CiteULike: GustavoLacerda's library [194 articles]

Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms

Tammy Cheng — 2008-07-26T13:54:09-00:00

PLoS Comput Biol, Vol. 4, No. 7. (25 July 2008), e1000135.

Recent analyses of human genome sequences have given rise to impressive advances in identifying non-synonymous single nucleotide polymorphisms (nsSNPs). By contrast, the annotation of nsSNPs and their links to diseases are progressing at a much slower pace. Many of the current approaches to analysing disease-associated nsSNPs use primarily sequence and evolutionary information, while structural information is relatively less exploited. In order to explore the potential of such information, we developed a structure-based approach, Bongo (Bonds ON Graph), to predict structural effects of nsSNPs. Bongo considers protein structures as residue–residue interaction networks and applies graph theoretical measures to identify the residues that are critical for maintaining structural stability by assessing the consequences on the interaction network of single point mutations. Our results show that Bongo is able to identify mutations that cause both local and global structural effects, with a remarkably low false positive rate. Application of the Bongo method to the prediction of 506 disease-associated nsSNPs resulted in a performance (positive predictive value, PPV, 78.5%) similar to that of PolyPhen (PPV, 77.2%) and PANTHER (PPV, 72.2%). As the Bongo method is solely structure-based, our results indicate that the structural changes resulting from nsSNPs are closely associated to their pathological consequences.

BLogo: A tool for visualization of bias in biological sequences

Wencheng Li — 2008-08-07T16:33:03-00:00

Bioinformatics (4 August 2008), btn407.

Summary: Blogo is a web-based tool that detects and displays statistically significant position-specific sequence bias with reduced background noise. The over-represented and under-represented symbols in a particular position are shown above and below the zero line. When the sequences are in open reading frames, the background frequency of nucleotides could be calculated separately for the three positions of a codon, thus greatly reducing the background noise. Thechi 2 test or fisher's exact test is used to evaluate the statistical significance of every symbol in every position and only those that are significant are highlighted in the resulting logo. The perl source code of the program is freely available and can be run locally. Availability: http://acephpx.cropdb.org/blogo/, http://www.bioinformatics.org/blogo/ Contact: lwcbio@yahoo.com.cn, xnwang@21cn.net 10.1093/bioinformatics/btn407

Sequences downstream of the start codon and their relations to G + C content and optimal growth temperature in prokaryotic genomes

Wencheng Li — 2008-08-07T15:58:45-00:00

Antonie van Leeuwenhoek, Vol. 92, No. 4. (26 November 2007), pp. 417-427.

Abstract The mechanism of translation initiation is responsible for shaping the mRNA sequences downstream of the start codon. However, this region has not been systematically analyzed in prokaryotes. We used sequence logos and statistic methods to analyze the patterns of overrepresented sequences in this region for 125 species of bacteria and 23 species of archaea. The specific positions are compared to the first 33 amino acids in the proteins. At the 2nd amino acid position, Lys, Ser or Thr is highly overrepresented for 68% to 84% of the genomes examined and Ala is highly overrepresented for 57% of the genomes. Overrepresentation of Lys2 is negatively correlated with the G + C content and overrepresentation of Ser2 or Thr2 is positively correlated with the G + C content of genomes. Ile at the 4th to the 8th positions were found to be overrepresented for 91% of the genomes analyzed and this seemed to be conserved for both bacteria and archaea. Organisms growing at high temperatures have relatively low extent of nucleotides bias at 5′ termini of open reading frames (ORFs). The extent of overrepresenting A and underrepresenting G at ORF 5′ termini is reduced in thermophiles and hyperthermophiles for both archaea and bacteria.

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

Juliane Dohm — 2008-07-29T20:45:04-00:00

Nucl. Acids Res. (26 July 2008), gkn425.

Novel sequencing technologies permit the rapid production of large sequence data sets. These technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. We generated and analyzed two Illumina 1G ultra-short read data sets, i.e. 2.8 million 27mer reads from a Beta vulgaris genomic clone and 12.3 million 36mers from the Helicobacter acinonychis genome. We found that error rates range from 0.3% at the beginning of reads to 3.8% at the end of reads. Wrong base calls are frequently preceded by base G. Base substitution error frequencies vary by 10- to 11-fold, with A > C transversion being among the most frequent and C > G transversions among the least frequent substitution errors. Insertions and deletions of single bases occur at very low rates. When simulating re-sequencing we found a 20-fold sequencing coverage to be sufficient to compensate errors by correct reads. The read coverage of the sequenced regions is biased; the highest read density was found in intervals with elevated GC content. High Solexa quality scores are over-optimistic and low scores underestimate the data quality. Our results show different types of biases and ways to detect them. Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis. 10.1093/nar/gkn425

Mycobiota and mycotoxin producing fungi from cocoa beans.

M Sánchez-Hervás — 2008-06-16T03:06:53-00:00

International journal of food microbiology (2 May 2008)

The present study reports on the natural mycobiota occurring in cocoa beans, paying special attention to the incidence of fungal species that are potential producers of mycotoxins. The results show that predominant fungi were different species of the genus Aspergillus belonging to section Flavi and Nigri. Of the 214 strains of Aspergillus section Flavi collected from cocoa beans, 120 were identified as A. flavus and 94 as A. tamarii. Of Aspergillus section Nigri 138 strains were isolated, with 132 belonging to A. niger aggregate and 6 to A. carbonarius species. Potential ability to produce aflatoxins (AFs) B1, B2, G1 and G2, cyclopiazonic acid (CPA) and ochratoxin A (OTA) was studied by isolate culture followed by HPLC analysis of these mycotoxins in the culture extracts. Results indicated that 64.1% and 34.2% of the A. flavus strains produced AFs and CPA, respectively. Most of the A. flavus strains presented moderate toxigenicity with mean levels of AFs ranging from 100 ng g(-1) to 1000 ng g(-1). All the CPA-producing strains of A. flavus were highly toxigenic producing >30 mug g(-1) of CPA. Furthermore, 98% of A. tamarii strains produced CPA and over 50% of them were highly CPA toxigenic. With respect to OTA-producing fungi, a high percentage of black aspergilli strains (49.2%) were able to produce OTA. Additionally, most of the OTA-producing isolates were of moderate toxigenicity, producing amounts of OTA from 10 mug g(-1) to 100 mug g(-1). These results indicate that there is a possible risk factor posed by AFs, CPA and OTA contamination of cocoa beans, and consequently, cocoa products.

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

John Marioni — 2008-06-11T20:56:53-00:00

Genome Res. (11 June 2008), gr.079558.108.

Ultra high-throughput sequencing is emerging as an attractive alternative to microarrays for genotyping, analysis of methylation patterns and identification of transcription factor binding sites. Here, we describe an application of the Illumina sequencing platform to study mRNA expression levels. Our goals were to estimate technical variance associated with Illumina sequencing in this context and to compare its ability to identify differentially expressed genes with existing array technologies. To do so, we estimated gene expression differences between liver and kidney RNA samples using multiple sequencing replicates, and compared the sequencing data to results obtained from Affymetrix arrays using the same RNA samples. We find that the Illumina sequencing data are highly replicable, with relatively little technical variation, and so, for many purposes, it may suffice to sequence each mRNA sample only once (i.e., using one lane). The information in a single lane of Illumina sequencing data appears comparable to that in a single array in enabling identification of differentially expressed genes, while allowing for additional analyses such as detection of low-expressed genes, alternative splice variants, and novel transcripts. Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra high-throughput sequencing technology. 10.1101/gr.079558.108

Recent Studies of the Enzymic Synthesis of Ricinoleic Acid by Developing Castor Beans.

Robert A Moreau — 2008-07-16T15:00:36-00:00

Plant physiology, Vol. 67, No. 4. (April 1981), pp. 672-676.

Oleate Delta(12)-hydroxylase activity was measured in extracts of developing castor bean seeds. Most of the hydroxylase activity is associated with microsomes. However, when microsomes are washed, the activity is completely lost. Some (50%) of the activity can be restored by addition of the 100,000g supernatant to the washed microsomes. Supernatant extracts (100,000g) of developing safflower seeds are able to restore all (100%) of the hydroxylase activity to the washed castor bean microsomes. In addition, purified mammalian catalase can restore some (25%) of the activity to the microsomes but is not as effective as either castor bean or safflower 100,000g supernatants. The K(m) of the hydroxylase for oxygen is 4 micromolar. Inasmuch as the activity was not inhibited by high concentrations of either carbon monoxide or cyanide, neither the involvement of cytochrome P450 nor other cytochrome systems is suggested. The enzyme system was not saturated by oleoyl-CoA, even at concentrations as high as 200 micromolar. When [(14)C]oleoyl-CoA is supplied as a substrate, the acyl component is rapidly transferred to phosphatidylcholine (PC). Hydroxylation may occur on PC or on a lipid which receives its acyl component from PC. However, exogeneously added 2-[1-(14)C]oleoyl-PC was hydroxylated at a much lower rate than was [1-(14)C]oleoyl-CoA added as the primary substrate.

Molecular species of PC and PE formed during castor oil biosynthesis

Jiann-Tsyh Lin — 2008-07-16T14:21:24-00:00

Lipids, Vol. 37, No. 10. (17 October 2002), pp. 991-995.

Abstract As part of a program to elucidate castor oil biosynthesis, we have identified 36 molecular species of PC and 35 molecular species of PE isolated from castor microsomes after incubations with [14C]-labeled FA. The six [14C]FA studied were ricinoleate, stearate, oleate, linoleate, linolenate, and palmitate, which were the only FA identified in castor microsomal incubations. The incorporation of each of the six FA into PC was better than that into PE. The [14C]FA were incorporated almost exclusively into the sn-2 position of both PC and PE. The incorporation of [14C]stearate and [14C]palmitate into 2-acyl-PC was slower compared to the other four [14C]FA. The incorporation does not show any selectivity for the various lysoPC molecular species. The level of incorporation of [14C]FA in PC was in the order of: oleate>linolenate>palmitate>linoleate >stearate>ricinoleate, and in PE: linoleate>linolenate> oleate>palmitate>stearate>ricinoleate. In general, at the sn-1 position of both PC and PE, linoleate was the most abundant FA, palmitate was the next, and oleate, linolenate, stearate, and ricinoleate were minor FA. The activities of oleoyl-12-hydroxylase, oleoyl-12-desaturase seem unaffected by the FA at the sn-1 position of 2-oleoyl-PC. The FA in the sn-1 position of PC does not significantly affect the activity of phospholipase A2, whereas ricinoleate is preferentially removed from the sn-2 position of PC. The results show that (i) [14C]oleate is most actively incorporated to form 2-oleoyl-PC, the immediate substrate of oleoyl-12-hydroxylase; (ii) 2-ricinoleoyl-PC is formed mostly by the hydroxylation of 2-oleoyl-PC, not from the incorporation of ricinoleate into 2-ricinoleoyl-PC; and (iii) 2-oleoyl-PF is less actively formed than 2-oleoyl-PC.

Ricinus communis Contains an Acyl-CoA Synthetase that Preferentially Activates Ricinoleate to Its CoA Thioester

Xiaohua He — 2008-07-16T14:20:34-00:00

Lipids, Vol. 42, No. 10. (19 October 2007), pp. 931-938.

Abstract As part of our effort to identify enzymes that are critical for producing large amounts of ricinoleate in castor oil, we have isolated three cDNAs encoding acyl-CoA synthetase (ACS) in the castor plant. Analysis of the cDNA sequences reveals that two of them, designated RcACS 2 and RcACS 4, contain complete coding regions corresponding to 694 and 690 amino acids, respectively. The third cDNA, RcACS 1, encodes a truncated gene sequence. The RcACS 2 and RcACS 4 share 77% identity at the amino acid sequence level. Complementation tests showed that both RcACS 2 and RcACS 4 successfully restored growth of a yeast mutant strain (YB525) deficient in ACS. Lysates from yeast cells expressing RcACS 2 and 4 were enzymatically active when using 14C-labeled oleic acid as a substrate. A cell fractionation study indicates that RcACS 2 and 4 are mainly associated with membranes. Substrate specificity assays indicate that the RcACS 2 preferentially activates ricinoleate, while the RcACS 4 has a preference for nonhydroxy fatty acids.

Cloning and characterization of a cDNA encoding diacylglycerol acyltransferase from castor bean

Xiaohua He — 2008-07-16T14:16:43-00:00

Lipids, Vol. 39, No. 4. (18 April 2004), pp. 311-318.

Abstract The oil from castor seed (Ricinus communis) contains 90% ricinoleate, a hydroxy FA that is used in producing numerous industrial products. Castor diacylglycerol acyltransferase (RcDGAT) is a critical enzyme, as it catalyzes the terminal step in castor oil biosynthesis in which the products contain two or three ricinoleoyl moieties. We have isolated a cDNA encoding RcDGAT from developing castor seeds. Analysis of the sequence reveals that this cDNA encodes a protein of 521 amino acids with a molecular mass of 59.9 kDa. Although there are regions of high similarity to other plant DGAT coding sequences, there are sequences that distinguish it as well. Southern blot analysis suggests that the castor genome contains a single copy of RcDGAT. Analysis by reverse transcription-PCR reveals that the accumulation of the mRNA reaches its highest level at 19 d after pollination and declines thereafter. Expression of the full-length cDNA for RcDGAT in the yeast Saccharomyces cerevisiae strain INVSc1 results in sevenfold higher DGAT activity compared with controls. When different molecular species of DAG were provided as substrates to the microsomal mixture, the RcDGAT showed a greater preference to catalyze the transfer of oleate from [14C]oleoyl-CoA to diricinolein than to diolein and dipalmitolein. With the addition of 0.25 mM substrates, diricinolein gave 318 pmol/mg/min diricinoleoyloleoylglycerol (RRO), while diolein and dipalmitolein gave only about 195 pmol/mg/min of triolein (OOO) and 120 pmol/mg/min dipalmitoyleoylglycerol (PoPoO), respectively. This work will facilitate investigation of the role of RcDGAT in castor oil biosynthesis.

Metabolism of 1-acyl-2-oleoyl-sn-glycero-3-phosphoethanolamine in castor oil biosynthesis

Jiann-Tsyh Lin — 2008-07-16T14:16:30-00:00

Lipids, Vol. 35, No. 5. (15 May 2000), pp. 481-486.

Abstract We have examined the role of 2-oleoyl-PE (phosphatidylethanolamine) in the biosynthesis of triacylglycerols (TAG) by castor microsomes. In castor microsomal incubation, the label from 14C-oleate of 1-palmitoyl-2-[1-14C]oleoyl-sn-glycero-3-phosphoethanolamine is incorporated into TAG containing ricinoleate. The enzyme characteristics, such as optimal pH, and the effect of incubation components of the oleoyl-12-hydroxylase using 2-oleoyl-PE as incubation substrate are similar to those for 2-oleoyl-PC (phosphatidylcholine). However, compared to 2-oleoyl-PC, 2-oleoyl-PE is a less efficient incubation substrate of oleoyl-12-hydroxylase in castor microsomes. Unlike 2-oleoyl-PC, 2-oleoyl-PE is not hydroxylated to 2-ricinoleoyl-PE by oleoyl-12-hydroxylase and is not desaturated to 2-linoleoyl-PE by oleoyl-12-desaturase. We have demonstrated the conversion of 2-oleoyl-PE to 2-oleoyl-PC and vice versa. The incorporation of label from 2-[14C]oleoyl-PE into TAG occurs after its conversion to 2-oleoyl-PC, which can then be hydroxylated or desaturated. We detected neither PE-N-monomethyl nor PE-N,N-dimethyl, the intermediates from PE to PC by N-methylation. The conversion of 2-oleoyl-PE to 2-oleoyl-PC likely occurs via hydrolysis to 1,2-diacyl-sn-glycerol by phospholipase C and then by cholinephosphotransferase. This conversion does not appear to play a key role in driving ricinoleate into TAG.

Polyamines are essential for the synthesis of 2-ricinoleoyl phosphatidic acid in developing seeds of castor

Mitsuhiro Tomosugi — 2008-07-16T14:15:57-00:00

Planta, Vol. 223, No. 2. (11 January 2006), pp. 349-358.

Abstract The major fatty acid component of castor (Ricinus communis L.) oil is ricinoleic acid (12-hydroxy-cis-9-octadecenoic acid), and unsaturated hydroxy acid accounts for >85% of the total fatty acids in triacylglycerol (TAG). TAG had a higher ricinoleate content at position 2 than at positions 1 and 3. Although lysophosphatidic acid (LPA) acyltransferase (EC 2.3.1.51), which catalyzes acylation of LPA at position 2, was expected to utilize ricinoleoyl-CoA preferentially over other fatty acyl-CoAs, no activity was found for ricinoleoyl-CoA in vitro at concentrations at which other unsaturated acyl-CoAs were incorporated rapidly. However, activity for ricinoleoyl-CoA appeared with addition of polyamines (putrescine, spermidine, and spermine), while polyamines decreased the rates of incorporation of other acyl-CoAs into position 2. The order of effect of polyamines on LPA acyltransferase activity was spermine > spermidine >> putrescine. At concentrations of spermine and spermidine of >0.1 mM, ricinoleoyl-CoA served as an effective substrate for LPA acyltransferase reaction. The concentrations of spermine and spermidine in the developing seeds were estimated at ∼0.09 and ∼0.63 mM, respectively. These stimulatory effects for incorporation of ricinoleate were specific to polyamines, but basic amino acids were ineffective as cations. In contrast, in microsomes from safflower seeds that do not contain ricinoleic acid, spermine and spermidine stimulated the LPA acyltransferase reaction for all acyl-CoAs tested, including ricinoleoyl-CoA. Although the fatty acid composition of TAG depends on both acyl-CoA composition in the cell and substrate specificity of acyltransferases, castor bean polyamines are crucial for incorporation of ricinoleate into position 2 of LPA. Polyamines are essential for synthesis of 2-ricinoleoyl phosphatidic acid in developing castor seeds.

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

Foissac — 2008-05-13T03:30:36-00:00

Current Bioinformatics, Vol. 3, No. 2. (May 2008), pp. 87-97.

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

Michael Brent — 2007-12-18T12:42:39-00:00

Nat Rev Genet, Vol. 9, No. 1. (January 2008), pp. 62-73.

Heuristic approach to deriving models for gene finding.

J Besemer — 2007-12-03T07:19:08-00:00

Nucleic Acids Res, Vol. 27, No. 19. (1 October 1999), pp. 3911-3920.

Computer methods of accurate gene finding in DNA sequences require models of protein coding and non-coding regions derived either from experimentally validated training sets or from large amounts of anonymous DNA sequence. Here we propose a new, heuristic method producing fairly accurate inhomogeneous Markov models of protein coding regions. The new method needs such a small amount of DNA sequence data that the model can be built 'on the fly' by a web server for any DNA sequence >400 nt. Tests on 10 complete bacterial genomes performed with the GeneMark.hmm program demonstrated the ability of the new models to detect 93.1% of annotated genes on average, while models built by traditional training predict an average of 93.9% of genes. Models built by the heuristic approach could be used to find genes in small fragments of anonymous prokaryotic genomes and in genomes of organelles, viruses, phages and plasmids, as well as in highly inhomogeneous genomes where adjustment of models to local DNA composition is needed. The heuristic method also gives an insight into the mechanism of codon usage pattern evolution.

Genome assembly forensics: finding the elusive mis-assembly

Adam Phillippy — 2008-03-15T05:14:17-00:00

Genome Biology, Vol. 9 (14 March 2008), R55.

Molecular biology: Power sequencing

Brenton Graveley — 2008-06-25T20:27:11-00:00

Nature, Vol. 453, No. 7199. (26 June 2008), pp. 1197-1198.

Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells

Dan Xie — 2008-05-27T08:52:20-00:00

Genome Res. (15 May 2008), gr.072769.107.

We introduce the GibbsModule algorithm for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the co-expressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs. Without using a pre-determined alignment result, GibbsModule iteratively updates the core motif shared by co-expressed genes and traces the homologous CRMs that contain the core motif. GibbsModule achieved substantial improvements in both precision and recall as compared to peer algorithms on a number of synthetic and real datasets. Applying GibbsModule to analyze the binding regions of the Kruppel-like factor (Klf) transcription factor in embryonic stem cells (ESCs), we discovered a motif that differs from a previously published Klf motif identified by a SELEX experiment, but the new motif is consistent with mutagenesis analysis. Sox2 motif was found to be a collaborating motif to the Klf motif in ESCs. We used quantitative chromatin immunoprecipitation (ChIP) analysis to test whether GibbsModule could distinguish functional and non-functional binding sites. All 7 tested binding sites in GibbsModule predicted CRMs had higher ChIP signals as compared to the other 7 tested binding sites located outside of predicted CRMs. GibbsModule is available at http://biocomp.bioen.uiuc.edu/GibbsModule. 10.1101/gr.072769.107

SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation

Morten Kloster — 2008-06-30T15:02:22-00:00

Nucl. Acids Res., Vol. 36, No. 11. (1 June 2008), pp. 3819-3827.

The genetic code is degenerate--most amino acids can be encoded by from two to as many as six different codons. The synonymous codons are not used with equal frequency: not only are some codons favored over others, but also their usage can vary significantly from species to species and between different genes in the same organism. Known causes of codon bias include differences in mutation rates as well as selection pressure related to the expression level of a gene, but the standard analysis methods can account for only a fraction of the observed codon usage variation. We here introduce an explicit model of codon usage bias, inspired by statistical physics. Combining this model with a maximum likelihood approach, we are able to clearly identify different sources of bias in various genomes. We have applied the algorithm to Saccharomyces cerevisiae as well as 325 prokaryote genomes, and in most cases our model explains essentially all observed variance. 10.1093/nar/gkn288

EagleView: a genome assembly viewer for next-generation sequencing technologies.

Weichun Huang — 2008-06-16T19:50:56-00:00

Genome research (11 June 2008)

The emergence of high-throughput next-generation sequencing technologies (e.g., 454, Illumina) has dramatically sped up whole-genome de novo sequencing and re-sequencing. While the low cost of these sequencing technologies provides an unparalleled opportunity for genome-wide polymorphism discovery, the analysis of the new data types and huge data volume poses formidable informatics challenges for base calling, read alignment and genome assembly, polymorphism detection, as well as data visualization. We introduce a new data integration and visualization tool EagleView to facilitate data analyses, visual validation, and hypothesis generation. EagleView can handle a large genome assembly of millions of reads. It supports a compact assembly view, multiple navigation modes, a pin-point view of technology specific trace information. Moreover, EagleView supports viewing co-assembly of mixed-type reads from different technologies, and supports integrating genome feature annotations into genome assemblies. EagleView has been used in our own lab and by over 100 research labs worldwide for next-generation sequence analyses. The EagleView software is freely available for not-for-profit use at http://bioinformatics.bc.edu/marthlab/EagleView.

Characterization of a new mitochondrial plasmid from Fusarium proliferatum

Miklós Láday — 2008-06-20T17:34:52-00:00

Plasmid, Vol. 59, No. 2. (March 2008), pp. 127-133.

A 10.3 kb linear mitochondrial DNA plasmid designated pFP1 was isolated from Fusarium proliferatum. The DNA sequence of the plasmid consists of 10,336 bp with perfect terminal inverted repeats of 400 bp. Two major, non-overlapping ORFs were identified on opposite strands, encoding a phage-type RNA polymerase and a family B type DNA polymerase, respectively. One additional minor ORF encoding a putative highly basic protein was also identified. The copy number of pFP1, as determined by RT-PCR, ranged between 1.8 and 3.1 per mtDNA copies depending on the host strain. Real-time PCR analysis of a total of 400 cultures surviving ethidium bromide curing indicated that no plasmid-free strains could be obtained by this treatment. Further single spore selections of the survivors with reduced plasmid content were needed to obtain plasmid-free clones. No phenotypic differences were found between the wild-type strains and their plasmid-free progenies.

The complete mitochondrial genome of the vascular wilt fungus Verticillium dahliae: a novel gene order for Verticillium and a diagnostic tool for species identification

Malena Pantou — 2008-06-20T17:12:28-00:00

Current Genetics, Vol. 50, No. 2. (2006), pp. 125-136.

Abstract The complete sequence (27,184 bp) of the mitochondrial (mt) genome of the phytopathogenic fungus Verticillium dahliae has been determined. It contains 14 protein-coding genes related to oxidative phosphorylation, two rRNA genes and a set of 25 tRNA genes. A single intron, that harbors an intronic ORF coding for a putative ribosomal protein (rps), is located within the large rRNA gene (rnl). Gene order comparisons of V. dahliae mtDNA and complete mt genomes of Pezizomycotina revealed four units of synteny for Sordariomycetes, namely rnl-trn (11–12)-nad2-nad3, nad4L-nad5-cob-cox1, nad1-nad4-atp8-atp6 and rns-trn (1–5)-cox3-trn (1–5)-nad6-trn (2–5). These four units, in different combinations, merged to single continuous unit in the orders of Hypocreales and Sordariales. V. dahliae (Phyllachorales) and all members of the genus showed a unique feature which is the translocation of the nad1-nad4-atp8-atp6-rns-cox3-nad6 region in between genes nad3 and atp9 of the Hypocreales mtDNA gene order. Analysis of mt intergenic sequences of Verticillium species permitted the design of a species-specific primer allowing the discrimination of V. longisporum against V. dahliae and V. albo-atrum. By considering the protein-coding gene sequences as one unit, a phylogenetic comparison with representatives of Ascomycota complete mtDNA was performed.

The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes

Nicolas Vidal — 2008-06-18T17:47:34-00:00

Comptes Rendus Biologies, Vol. 328, No. 10-11. ( 2005), pp. 1000-1008.

Squamate reptiles number approximately 8000 living species and are a major component of the world's terrestrial vertebrate diversity. However, the established relationships of the higher-level groups have been questioned in recent molecular analyses. Here we expand the molecular data to include DNA sequences, totaling 6192 base pairs (bp), from nine nuclear protein-coding genes (C-mos, RAG1, RAG2, R35, HOXA13, JUN, [alpha]-enolase, amelogenin and MAFB) for 19 taxa representing all major lineages. Our phylogenetic analyses yield a largely resolved phylogeny that challenges previous morphological analyses and requires a new classification. The limbless dibamids are the most basal squamates. Of the remaining taxa (Bifurcata), the gekkonids form a basal lineage. The Unidentata, squamates that are neither dibamids nor gekkonids, are divided into the Scinciformata (scincids, xantusiids, and cordylids) and the Episquamata (remaining taxa). Episquamata includes Laterata (Teiformata, Lacertiformata, and Amphisbaenia, with the latter two joined in Lacertibaenia) and Toxicofera (iguanians, anguimorphs and snakes). Our results reject several previous hypotheses that identified either the varanids, or a burrowing lineage such as amphisbaenians or dibamids, as the closest relative of snakes. Our study also rejects the monophyly of both Scleroglossa and Autarchoglossa, because Iguania, a species-rich lineage (ca. 1440 sp.), is in a highly nested position rather than being basal among Squamata. Thus iguanians should not be viewed as representing a primitive state of squamate evolution but rather a specialized and successful clade combining lingual prehension, dependence on visual cues, and ambush foraging mode, and which feeds mainly on prey avoided by other squamates. Molecular time estimates show that the Triassic and Jurassic (from 250 to 150 Myr) were important times for squamate evolution and diversification. To cite this article: N. Vidal, S.B. Hedges, C. R. Biologies 328 (2005).

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

Oliver Keller — 2008-06-13T20:15:59-00:00

BMC Bioinformatics, Vol. 9 (13 June 2008), 278.

Everything you wanted to know about small RNA but were afraid to ask

Scott Boyd — 2008-04-21T17:31:41-00:00

Laboratory Investigation, Vol. aop, No. current.

Genome sequencing in microfabricated high-density picolitre reactors

Marcel Margulies — 2005-07-31T21:14:04-00:00

Nature (31 July 2005)

The new paradigm of flow cell sequencing

Robert Holt — 2008-06-02T17:49:08-00:00

Genome Res., Vol. 18, No. 6. (1 June 2008), pp. 839-846.

DNA sequencing is in a period of rapid change, in which capillary sequencing is no longer the technology of choice for most ultra-high-throughput applications. A new generation of instruments that utilize primed synthesis in flow cells to obtain, simultaneously, the sequence of millions of different DNA templates has changed the field. We compare and contrast these new sequencing platforms in terms of stage of development, instrument configuration, template format, sequencing chemistry, throughput capability, operating cost, data handling issues, and error models. While these platforms outperform capillary instruments in terms of bases per day and cost per base, the short length of sequence reads obtained from most instruments and the limited number of samples that can be run simultaneously imposes some practical constraints on sequencing applications. However, recently developed methods for paired-end sequencing and for array-based direct selection of desired templates from complex mixtures extend the utility of these platforms for genome analysis. Given the ever increasing demand for DNA sequence information, we can expect continuous improvement of this new generation of instruments and their eventual replacement by even more powerful technology. 10.1101/gr.073262.107

Synonymous codon usage bias and the expression of human glucocerebrosidase in the methylotrophic yeast, Pichia pastoris

Graham Sinclair — 2008-06-11T17:29:08-00:00

Protein Expression and Purification, Vol. 26, No. 1. (October 2002), pp. 96-105.

Codon bias and heterologous protein expression

Claes Gustafsson — 2008-06-11T17:21:23-00:00

Trends in Biotechnology, Vol. 22, No. 7. (July 2004), pp. 346-353.

The expression of functional proteins in heterologous hosts is a cornerstone of modern biotechnology. Unfortunately, proteins are often difficult to express outside their original context. They might contain codons that are rarely used in the desired host, come from organisms that use non-canonical code or contain expression-limiting regulatory elements within their coding sequence. Improvements in the speed and cost of gene synthesis have facilitated the complete redesign of entire gene sequences to maximize the likelihood of high protein expression. Redesign strategies are discussed here, including modification of translation initiation regions, alteration of mRNA structural elements and use of different codon biases.

The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom)

Yong Wang — 2008-06-10T22:28:51-00:00

FEMS Microbiology Letters, Vol. 280, No. 1. (2008), pp. 34-41.

Abstract In this study, the full mitochondrial genome of a basidiomycete fungus, Pleurotus ostreatus, was sequenced and analyzed. It is a circular DNA molecule of 73 242 bp and contains 44 known genes encoding 18 proteins and 26 RNA genes. The protein-coding genes include 14 common mitochondrial genes, one ribosomal small subunit protein 3 gene, one RNA polymerase gene and two DNA polymerase genes. In addition, one RNA and one DNA polymerase genes were identified in a mitochondrial plasmid. These two genes show relatively low similarities to their homologs in the mitochondrial genome but they are nearly identical to the known mitochondrial plasmid genes from another Pleurotus ostreatus strain. This suggests that the plasmid may mediate the horizontal gene transfer of the DNA and RNA polymerase genes into mitochondrial genome, and such a transfer may be an ancient event. Phylogenetic analysis based on the cox1 ORFs verified the traditional classification of Pleurotus ostreatus among fungi. However, the discordances were observed in the phylogenetic trees based on the six cox1 intronic ORFs of Pleurotus ostreatus and their homologs in other species, suggesting that these intronic ORFs are foreign DNA sequences obtained through HGT. In summary, this analysis provides valuable information towards the understanding of the evolution of fungal mtDNA.

The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts

Patrick Woo — 2008-06-10T22:28:36-00:00

FEBS Letters, Vol. 555, No. 3. (18 December 2003), pp. 469-477.

We report the complete sequence of the mitochondrial genome of Penicillium marneffei, the first complete mitochondrial DNA sequence of a thermal dimorphic fungus. This 35 kb mitochondrial genome contains the genes encoding ATP synthase subunits 6, 8, and 9 (atp6, atp8, and atp9), cytochrome oxidase subunits I, II, and III (cox1, cox2, and cox3), apocytochrome b (cob), reduced nicotinamide adenine dinucleotide ubiquinone oxireductase subunits (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), ribosomal protein of the small ribosomal subunit (rps), 28 tRNAs, and small and large ribosomal RNAs. Analysis of gene contents, gene orders, and gene sequences revealed that the mitochondrial genome of P. marneffei is more closely related to those of molds than yeasts.

The Agrocybe aegerita mitochondrial genome contains two inverted repeats of the nad4 gene arisen by duplication on both sides of a linear plasmid integration site

C Ferandon — 2008-06-10T22:28:15-00:00

Fungal Genetics and Biology, Vol. 45, No. 3. (March 2008), pp. 292-301.

The Agrocybe aegerita mitochondrial genome possesses two polB genes with linear plasmid origin. The cloning and sequencing of the regions flanking Aa-polB P1 revealed two large inverted repeats (higher than 2421 nt) separated by a single copy region of 5834 nt. Both repeats contain identical copies of the nad4 gene. The single copy region contains two disrupted genes with plasmid origin Aa-polB P1 and a small ORF homologous to a small gene described in two basidiomycete linear plasmids. The phylogenetic analyses argue in favor of a same plasmid origin for both genes but, surprisingly, these genes were separated by a mitochondrial tRNA-Met. Both strands of the complete region containing the two nad4 inverted copies and the tRNA-Met appear to be transcribed on large polycistronic mRNAs. A model summarizing the events that would have occurred is proposed: (1) capture of the tRNA by the plasmid before its integration in the mtDNA or acquisition of the tRNA gene by recombination after the plasmid integration, (2) integration of the plasmid in the mtDNA, accompanied by a large duplication containing the nad4 gene and (3) erosion of the plasmid sequences by large deletions and mutations.

Modeling Transcriptome Based on Transcript-Sampling Data

Jiang Zhu — 2008-06-10T05:57:07-00:00

PLoS ONE, Vol. 3, No. 2. (20 February 2008), e1659.

Background: Newly-evolved multiplex sequencing technology has been bringing transcriptome sequencing into an unprecedented depth. Millions of transcript tags now can be acquired in a single experiment through parallelization. The significant increase in throughput and reduction in cost required us to address some fundamental questions, such as how many transcript tags do we have to sequence for a given transcriptome? How could we estimate the total number of unique transcripts for different cell types (transcriptome diversity) and the distribution of their copy numbers (transcriptome dynamics)? What is the probability that a transcript with a given expression level to be detected at a certain sampling depth? Methodology/Principal Findings: We developed a statistical model to evaluate these parameters based on transcriptome-sampling data. Three mixture models were exploited for their potentials to model the sampling frequencies. We demonstrated that relative abundances of all transcripts in a transcriptome follow the generalized inverse Gaussian distribution. The widely known beta and gamma distributions failed to fulfill the singular characteristics of relative abundance distribution, i.e., highly skewed toward zero and with a long tail. An estimator of transcriptome diversity and an analytical form of sampling growth curve were proposed in a coherent framework. Experimental data fitted this model very well and Monte Carlo simulations based on this model replicated sampling experiments in a remarkable precision. Conclusions: Taking human embryonic stem cell as a prototype, we demonstrated that sequencing tens of thousands of transcript tags in an ordinary EST/SAGE experiment was far from sufficient. In order to fully characterize a human transcriptome, millions of transcript tags had to be sequenced. This model lays a statistical basis for transcriptome-sampling experiments and in essence can be used in all sampling-based data.

An analysis of expressed sequence tags of developing castor endosperm using a full-length cDNA library

Chaofu Lu — 2007-08-01T18:06:53-00:00

BMC Plant Biology, Vol. 7 (31 July 2007), 42.

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes.

S Schwartz — 2008-01-04T13:15:46-00:00

Genome Res, Vol. 18, No. 1. (January 2008), pp. 88-103.

Introns are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5' splice site (5'ss), the branch site (BS), and the polypyrimdine tract/3'splice site (PPT-3'ss). To study the evolution of these splicing signals, we have conducted a systematic comparative analysis of these signals in over 1.2 million introns from 22 eukaryotes. Our analyses suggest that all these signals have dramatically evolved: The PPT is weak among most fungi, intermediate in plants and protozoans, and strongest in metazoans. Within metazoans it shows a gradual strengthening from Caenorhabditis elegans to human. The 5'ss and the BS were found to be degenerate among most organisms, but highly conserved among some fungi. A maximum parsimony-based algorithm for reconstructing ancestral position-specific scoring matrices suggested that the ancestral 5'ss and BS were degenerate, as in metazoans. To shed light on the evolutionary variation in splicing signals, we have analyzed the evolutionary changes in the factors that bind these signals. Our analysis reveals coevolution of splicing signals and their corresponding splicing factors: The strength of the PPT is correlated to changes in key residues in its corresponding splicing factor U2AF2; limited correlation was found between changes in the 5'ss and U1 snRNA that binds it; but not between the BS and U2 snRNA. Thus, although the basic ability of eukaryotes to splice introns has remained conserved throughout evolution, the splicing signals and their corresponding splicing factors have considerably evolved, uniquely shaping the splicing mechanisms of different organisms.

ALLPATHS: De novo assembly of whole-genome shotgun microreads.

Jonathan Butler — 2008-03-18T00:16:38-00:00

Genome Res (13 March 2008)

New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial, theoretical solution to the challenge of de novo assembly from whole-genome shotgun "microreads." For 11 genomes of sizes up to 39 Mb, we generated high-quality assemblies from 80x coverage by paired 30-base simulated reads modeled after real Illumina-Solexa reads. The bacterial genomes of Campylobacter jejuni and Escherichia coli assemble optimally, yielding single perfect contigs, and larger genomes yield assemblies that are highly connected and accurate. Assemblies are presented in a graph form that retains intrinsic ambiguities such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. For both C. jejuni and E. coli, this assembly graph is a single edge encompassing the entire genome. Larger genomes produce more complicated graphs, but the vast majority of the bases in their assemblies are present in long edges that are nearly always perfect. We describe a general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads.

Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs

Daniel Zerbino — 2008-04-01T20:50:59-00:00

Genome Res. (18 March 2008), gr.074492.107.

We have developed a new set of algorithms, collectively called Velvet, to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) which is ideal for high coverage, very short read (25-50bp) datasets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50Kb N50 length in simulations of prokaryotic data and 3Kb N50 on simulated mammalian BACs. When applied to real Solexa datasets without readpairs, Velvet generated contigs of around 8Kb in a prokaryote and 2Kb in a mammalian BAC, in close agreement with our simulated results without readpair information. Velvet represents a new approach to assembly which can leverage very short reads in combination with read pairs to produce useful assemblies. 10.1101/gr.074492.107

Mireval: a web tool for simple microRNA prediction in genome sequences

William Ritchie — 2008-05-20T18:02:57-00:00

Bioinformatics, Vol. 24, No. 11. (1 June 2008), pp. 1394-1396.

Summary: We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative. It will allow users with no prior knowledge of in-silico detection of microRNAs to take advantage of the most successful approaches to investigate sequences of interest. Availability: The mirEval web server is available at http://tagc.univ-mrs.fr/mireval Contact: W.Ritchie@centenary.org.au Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btn137

Lachesis muta (Viperidae) cDNAs reveal diverging pit viper molecules and scaffolds typical of cobra (Elapidae) venoms: implications for snake toxin repertoire evolution.

IL Junqueira-de-Azevedo — 2008-05-19T12:59:19-00:00

Genetics, Vol. 173, No. 2. (June 2006), pp. 877-889.

Efforts to describe toxins from the two major families of venomous snakes (Viperidae and Elapidae) usually reveal proteins belonging to few structural types, particular of each family. Here we carried on an effort to determine uncommon cDNAs that represent possible new toxins from Lachesis muta (Viperidae). In addition to nine classes of typical toxins, atypical molecules never observed in the hundreds of Viperidae snakes studied so far are highly expressed: a diverging C-type lectin that is related to Viperidae toxins but appears to be independently originated; an ohanin-like toxin, which would be the third member of the most recently described class of Elapidae toxins, related to human butyrophilin and B30.2 proteins; and a 3FTx-like toxin, a new member of the widely studied three-finger family of proteins, which includes major Elapidae neurotoxins and CD59 antigen. The presence of these common and uncommon molecules suggests that the repertoire of toxins could be more conserved between families than has been considered, and their features indicate a dynamic process of venom evolution through molecular mechanisms, such as multiple recruitments of important scaffolds and domain exchange between paralogs, always keeping a minimalist nature in most toxin structures in opposition to their nontoxin counterparts.

CompariMotif: quick and easy comparisons of sequence motifs

Richard Edwards — 2008-05-07T14:30:49-00:00

Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1307-1309.

Summary: CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. Availability: CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/ Contact: r.edwards@southampton.ac.uk Supplementary information: Further details are available at http://bioinformatics.ucd.ie/shields/software/comparimotif/ 10.1093/bioinformatics/btn105

EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome.

Monica Jain — 2007-04-20T07:57:58-00:00

Nucleic Acids Res (1 April 2007)

Clustering and assembly of expressed sequence tags (ESTs) constitute the basis for most genomewide descriptions of a transcriptome. This approach is limited by the decline in sequence quality toward the end of each EST, impacting both sequence clustering and assembly. Here, we exploit the available draft genome sequence of the unicellular green alga Chlamydomonas reinhardtii to guide clustering and to correct errors in the ESTs. We have grouped all available EST and cDNA sequences into 12 063 ACEGs (assembly of contiguous ESTs based on genome) and generated 15 857 contigs of average length 934 nt. We predict that roughly 3000 of our contigs represent full-length transcripts. Compared to previous assemblies, ACEGs show extended contig length, increased accuracy and a reduction in redundancy. Because our assembly protocol also uses ESTs with no corresponding genomic sequences, it provides sequence information for genes interrupted by sequence gaps. Detailed analysis of randomly sampled ACEGs reveals several hundred putative cases of alternative splicing, many overlapping transcription units and new genes not identified by gene prediction algorithms. Our protocol, although developed for and tailored to the C. reinhardtii dataset, can be exploited by any eukaryotic genome project for which both a draft genome sequence and ESTs are available.

Quality scores and SNP detection in sequencing-by-synthesis systems

William Brockman — 2008-05-01T08:10:43-00:00

Genome Res. (22 January 2008), gr.070227.107.

Promising new sequencing technologies, based on sequencing by synthesis (SBS), are starting to deliver large amounts of DNA sequence at very low cost. Polymorphism detection is a key application. We describe general methods for improved quality scores and accurate automated polymorphism detection, and apply them to data from the Roche (454) Genome Sequencer 20. We assess our methods using known-truth data sets, which is critical to the validity of the assessments. 1. Improved quality scores. We developed informative, base-by-base error predictors for this sequencer and used a variant of the PHRED binning algorithm to combine them into a single empirically derived quality score. These quality scores are more useful than those produced by the system software: they both better predict actual error rates and identify many more high-quality bases. 2. Polymorphism detection. We developed a SNP detection method, with variants for low coverage, high coverage, and PCR amplicon applications, and evaluated it on known-truth data sets. We demonstrate good specificity in single reads, and excellent specificity (no false positives in 215 kb of genome) in high-coverage data. 10.1101/gr.070227.107

Empirical comparison of ab initio repeat finding programs

Surya Saha — 2008-03-05T13:06:57-00:00

Nucl. Acids Res. (20 February 2008), gkn064.

Identification of dispersed repetitive elements can be difficult, especially when elements share little or no homology with previously described repeats. Consequently, a growing number of computational tools have been designed to identify repetitive elements in an ab initio manner, i.e. without using prior sequence data. Here we present the results of side-by-side evaluations of six of the most widely used ab initio repeat finding programs. Using sequence from rice chromosome 12, tools were compared with regard to time requirements, ability to find known repeats, utility in identifying potential novel repeats, number and types of repeat elements recognized and compactness of family descriptions. The study reveals profound differences in the utility of the tools with some identifying virtually their entire substrate as repetitive, others making reasonable estimates of repetition, and some missing almost all repeats. Of note, even when tools recognized similar numbers of repeats they often showed marked differences in the nature and number of repeat families identified. Within the context of this comparative study, ReAS and RepeatScout showed the most promise in analysis of sequence reads and assembled genomic regions, respectively. Our results should help biologists identify the program(s), if any, that is best suited for their needs. 10.1093/nar/gkn064

Comparative analysis of sequence features involved in the recognition of tandem splice sites

Ralf Bortfeldt — 2008-04-30T22:22:05-00:00

BMC Genomics, Vol. 9 (30 April 2008), 202.

What is principal component analysis?

Markus Ringnér — 2008-03-09T04:13:08-00:00

Nature Biotechnology, Vol. 26, No. 3., pp. 303-304.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

Qi Liu — 2008-03-31T18:19:31-00:00

BMC Bioinformatics, Vol. 9 (31 March 2008), 176.

Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia

Tom Walsh — 2008-03-28T13:34:50-00:00

Science (27 March 2008), 1155174.

Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications >100 kb were identified by microarray comparative genomic hybridization (CGH) of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases (P = 0.0008) and 20% of young onset cases (P = 0.0001). The association was independently replicated in patients with childhood-onset schizophrenia compared to their parents (P = 0.03). Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations impacting genes in neurodevelopmental pathways contribute to schizophrenia. 10.1126/science.1155174

Origins and evolution of spliceosomal introns.

F Rodríguez-Trelles — 2007-01-15T18:01:39-00:00

Annu Rev Genet, Vol. 40 (2006), pp. 47-76.

Research into the origins of introns is at a critical juncture in the resolution of theories on the evolution of early life (which came first, RNA or DNA?), the identity of LUCA (the last universal common ancestor, was it prokaryotic- or eukaryotic-like?), and the significance of noncoding nucleotide variation. One early notion was that introns would have evolved as a component of an efficient mechanism for the origin of genes. But alternative theories emerged as well. From the debate between the "introns-early" and "introns-late" theories came the proposal that introns arose before the origin of genetically encoded proteins and DNA, and the more recent "introns-first" theory, which postulates the presence of introns at that early evolutionary stage from a reconstruction of the "RNA world." Here we review seminal and recent ideas about intron origins. Recent discoveries about the patterns and causes of intron evolution make this one of the most hotly debated and exciting topics in molecular evolutionary biology today.

Mitochondrial introns: a critical view

Franz Lang — 2008-03-18T19:23:55-00:00

Trends in Genetics, Vol. 23, No. 3. (March 2007), pp. 119-125.

Although group I and group II introns were discovered more than 25 years ago, they are still difficult to identify. Modeling their RNA structure also remains particularly challenging for organelle sequences, owing to their great diversity. In fact, accelerated evolution in organelles often results in a reduced RNA structure and a loss of autocatalytic splicing and intron mobility. We set out to identify all mitochondrial group I and II introns in published sequences, and, to this end, we developed and applied a new search approach: RNAweasel. On the basis of the results, we focus here on building a comprehensive picture of mitochondrial group I introns, including a modified (reduced) consensus RNA secondary structure and a concise phylogeny-based subclassification.

prot4EST: Translating Expressed Sequence Tags from neglected genomes

James Wasmuth — 2008-03-18T17:41:28-00:00

BMC Bioinformatics, Vol. 5, No. 1. (2004)

BACKGROUND:The genomes of an increasing number of species are being investigated through generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects.RESULTS:As part of our ongoing EST programs investigating these "neglected" genomes, we have developed a polypeptide prediction pipeline, prot4EST. It incorporates freely available software to produce final translations that are more accurate than those derived from any single method. We show that this integrated approach goes a long way to overcoming the deficit in training data.CONCLUSIONS:prot4EST provides a portable EST translation solution and can be usefully applied to >95% of EST projects to improve downstream annotation. It is freely available from http://www.nematodes.org/PartiGene.