InterProScan: protein domains identifier

Quévillon, Emmanuel; Silventoinen, Ville; Pillai, Sharmila; Harte, Nicola; Mulder, Nicola; Apweiler, Rolf; López, Rodrigo

doi:10.1093/nar/gki442

Cited by 2,602 publications

(2,101 citation statements)

References 18 publications

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“…tRNAs were predicted using tRNAscan-SE 40 . All predicted proteins were functionally annotated using SignalP 41 for signal sequences, TMHMM 42 for transmembrane domains, interProScan 43 59 and a Yule tree prior 60 .…”

Section: Methodsmentioning

confidence: 99%

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Möck

Otillar

Strauss

et al. 2017

Nature

328

303

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The Southern Ocean houses a diverse and productive community of organisms 1,2 . Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice 3-7 . How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus 8,9 , based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation.

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Section: Methodsmentioning

confidence: 99%

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Möck

Otillar

Strauss

et al. 2017

Nature

328

303

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“…Protein sequences from genes predicted by Maker were functionally annotated using NCBI blastp v.2.2.30+ versus the NCBI non-redundant refseq protein database (http://www.ncbi.nlm.nih.gov/refseq/), versus the UniProt database 48 , and using InterProScan (v. 5.6-48.0) 49 .…”

Section: Methodsmentioning

confidence: 99%

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

VanBuren

Bryant

Edger

et al. 2015

Nature

290

271

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Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly 1 . The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE) 2 . Here we report the whole-genome sequencing and assembly of the desiccationtolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.The genomes of Arabidopsis 3 , rice 4 , poplar, grape and Sorghum 5 were first sequenced using high-quality and reiterative Sanger-based approaches producing a series of 'gold standard' reference genomes. The advent of next-generation sequencing (NGS) technologies reduced costs of sequencing substantially, which has enabled sequencing of over 100 plant genomes 1 . The quality of plant genome assemblies depends on genome size, ploidy, heterozygosity and sequence coverage, but most NGS-based genomes have on the order of tens of thousands of short contigs distributed in thousands of scaffolds. The short read lengths of NGS, inherent biases and non-random sequencing errors have resulted in highly fragmented draft genome assemblies that are not complete, which means they are missing biologically meaningful sequences including entire genes, regulatory regions, transposable elements, centromeres, telomeres and haplotype-specific structural variations. It is becoming clear from ENCODE projects that complete genomes are needed to better understand the importance of the non-coding regions of genomes 2 .More than 40% of calories consumed by humans are derived from grasses, and the grass family (Poaceae) is arguably the most important plant family with regard to global food security 6 . The size and complexity of most grass genomes has challenged progress in gene discovery and comparative genomics, although draft genomes are now available for most agriculturally important grasses 1 . The largest genome assemblies, such as maize (2,300 megabases (Mb)) 7 , barley (5,100 Mb) 8 and wheat (hexaploid, 1...

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“…26) on Refseq protein, Swissprot, and Ensembl protein reference files from Crassostrea gigas, Lottia gigantea, and Lingula anatina to retrieve the corresponding annotations. The contigs were also processed with rnammer (Lagesen et al 2007) (standard parameters, version 1.2) to find ribosomal genes, with repeatmasker (Smith et al n.d.) (-engine crossmatch -gccalc -species Danio rerio parameters, version open-4-0-3) to list the contained repeats and with interproscan (Quevillon et al 2005) (-goterms -pathways parameters, version 4.8) for gene ontology and structural annotation. Reads have been realigned back to contigs with bwa (Li and Durbin 2009) (standard parameters, mem algorithm, version 0.7.12).…”

Section: Methodsologymentioning

confidence: 99%

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Bertucci

Pierron

Thébault

et al. 2017

Environ Sci Pollut Res

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The freshwater pearl mussel Margaritifera margaritifera is one of the most threatened freshwater bivalves worldwide. In this study, we aimed (i) to study the processes by which water quality might affect freshwater mussels in situ and (ii) to provide insights into the ecotoxicological significance of water pollution to natural populations in order to provide necessary information to enhance conservation strategies. M. margaritifera specimens were sampled in two close sites located upstream or downstream from an illegal dumping site. The renal transcriptome of these animals was assembled and gene transcription determined by RNA-seq. Correlations between transcription levels of each single transcript and the bioaccumulation of nine trace metals, age (estimated by sclerochronology), and condition index were determined in order to identify genes likely to respond to a specific factor. Amongst the studied metals, Cr, Zn, Cd, and Ni were the main factors correlated with transcription levels, with effects on translation, apoptosis, immune response, response to stimulus, and transport pathways.However, the main factor explaining changes in gene transcription appeared to be the age of individuals with a negative correlation with the transcription of retrotransposon-related genes. To investigate this effect further, mussels were classified into three age classes. In young, middle-aged and old animals, transcription levels were mainly explained by Cu, Zn and age, respectively. This suggests differences in the molecular responses of this species to metals during its lifetime that must be better assessed in future ecotoxicology studies.

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InterProScan: protein domains identifier

Cited by 2,602 publications

References 18 publications

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

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