<scp>M</scp>ercator: a fast and simple web server for genome scale functional annotation of plant sequence data

The halotolerant green alga Dunaliella bardawil is unique in that it accumulates under stress two types of lipid droplets: cytoplasmatic lipid droplets (CLD) and b-carotene-rich (bC) plastoglobuli. Recently, we isolated and analyzed the lipid and pigment compositions of these lipid droplets. Here, we describe their proteome analysis. A contamination filter and an enrichment filter were utilized to define core proteins. A proteome database of Dunaliella salina/D. bardawil was constructed to aid the identification of lipid droplet proteins. A total of 124 and 42 core proteins were identified in bC-plastoglobuli and CLD, respectively, with only eight common proteins. Dunaliella spp. CLD resemble cytoplasmic droplets from Chlamydomonas reinhardtii and contain major lipid droplet-associated protein and enzymes involved in lipid and sterol metabolism. The bC-plastoglobuli proteome resembles the C. reinhardtii eyespot and Arabidopsis (Arabidopsis thaliana) plastoglobule proteomes and contains carotene-globule-associated protein, plastid-lipid-associated protein-fibrillins, SOUL hemebinding proteins, phytyl ester synthases, b-carotene biosynthesis enzymes, and proteins involved in membrane remodeling/lipid droplet biogenesis: VESICLE-INDUCING PLASTID PROTEIN1, synaptotagmin, and the eyespot assembly proteins EYE3 and SOUL3. Based on these and previous results, we propose models for the biogenesis of bC-plastoglobuli and the biosynthesis of b-carotene within bCplastoglobuli and hypothesize that bC-plastoglobuli evolved from eyespot lipid droplets.

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“…The mass spectrometry results were further annotated using Mercator (Lohse et al, 2014) and WebMGA (Kegg and Kog; Wu et al, 2011).…”

Section: Annotation Of Mass Spectrometry Resultsmentioning

confidence: 99%

Proteome Analysis of Cytoplasmatic and Plastidic β-Carotene Lipid Droplets in Dunaliella bardawil

et al. 2014

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“…In addition to using established techniques such as BUSCO, comparing the whole plant gene set data against the backdrop of closely related species promises to become a versatile tool (Bolger et al, 2017) and the comparison can be largely automated (Lohse et al, 2014;Lyons and Freeling, 2008).…”

Section: Genome Assemblies Made Cheaper and Easiermentioning

confidence: 99%

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

et al. 2017

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Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii. Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.

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“…GO terms were augmented with Interpro annotations using ANNEX (Myhre et al 2006). MapMan bins were annotated with Mercator (Lohse et al 2014). Interspersed repeats and low-complexity regions were identified using RepeatMasker (version 4.0.3) (Smit et al 2013(Smit et al -2015.…”

Section: Feature Annotationmentioning

confidence: 99%

Venus flytrap carnivorous lifestyle builds on herbivore defense strategies

et al. 2016

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Although the concept of botanical carnivory has been known since Darwin's time, the molecular mechanisms that allow animal feeding remain unknown, primarily due to a complete lack of genomic information. Here, we show that the transcriptomic landscape of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death–related genes/processes. We hypothesize that the carnivory syndrome of Dionaea evolved by exaptation of ancient defense pathways, replacing cell death with nutrient acquisition.

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Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Cited by 547 publications

References 52 publications

Proteome Analysis of Cytoplasmatic and Plastidic β-Carotene Lipid Droplets in Dunaliella bardawil

Proteome Analysis of Cytoplasmatic and Plastidic β-Carotene Lipid Droplets in Dunaliella bardawil

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

Venus flytrap carnivorous lifestyle builds on herbivore defense strategies

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