Odorant Binding Proteins of the Red Imported Fire Ant, Solenopsis invicta: An Example of the Problems Facing the Analysis of Widely Divergent Proteins
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{"title"=>"Odorant binding proteins of the red imported fire ant, Solenopsis invicta: An example of the problems facing the analysis of widely divergent proteins", "type"=>"journal", "authors"=>[{"first_name"=>"Dietrich", "last_name"=>"Gotzek", "scopus_author_id"=>"24166584500"}, {"first_name"=>"Hugh M.", "last_name"=>"Robertson", "scopus_author_id"=>"7203066280"}, {"first_name"=>"Yannick", "last_name"=>"Wurm", "scopus_author_id"=>"15766615600"}, {"first_name"=>"De Wayne", "last_name"=>"Shoemaker", "scopus_author_id"=>"7006175202"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-79551627011", "sgr"=>"79551627011", "pui"=>"361218274", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"21305009", "doi"=>"10.1371/journal.pone.0016289"}, "id"=>"3c4c8aa4-0b20-3c10-9106-dd1bcce37476", "abstract"=>"We describe the odorant binding proteins (OBPs) of the red imported fire ant, Solenopsis invicta, obtained from analyses of an EST library and separate 454 sequencing runs of two normalized cDNA libraries. We identified a total of 18 putative functional OBPs in this ant. A third of the fire ant OBPs are orthologs to honey bee OBPs. Another third of the OBPs belong to a lineage-specific expansion, which is a common feature of insect OBP evolution. Like other OBPs, the different fire ant OBPs share little sequence similarity (∼ 20%), rendering evolutionary analyses difficult. We discuss the resulting problems with sequence alignment, phylogenetic analysis, and tests of selection. As previously suggested, our results underscore the importance for careful exploration of the sensitivity to the effects of alignment methods for data comprising widely divergent sequences.", "link"=>"http://www.mendeley.com/research/odorant-binding-proteins-red-imported-fire-ant-solenopsis-invicta-example-problems-facing-analysis-w", "reader_count"=>65, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Researcher"=>19, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>4, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Researcher"=>19, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>4, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>55, "Neuroscience"=>1, "Chemical Engineering"=>1, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>55}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>4}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Austria"=>1, "Sweden"=>1, "United States"=>3, "China"=>1, "Denmark"=>1, "Brazil"=>1, "Italy"=>1, "Chile"=>1, "Germany"=>6}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/801973"], "description"=>"<p>Given are the log-likelihoods of the null hypotheses (H<sub>0</sub>), which assume no selection, and alternative hypotheses (H<sub>a</sub>), which allow for positive selection. Likelihood-ratio tests (LRT) of positive selection are conducted to compare the two hypotheses. Levels of significance are 3.84 at 5% and 6.63 at 1% for the site model and 3.84 at 5% and 5.99 at 1% for the branch and branch-site models, following the χ<sub>1</sub><sup>2</sup> distribution to guide against violations of model assumptions. Statistically significant LRTs for positive selection are indicated by italics and *** for p≪0.01. Note that inference of positive selection greatly depends on the alignment method used.</p>", "links"=>[], "tags"=>["analyses", "alignment", "dataset"], "article_id"=>472340, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Dietrich Gotzek", "Hugh M. Robertson", "Yannick Wurm", "DeWayne Shoemaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016289.t003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_the_selection_analyses_for_the_best_alignment_method_PRANK_and_two_others_CLUSTAL_and_MUSCLE_and_the_MAP_dataset_of_Solenopsis_/472340", "title"=>"Results of the selection analyses for the best alignment method (PRANK), and two others (CLUSTAL and MUSCLE) and the MAP dataset of <i>Solenopsis</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 20:53:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/801937"], "description"=>"<p>We define the core length as the number of character positions from the first to the last of the characteristic cysteine residues (C1–C6) of the OBPs. The log-likelihoods (LnL), parsimony informative characters, tree size, and average approximate likelihood-ratio tests (aLRT) are derived from the ML analyses. Robinson-Foulds tree distances (RF distance) are calculated by comparing the ant and bee MAP trees to the ML trees derived under the other MSA methods. Best scores of the MSAs compared to the BAli-Phy MAP are in highlighted in bold italics.</p>", "links"=>[], "tags"=>["alignment", "methods", "phylogenies"], "article_id"=>472310, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Dietrich Gotzek", "Hugh M. Robertson", "Yannick Wurm", "DeWayne Shoemaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016289.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Details_of_the_multiple_sequence_alignment_MSA_methods_used_and_maximum_likelihood_phylogenies_estimated_from_them_/472310", "title"=>"Details of the multiple sequence alignment (MSA) methods used and maximum likelihood phylogenies estimated from them.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 20:53:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/801598"], "description"=>"<p>A. The <i>S. invicta</i> MAP phylogeny. The branch in grey is collapsed in the 50% consensus tree. Branch support is posterior probabilities derived from 3241 samples taken after the burn-in was discarded. Even though the node support in the conserved ortholog clade is relatively poor, the exact same topology of the orthologs was recovered in the honey bee MAP tree (not shown), suggesting that the branching pattern is accurate. B. The <i>S. invicta</i> MAP-AU plot. The quality of the alignment is indicated through a heat map. Red (warm colors) indicates areas of high quality alignment, blue (cold colors) signifies areas of low certainty. Note that there are considerable high quality alignment blocks in the N-terminal signal peptide and the C-terminal protein tail.</p>", "links"=>[], "tags"=>["a-posteriori", "phylogeny", "alignment", "odorant", "binding"], "article_id"=>471963, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Dietrich Gotzek", "Hugh M. Robertson", "Yannick Wurm", "DeWayne Shoemaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016289.g001", "stats"=>{"downloads"=>2, "page_views"=>60, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_a_posteriori_MAP_phylogeny_and_alignment_of_the_Solenopsis_invicta_SiOBP_odorant_binding_proteins_/471963", "title"=>"Maximum a-posteriori (MAP) phylogeny and alignment of the <i>Solenopsis invicta</i> (SiOBP) odorant binding proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 20:51:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/801907"], "description"=>"<p>*This single Sanger read appears to be partially unspliced and frameshifted.</p><p>**The total number of 454 reads contributing to this SiOBP3/<i>Gp-9</i> contig is unclear, because it strangely assembled in several different non-overlapping contigs.</p><p>The columns are: Gene – number we are assigning; cDNA – length of cDNA in base pairs, excluding polyA tail; TotAA – conceptual precursor protein length including signal sequence; MatAA – mature secreted protein length excluding signal sequence according to PSORTII; 454 – number of 454 reads contributing to contig; Sanger – number of Sanger reads contributing to contig; C – number of conserved cysteines; PolyA – presence of single or multiple poly-adenylation sites.</p>", "links"=>[], "tags"=>["odorant", "binding"], "article_id"=>472276, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Dietrich Gotzek", "Hugh M. Robertson", "Yannick Wurm", "DeWayne Shoemaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016289.t001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Details_of_the_Solenopsis_invicta_odorant_binding_proteins_/472276", "title"=>"Details of the <i>Solenopsis invicta</i> odorant binding proteins.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 20:53:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/801758"], "description"=>"<p>The phylogenies are based on the two best alignments (top: MUSCLE, bottom: PRANK). All trees are midpoint rooted in the absence of a suitable outgroup. Branch support is SH-like aLRT derived from PhyML analyses.</p>", "links"=>[], "tags"=>["phylogenies", "ant", "obps"], "article_id"=>472127, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Dietrich Gotzek", "Hugh M. Robertson", "Yannick Wurm", "DeWayne Shoemaker"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016289.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenies_of_the_fire_ant_OBPs_SiOBPs_and_honey_bee_OBPs_AmOBPs_/472127", "title"=>"Maximum likelihood phylogenies of the fire ant OBPs (SiOBPs) and honey bee OBPs (AmOBPs).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 20:52:31"}

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