcoRI fragments A to P. The clone pHT1100, containing EcoRI fragments A (12.6 kbp) and H (3.5 kbp), conferred the bacteriocin activity on E. faecalis strains. Genetic analysis showed that the determinant was located in a 6.6-kbp region within the EcoRI AH fragments. Six open reading frames (ORFs) were identified in this region and designated ORF7 (bacL1 ) ORF8 (bacL2 ), ORF9, ORF10, ORF11 (bacA), and ORF12 (bacI). They were aligned in this order and oriented in the same direction. ORFs bacL1 , bacL2 , bacA, and bacI were essential for expression of the bacteriocin in E. faecalis. Extracellular complementation of bacteriocin expression was possible for bacL1 and -L2 and bacA mutants. bacL1 and -L2 and bacA encoded bacteriocin component L and activator component A, respectively. The products of these genes are secreted into the culture medium and extracellularly complement bacteriocin expression. bacI encoded immunity, providing the host with resistance to its own bacteriocin activity. The bacL1 -encoded protein had significant homology with lytic enzymes that attack the gram-positive bacterial cell wall. Sequence data for the deduced bacL1 -encoded protein suggested that it has a domain structure consisting of an N-terminal signal peptide, a second domain with the enzymatic activity, and a third domain with a three-repeat structure directing the proenzyme to its cell surface receptor.

scholarly journals Identification and analysis of proton-translocating pyrophosphatases in the methanogenic archaeonMethanosarcina mazei

Archaea ◽  
2002 ◽  
Vol 1 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Sebastian Bäumer ◽  
Sabine Lentes ◽  
Gerhard Gottschalk ◽  
Uwe Deppenmeier
Keyword(s):  
Specific Activity ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Inorganic Pyrophosphatase ◽  
Amino Acid Sequence Similarity ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Inorganic Pyrophosphate ◽  
Reading Frames

Analysis of genome sequence data from the methanogenic archaeonMethanosarcina mazeiGö1 revealed the existence of two open reading frames encoding proton-translocating pyrophosphatases (PPases). These open reading frames are linked by a 750-bp intergenic region containing TC-rich stretches and are transcribed in opposite directions. The corresponding polypeptides are referred to as Mvp1 and Mvp2 and consist of 671 and 676 amino acids, respectively. Both enzymes represent extremely hydrophobic, integral membrane proteins with 15 predicted transmembrane segments and an overall amino acid sequence similarity of 50.1%. Multiple sequence alignments revealed that Mvp1 is closely related to eukaryotic PPases, whereas Mvp2 shows highest homologies to bacterial PPases. Northern blot experiments with RNA from methanol-grown cells harvested in the mid-log growth phase indicated that only Mvp2 was produced under these conditions. Analysis of washed membranes showed that Mvp2 had a specific activity of 0.34 U mg (protein)–1. Proton translocation experiments with inverted membrane vesicles prepared from methanol-grown cells showed that hydrolysis of 1 mol of pyrophosphate was coupled to the translocation of about 1 mol of protons across the cytoplasmic membrane. Appropriate conditions formvp1 expression could not be determined yet. The pyrophosphatases ofM. mazeiGö1 represent the first examples of this enzyme class in methanogenic archaea and may be part of their energy-conserving system. Abbreviations: DCCD,N,N′-dicyclohexylcarbodiimide; PPase, inorganic pyrophosphatase; PPi, inorganic pyrophosphate; Δp, proton motive force.

scholarly journals EST analysis of gene expression in early cleavage-stage sea urchin embryos

Development ◽  
1999 ◽  
Vol 126 (17) ◽  
pp. 3857-3867
Author(s):  
Y.H. Lee ◽  
G.M. Huang ◽  
R.A. Cameron ◽  
G. Graham ◽  
E.H. Davidson ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Expressed Sequence Tags ◽  
Early Embryo ◽  
Cytoskeletal Proteins ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Est Analysis ◽  
Signaling Systems ◽  
Sea Urchin Embryos ◽  
Expressed Sequence

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts.

scholarly journals Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms

2021 ◽  
Author(s):  
Claudia Ortiz-Sepulveda ◽  
Mathieu Genete ◽  
Christelle Blassiau ◽  
Cécile Godé ◽  
Christian Albrecht ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Early Stage ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Model Organisms ◽  
Recent Common Ancestor ◽  
Ultraconserved Elements ◽  
Most Recent Common Ancestor ◽  
Reading Frames

Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced a substantial dataset. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites), although some branches lack support in the latter case. Variant calling on the exome of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Nucleotide diversity and population differentiation was low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming non-specific sequence data obtained for Coelaturini of the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays an identical gene order to that of the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for the development of integrative genomic studies on micro- and macroevolutionary dynamics in non-model organisms.

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