ORFcor: Identifying and Accommodating ORF Prediction Inconsistencies for Phylogenetic Analysis

<div><p>The high-throughput annotation of open reading frames (ORFs) required by modern genome sequencing projects necessitates computational protocols that sometimes annotate orthologous ORFs inconsistently. Such inconsistencies hinder comparative analyses by non-uniformly extending or truncating 5′ and/or 3′ sequence ends, causing ORFs that are in fact identical to artificially diverge. Whereas strategies exist to correct such inconsistencies during whole-genome annotation, equivalent software designed to correct subsets of these data without genome reannotation is lacking. We therefore developed ORFcor, which corrects annotation inconsistencies using consensus start and stop positions derived from sets of closely related orthologs. ORFcor corrects inconsistent ORF annotations in diverse test datasets with specificities and sensitivities approaching 100% when sufficiently related orthologs (e.g., from the same taxonomic family) are available for comparison. The ORFcor package is implemented in Perl, multithreaded to handle large datasets, includes related scripts to facilitate high-throughput phylogenomic analyses, and is freely available at <a href="http://www.currielab.wisc.edu/downloads.html" target="_blank">www.currielab.wisc.edu/downloads.html</a>.</p></div

Illustrative examples of the ORFcor approach.

<p>A sequence alignment is given where one sequence is overextended (red box), one is chimeric (green box) and one is truncated (blue box). For each altered sequence, the consensus unaligned sequence positions for both the query and reference are indicated, compared with the relevant (non-default) parameters, and the resulting alterations to the sequences indicated.</p

Effect of varying <i>d</i> (the minimum identity required between two protein sequences to be used for correction) on ORFcor performance measured using the F-score.

<p>Simulations using test datasets #1 and #2 are shown in panels A and B, respectively.</p

Performance of ORFcor on 123 complete genome sequences belonging to the <i>Enterobacteriaceae</i> using default settings, except as indicated.

<p>Performance of ORFcor on 123 complete genome sequences belonging to the <i>Enterobacteriaceae</i> using default settings, except as indicated.</p

Table_1.xlsx

<p>Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.</p

Table_3.xlsx

<p>Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.</p

Table_2.xlsx

<p>Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.</p

Image_1.tif

<p>Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.</p

Sceliphrolactam, a Polyene Macrocyclic Lactam from a Wasp-Associated <i>Streptomyces</i> sp.

A previously unreported 26-membered polyene macrocyclic lactam, sceliphrolactam, was isolated from an actinomycete, <i>Streptomyces</i> sp., associated with the mud dauber, Sceliphron caementarium. Sceliphrolactam’s structure was determined by 1D- and 2D-NMR, MS, UV, and IR spectral analysis. Sceliphrolactam displays antifungal activity against amphotericin B-resistant <i>Candida albicans</i> (MIC = 4 μg/mL, 8.3 μM)

16S <i>Pseudonocardia</i> phylogenetic tree.

<p>A phylogeny showing bacterial sequences associated with individual leaf-cutting ant colonies over time and their free-living relatives (<i>italics</i>). The phylogenetic tree was generated by the maximum likelihood method based on the Tamura-Nei model and bootstrapped 1000 times. The scale bar represents the genetic distance between samples, reflecting the number of nucleotide changes per site. The tree was created from 16 S rDNA sequences of <i>Pseudonocardia</i> exosymbionts obtained from leaf-cutting ants at the time of colony collection (regular text) and up to 9 years later (bold text). Year(s) of isolation noted in parenthesis after the colony code. Identical sequences obtained at different times are represented by a single sequence with multiple dates. Clades of <i>Pseudonocardia</i> associated with leaf-cutting ants are labeled with roman numerals <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103269#pone.0103269-Cafaro1" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103269#pone.0103269-Poulsen4" target="_blank">[19]</a> and depicted in grey boxes. Ant-isolates are labeled by colony number, followed by the year isolated and GenBank identification number in parenthesis. The percentage sequence identity with original isolates is given in brackets after all re-isolates. Isolations from the same colony are boxed in the same color to facilitate comparison. Note that bacteria isolated from all colonies remain in the same phylogenetic clade over time, with the exception of a different morphological type (*) isolated once from a colony with two other independent re-isolates identical to the original sequence isolated.</p