Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

Berendzen, Joel; Bruno, William; Cohn, Judith D.; Hengartner, Nicolas W.; Kuske, Cheryl R.; McMahon, Benjamin H.; Wolinsky, Murray; Xie, Gary

doi:10.1186/1756-0500-5-460

Cited by 24 publications

(28 citation statements)

References 59 publications

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“…These treatments included those that induce oil accumulation (glucose or decane addition), increased temperature (37°C) and decreased temperature (4°C), and controls for daylight and at midnight. The transcriptomes were collectively analyzed using the Sequedex program for rapid gene annotation based on kmers of 10 amino acids [43,44]. Fig.…”

Section: Transcriptome Analysis Of Lipid Production In a Protothecoidesmentioning

confidence: 99%

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

et al. 2017

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In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

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Section: Transcriptome Analysis Of Lipid Production In a Protothecoidesmentioning

confidence: 99%

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

et al. 2017

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“…Shotgun metagenome reads were annotated to SEED (http://pubseed .theseed.org/) subsystems using Sequedex with default parameters (38), and annotations in MG-RAST (39) produced nearly identical functional profiles. A comparison of functional profiles was performed within the STAMP software package (35).…”

Section: Methodsmentioning

confidence: 99%

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Steven

Kuske

Gallegos‐Graves

et al. 2015

Appl Environ Microbiol

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bBiological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.

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“…A complementary approach is to use a metagenomic assembler; however, low coverage of individual microbial genomes can limit the potential for good quality assemblies in complex samples (Howe et al 2014) or samples dominated by host background. Marker-based approaches present an important option for fast estimation of microbial content but only tag a small fraction of the input leaving potentially interesting fragments hidden in a large collection of unlabeled reads (Liu et al 2011;Berendzen et al 2012;Segata et al 2012;Sunagawa et al 2013;Minot et al 2014;Tu et al 2014). Recent efforts have demonstrated substantial progress in labeling all reads by applying ordered searches that attempt to reserve the most computationally expensive analysis for the fewest reads (Nakamura et al 2009;Zhao et al 2013;Byrd et al 2014;Cotten et al 2014;Takeuchi et al 2014).…”

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confidence: 99%

Using populations of human and microbial genomes for organism detection in metagenomes

et al. 2015

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Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.

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Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

Cited by 24 publications

References 59 publications

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Using populations of human and microbial genomes for organism detection in metagenomes

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