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Aphids acquired symbiotic genes via lateral gene transfer

BMC BIOLOGY 2009年第2009期7卷 1-13页

作者： Nikoh, Naruo Nakabachi, Atsushi RIKEN Adv Sci Inst Saitama Japan Open Univ Japan Div Nat Sci Chiba Japan

Background: Aphids possess bacteriocytes, which are cells specifically differentiated to harbour the obligate mutualist Buchnera aphidicola (gamma-Proteobacteria). Buchnera has lost many of the genes that appear to be essential for bacterial life. From the bacteriocyte of the pea aphid Acyrthosiphon pisum, we previously identified two clusters of expressed sequence tags that display similarity only to bacterial genes. Southern blot analysis demonstrated that they are encoded in the aphid genome. In this study, in order to assess the possibility of lateral gene transfer, we determined the full-length sequences of these transcripts, and performed detailed structural and phylogenetic analyses. We further examined their expression levels in the bacteriocyte using real-time quantitative RT-PCR. Results: Sequence similarity searches demonstrated that these fully sequenced transcripts are significantly similar to the bacterial genes ldcA (product, LD-carboxypeptidase) and rlpA (product, rare lipoprotein A), respectively. Buchnera lacks these genes, whereas many other bacteria, including Escherichia coli, a close relative of Buchnera, possess both ldcA and rlpA. Molecular phylogenetic analysis clearly demonstrated that the aphid ldcA was derived from a rickettsial bacterium closely related to the extant Wolbachia spp. (alpha-Proteobacteria, Rickettsiales), which are intracellular symbionts of various lineages of arthropods. The evolutionary origin of rlpA was not fully resolved, but it was clearly demonstrated that its double-psi beta-barrel domain is of bacterial origin. Real-time quantitative RT-PCR demonstrated that ldcA and rlpA are expressed 11.6 and 154-fold higher in the bacteriocyte than in the whole body, respectively. LdcA is an enzyme required for recycling murein (peptidoglycan), which is a component of the bacterial cell wall. As Buchnera possesses a cell wall composed of murein but lacks ldcA, a high level of expression of the aphid ldcA in the bacteriocyte ma

关键词： basic local alignment search tool Lateral Gene Transfer Aphid Species Molecular Phylogenetic Analysis basic local alignment search tool search

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Are there unequivocal criteria to label a given protein as a toxin? Permissive versus conservative annotation processes

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GENOME BIOLOGY 2013年第9期14卷 406/1-406/7页

作者： Terrat, Yves Ducancel, Frederic Univ Montreal Inst Plant Biol Montreal Bot Garden Montreal PQ H1X 2B2 Canada CEA iBiTecS SPI LIAS Antibody Engn Hlth Lab LIAS F-91191 Gif Sur Yvette France

A response to Novel venom gene discovery in the platypus by Whittington CM, Papenfuss AT, Locke DP, Mardis ER, Wilson RK, Abubucker S, Mitreva M, Wong ESW, Hsu AL, Kuchel PW, Belov K, Warren WC. Genome Biol 2010, 11:R95. During the past decade, the field of toxin discovery haschanged in many aspects, including the study of newphyla and the application of new discovery ***-throughput screening at the cDNA level has beensuccessful in characterizing a broad range of toxinsequences [1-7]. In an article published in GenomeBiology, Whittington and colleagues [8] report the discovery of novel toxin genes in the platypus, expandingthe small list of previously characterized venom compounds in this fascinating species [9-15]. At fi rst glance,we were surprised to fi nd the expression of sarafotoxinlike sequences as, to date, no similar sequences have beenidentifi ed outside the small genus of burrowing snakes(Atractaspis). A preliminary analysis yielded strongevidence for the non-toxin function of these sarafotoxinlike sequences. Hence, we decided to re-evaluate theoriginal venom-gene list, which includes 83 ***, we address issues that question the validity of theannotation method adopted by Whittington et al., whichis largely based on similarity searches using toxin-relatedgenes and on a tissue-expression criterion that might leadto false positives.

关键词： basic local alignment search tool Venom Gland basic local alignment search tool search Putative Toxin Platypus Genome

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Diversity and abundance of photosynthetic sponges in temperate Western Australia

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BMC Ecology 2009年第1期9卷 1-13页

作者： Lemloh, Marie-Louise Fromont, Jane Brümmer, Franz Usher, Kayley M Abteilung Zoologie Biologisches Institut Universität Stuttgart 70569 Stuttgart Pfaffenwaldring 57 Germany Department of Aquatic Zoology Western Australian Museum Welshpool DC WA 6986 Locked Bag 49 Australia School of Plant Biology University of Western Australia Crawley WA 6009 35 Stirling Highway Australia

Background. Photosynthetic sponges are important components of reef ecosystems around the world, but are poorly understood. It is often assumed that temperate regions have low diversity and abundance of photosynthetic sponges, but to date no studies have investigated this question. The aim of this study was to compare the percentages of photosynthetic sponges in temperate Western Australia (WA) with previously published data on tropical regions, and to determine the abundance and diversity of these associations in a range of temperate environments. Results. We sampled sponges on 5 m belt transects to determine the percentage of photosynthetic sponges and identified at least one representative of each group of symbionts using 16S rDNA sequencing together with microscopy techniques. Our results demonstrate that photosynthetic sponges are abundant in temperate WA, with an average of 63% of sponge individuals hosting high levels of photosynthetic symbionts and 11% with low to medium levels. These percentages of photosynthetic sponges are comparable to those found on tropical reefs and may have important implications for ecosystem function on temperate reefs in other areas of the world. A diverse range of symbionts sometimes occurred within a small geographic area, including the three "big" cyanobacterial clades, Oscillatoria spongeliae, "Candidatus Synechococcus spongiarum" and Synechocystis species, and it appears that these clades all occur in a wide range of sponges. Additionally, spongin-permeating red algae occurred in at least 7 sponge species. This study provides the first investigation of the molecular phylogeny of rhodophyte symbionts in sponges. Conclusion. Photosynthetic sponges are abundant and diverse in temperate WA, with comparable percentages of photosynthetic to non-photosynthetic sponges to tropical zones. It appears that there are three common generalist clades of cyanobacterial symbionts of sponges which occur in a wide range of sponges in a wide ran

关键词： Western Australia Sponge Species Sponge Tissue basic local alignment search tool search Rapid Light Curve

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New finite-size correction for local alignment score distributions

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BMC Research Notes 2012年第1期5卷 1-6页

作者： Park, Yonil Sheetlin, Sergey Ma, Ning Madden, Thomas L. Spouge, John L. National Center for Biotechnology Information National Library of Medicine Bethesda MD 20894 United States

Background: local alignment programs often calculate the probability that a match occurred by chance. The calculation of this probability may require a finite-size correction to the lengths of the sequences, as an alignment that starts near the end of either sequence may run out of sequence before achieving a significant score. Findings. We present an improved finite-size correction that considers the distribution of sequence lengths rather than simply the corresponding means. This approach improves sensitivity and avoids substituting an ad hoc length for short sequences that can underestimate the significance of a match. We use a test set derived from ASTRAL to show improved ROC scores, especially for shorter sequences. Conclusions: The new finite-size correction improves the calculation of probabilities for a local alignment. It is now used in the BLAST+ package and at the NCBI BLAST web site (). © 2012Park et al.;licensee BioMed Central Ltd.

关键词： Receiver Operator Characteristic local alignment basic local alignment search tool basic local alignment search tool search Optimal local alignment

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SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

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BMC BIOINFORMATICS 2004年第1期5卷 171-171页

作者： Wang, CL Lefkowitz, EJ Univ Alabama Birmingham Dept Microbiol Birmingham AL 35294 USA

Background: Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool ( BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results: We describe the implementation of SS-Wrapper ( Similarity search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single

关键词： Query Sequence basic local alignment search tool Message Passing Interface Sequence Similarity search basic local alignment search tool search

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PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results

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BMC BIOINFORMATICS 2007年第1期8卷 53-53页

作者： He, Ji Dai, Xinbin Zhao, Xuechun Samuel Roberts Noble Fdn Inc Div Plant Biol Bioinformat Lab Ardmore OK 73401 USA

Background: BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Results: Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. Conclusion: PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interfa

关键词： Query Sequence basic local alignment search tool Laboratory Information Management System basic local alignment search tool search search Session

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Multiple homoplasious insertions and deletions of a Triticeae (Poaceae) DNA transposon: a phylogenetic perspective

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BMC EVOLUTIONARY BIOLOGY 2007年第1期7卷 92-92页

作者： Mason-Gamer, Roberta J. Univ Illinois Dept Biol Sci Chicago IL 60680 USA

Background: Stowaway elements are short, non-autonomous DNA transposons categorized as miniature inverted-repeat transposable elements (MITEs). The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing Stowaway activity has never been observed. Thus, a phylogenetic perspective on presence vs. absence of elements in an aligned data set can provide valuable historical insights into the dynamics of MITE acquisition and loss. Results: A Stowaway-like element resides within the fourth intron of a beta-amylase gene in representatives of five genera in the wheat tribe, Triticeae. Its presence vs. absence was examined with reference to the beta-amylase gene tree topology, and in light of sequence comparisons of the beta-amylase elements to Triticeae Stowaway elements in the Entrez nucleotide database. Among the sequences lacking the element, there are five distinct putative excision footprints (one widespread and four restricted to unrelated lineages) and two flanking deletions. The sequences that do contain elements are polyphyletic on the beta-amylase tree, and their elements are divergent at the sequence level. The beta-amylase elements do not form a monophyletic group relative to other Stowaway elements in Entrez;most are more similar to elements from other loci in other Triticeae genomes than they are to one another. Conclusion: Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a Stowaway- like element has undergone multiple deletions from and insertions into the same site in beta-amylase intron 4 during the history of the tribe. The elements currently at the site represent multiple, distinct lineages that transcend generic boundaries. While patterns of Stowaway polymorphism across a phylogenetic data set do not allow evolutionary mechanisms to be inferred with certainty, they do provide insights into the

关键词： Phylogenetic Distribution Empty Site basic local alignment search tool search Triticeae Genome Palindromic Structure

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Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex

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BMC GENOMICS 2009年第1期10卷 500-500页

作者： Thomson, Susanne A. Baldwin, William S. Wang, Ying H. Kwon, Gwijun LeBlanc, Gerald A. N Carolina State Univ Dept Environm & Mol Toxicol Raleigh NC 27695 USA Clemson Univ Dept Biol Sci Pendleton SC USA Clemson Univ Environm Toxicol Program Pendleton SC USA

Background: The nuclear receptor superfamily currently consists of seven gene subfamilies that encompass over 80 distinct receptor proteins. These transcription factors typically share a common five-domain structure with a highly conserved DNA-binding domain. Some nuclear receptors are ubiquitous among the metazoans, while others are unique to specific phylogenetic groups. Crustaceans represent the second largest group of arthropods with insects being the largest. However, relative to insects, little is known about the nuclear receptors of crustaceans. The aim of this study was to identify putative nuclear receptors from the first assembled genome of a crustacean Daphnia pulex http://***. Nuclear receptor expression was evaluated and receptors were subjected to phylogenetic analyses to gain insight into evolution and function. Results: Twenty-five putative nuclear receptors were identified in D. pulex based on the presence of a conserved DNA-binding domain. All of the nuclear receptor protein sequences contain a highly homologous DNA-binding domain and a less conserved ligand-binding domain with the exception of the NR0A group. These receptors lack a ligand-binding domain. Phylogenetic analysis revealed the presence of all seven receptor subfamilies. The D. pulex genome contains several nuclear receptors that have vertebrate orthologs. However, several nuclear receptor members that are represented in vertebrates are absent from D. pulex. Notable absences include receptors of the 1C group (peroxisome proliferators-activated receptors), the 3A group (estrogen receptor), and the 3C group (androgen, progestogen, mineralcorticoid, and glucocorticoid receptors). The D. pulex genome also contains nuclear receptor orthologs that are present in insects and nematodes but not vertebrates, including putative nuclear receptors within the NR0A group. A novel group of receptors, designated HR97, was identified in D. pulex that groups with the HR96/CeNHR8/48/DAF12 clade,

关键词： Nuclear Receptor basic local alignment search tool Receptor Group basic local alignment search tool search Hormone Response Element

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Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring

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BMC GENOMICS 2011年第1期12卷 234-234页

作者： Milan, Massimo Coppe, Alessandro Reinhardt, Richard Cancela, Leonor M. Leite, Ricardo B. Saavedra, Carlos Ciofi, Claudio Chelazzi, Guido Patarnello, Tomaso Bortoluzzi, Stefania Bargelloni, Luca Univ Padua Dept Publ Hlth Comparat Pathol & Vet Hyg Fac Vet Med I-35020 Legnaro Italy Univ Florence Dept Evolutionary Biol I-50125 Florence Italy Univ Padua Dept Biol I-35131 Padua Italy Max Planck Inst Mol Genet D-14195 Berlin Germany Univ Algarve CCMAR Faro Portugal CSIC IATS Ribera De Cabanes 12595 Castellon Spain

Background: The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam. Results: A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring. Conclusions: The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.

关键词： Gene Ontology Digestive Gland Venice Lagoon Manila Clam basic local alignment search tool search

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Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

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BMC GENOMICS 2012年第1期13卷 60-60页

作者： Miao, Zhenyan Li, Daofeng Zhang, Zhenhai Dong, Jiangli Su, Zhen Wang, Tao China Agr Univ Coll Biol Sci State Key Lab Plant Physiol & Biochem Beijing 100193 Peoples R China China Agr Univ Coll Biol Sci State Key Lab Agrobiotechnol Beijing 100193 Peoples R China

Background: Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula. Description: The M. truncatula transporter database (MTDB) contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG) V3.5 V3 and the M. truncatula Gene Index (MTGI) V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based basic local alignment search tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments. Conclusions: In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://***/MtTransporter/.

关键词： Protein Data Bank Transporter Gene basic local alignment search tool basic local alignment search tool search Tentative Consensus

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