EC2KEGG: a command line tool for comparison of metabolic pathways

Porollo, Aleksey

doi:10.1186/1751-0473-9-19

Cited by 17 publications

(15 citation statements)

References 11 publications

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“…Although microalgal species clustered tightly according to their clades and habitats in our Pfam analyses, biclustering based on EC (Enzyme Commission) assignments (Alborzi et al., 2017) within Kyoto Encyclopedia for Genes and Genomes (KEGG) pathways (Data S5) (Porollo, 2014) was inconsistent with Pfam-only biclustering, and species from the same clade did not always cluster together (Figure 4). This discrepancy between our Pfam analyses and KEGG pathway analyses could partially result from the distance each descriptor has to experimental evidence of function.…”

Section: Resultsmentioning

confidence: 91%

Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae

Nelson

Chaiboonchoe²,

Fu³

et al. 2019

iScience

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SummaryThe activities of microalgae support nutrient cycling that helps to sustain aquatic and terrestrial ecosystems. Most microalgal species, especially those from the subtropics, are genomically uncharacterized. Here we report the isolation and genomic characterization of 22 microalgal species from subtropical coastal regions belonging to multiple clades and three from temperate areas. Halotolerant strains including Halamphora, Dunaliella, Nannochloris, and Chloroidium comprised the majority of these isolates. The subtropical-based microalgae contained arrays of methyltransferase, pyridine nucleotide-disulfide oxidoreductase, abhydrolase, cystathionine synthase, and small-molecule transporter domains present at high relative abundance. We found that genes for sulfate transport, sulfotransferase, and glutathione S-transferase activities were especially abundant in subtropical, coastal microalgal species and halophytic species in general. Our metabolomics analyses indicate lineage- and habitat-specific sets of biomolecules implicated in niche-specific biological processes. This work effectively expands the collection of available microalgal genomes by ∼50%, and the generated resources provide perspectives for studying halophyte adaptive traits.

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Section: Resultsmentioning

confidence: 91%

Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae

Nelson

Chaiboonchoe²,

Fu³

et al. 2019

iScience

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“…Shared metabolic capacity among NJAY, AY-WB and OY-M was determined in two manners: the first utilized existing annotations for AY-WB and OY-M, and the second involved reannotating genic content for these two reference taxa. Prodigal-predicted NJAY protein sequences were annotated using Blast2GO [ 42 ], from which Enzyme Commission (EC) numbers were extracted and compared in pairwise fashion with each of AY-WB and OY-M using the EC2KEGG program [ 43 ]. The Prodigal gene finder was then run independently on AY-WB and OY-M, and resultant protein sequences were assigned EC numbers using Blast2GO.…”

Section: Methodsmentioning

confidence: 99%

Draft genome sequence of the New Jersey aster yellows strain of ‘Candidatus Phytoplasma asteris’

Sparks¹,

Bottner-Parker

Gundersen‐Rindal³

et al. 2018

PLoS ONE

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The NJAY (New Jersey aster yellows) strain of ‘Candidatus Phytoplasma asteris’ is a significant plant pathogen responsible for causing severe lettuce yellows in the U.S. state of New Jersey. A draft genome sequence was prepared for this organism. A total of 177,847 reads were assembled into 75 contigs > 518 bp with a total base value of 652,092 and an overall [G+C] content of 27.1%. A total of 733 protein coding genes were identified. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession MAPF00000000. This draft genome was used for genome- and gene-based comparative phylogenetic analyses with other phytoplasmas, including the closely related ‘Ca. Phytoplasma asteris’ strain, aster yellows witches’- broom (AY-WB). NJAY and AY-WB exhibit approximately 0.5% dissimilarity at the nucleotide level among their shared genomic segments. Evidence indicated that NJAY harbors four plasmids homologous to those known to encode pathogenicity determinants in AY-WB, as well as a chromosome-encoded mobile unit. Apparent NJAY orthologs to the important AY-WB virulence factors, SAP11 and SAP54, were identified. A number of secreted proteins, both membrane-bound and soluble, were encoded, with many bearing similarity to known AY-WB effector molecules and others representing possible secreted proteins that may be novel to the NJAY lineage.

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“…Functional annotation was carried out using Blast2GO 2.8.0 (Conesa et al, 2005 ). Statistical analysis of KEGG pathways was carried out using EC2KEGG (Porollo, 2014 ) and full results are shown in Table S5 .…”

Section: Methodsmentioning

confidence: 99%

Deep Sequencing of Suppression Subtractive Hybridisation Drought and Recovery Libraries of the Non-model Crop Trifolium repens L.

et al. 2017

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White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. The aim of this work was to characterize its molecular response to water deficit and recovery following re-hydration to identify targets for the breeding of tolerant varieties. We created a white clover reference transcriptome of 16,193 contigs by deep sequencing (mean base coverage 387x) four Suppression Subtractive Hybridization (SSH) libraries (a forward and a reverse library for each treatment) constructed from young leaf tissue of white clover at the onset of the response to drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data. The pipeline generated four robust sets of transcripts induced and repressed in the leaves of plants subjected to water deficit stress (6,937 and 3,142, respectively) and following re-hydration (6,695 and 4,897, respectively). Semi-quantitative polymerase chain reaction was used to verify the expression pattern of 16 genes. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways. In agreement with similar studies in other crops, the majority of transcripts up-regulated in response to drought belonged to metabolic processes, such as amino acid, carbohydrate, and lipid metabolism, while transcripts involved in photosynthesis, such as components of the photosystem and the biosynthesis of photosynthetic pigments, were up-regulated during recovery. The data also highlighted the role of raffinose family oligosaccharides (RFOs) and the possible delayed response of the flavonoid pathways in the initial response of white clover to water withdrawal. The work presented in this paper is to our knowledge the first large scale molecular analysis of the white clover response to drought stress and re-hydration. The data generated provide a valuable genomic resource for marker discovery and ultimately for the improvement of white clover.

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EC2KEGG: a command line tool for comparison of metabolic pathways

Cited by 17 publications

References 11 publications

Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae

Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae

Draft genome sequence of the New Jersey aster yellows strain of ‘Candidatus Phytoplasma asteris’

Deep Sequencing of Suppression Subtractive Hybridisation Drought and Recovery Libraries of the Non-model Crop Trifolium repens L.

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