InterPro: the integrative protein signature database

Hunter, Sarah; Apweiler, Rolf; Attwood, Teresa K.; Bairoch, Amos Marc; Bateman, Alex; Binns, David; Bork, Peer; Das, Ujjwal; Daugherty, Louise C.; Duquenne, Lauranne; Finn, Robert D.; Gough, Julian; Haft, Daniel H.; Hulo, Nicolas; Kahn, Daniel; Kelly, Elizabeth A.; Laugraud, Aurélie; Letunić, Ivica; Lonsdale, David; López, Rodrigo; Madera, Martin; Maslen, John; McAnulla, Craig; McDowall, Jennifer; Mistry, Jaina; Mitchell, Alex L.; Mulder, Nicola; Natale, Darren A.; Orengo, Christine A.; Quinn, Antony F.; Selengut, Jeremy D.; Sigrist, Christian J. A.; Thimma, Manjula; Thomas, Paul D.; Valentin, Franck; Wilson, Derek A.; Wu, Cathy H.; Yeats, Corin

doi:10.1093/nar/gkn785

Cited by 1,790 publications

(1,497 citation statements)

References 26 publications

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“…A functional annotation pipeline similar to the one used for strawberry genome annotation 10 was used to infer Gene Ontology 55 assignments to 29,841 protein coding genes (,82%). Peptide sequences were analysed through an integrated approach involving Interproscan 40 , SignalP 41 , Predotar 42 , TMHMM 43 and orthology-based projections from Arabidopsis. Green plant phylogeny.…”

Section: Research Article Methodsmentioning

confidence: 99%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

761

750

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Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled .94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.A major opportunity for a sustainable energy and biomaterials economy in many parts of the world lies in a better understanding of the molecular basis of superior growth and adaptation in woody plants. Part of this opportunity involves species of Eucalyptus L'Hér, a genus of woody perennials native to Australia 1 . The remarkable adaptability of eucalypts coupled with their fast growth and superior wood properties has driven their rapid adoption for plantation forestry in more than 100 countries across six continents (.20 million ha) 2 , making eucalypts the most widely planted hardwood forest trees in the world. The subtropical E. grandis and the temperate E. globulus stand out as targets of breeding programmes worldwide. Planted eucalypts provide key renewable resources for the production of pulp, paper, biomaterials and bioenergy, while mitigating human pressures on native forests 3 . Eucalypts also have a large diversity and high concentration of essential oils (mixtures of mono-and sesquiterpenes), many of which have ecological functions as well as medicinal and industrial uses. Predominantly outcrossers 1 with hermaphroditic animal-pollinated flowers, eucalypts are highly heterozygous and display pre-and postzygotic barriers to selfing to reduce inbreeding depression for fitness and survival 4 .To mitigate the challenge of assembling a highly heterozygous genome, we sequenced the genome of 'BRASUZ1', a 17-year-old E. grandis genotype derived from one generation of selfing. The availability of annotated forest tree genomes from two separately evolving rosid lineages, Eucalyptus (order Myrtales) and Populus (order Malpighiales 5 ), in combination with genomes from domesticated woody plants (for example, Vitis, Prunus, Citrus), provides a comparative foundation for addressing

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Section: Research Article Methodsmentioning

confidence: 99%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

761

750

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“…The integrated gene set was translated into aminoacid sequences, which were used to search the InterPro database 48 by Iprscan (v 4.7) 49 . We used BLAST to search the metabolic pathway database 50 (release58) in KEGG and homologs in the SwissProt and TrEMBL databases in UniProt 51 (release 2011-01).…”

Section: Digital Gene Expression (Dge)mentioning

confidence: 99%

A heterozygous moth genome provides insights into herbivory and detoxification

et al. 2013

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l e t t e r sHow an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants 1 , but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood 2 . We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.The global pest P. xylostella (Lepidoptera: Yponomeutidae) is thought to have coevolved with the crucifer plant family 3 ( Supplementary Fig. 1) and has become the most destructive pest of economically important food crops, including rapeseed, cauliflower and cabbage 4 . Recently, the total cost of damage and management worldwide was estimated at $4-5 billion per annum 5,6 . This insect is the first species to have evolved resistance to dichlorodiphenyltrichloroethane (DDT) in the 1950s 7 and to Bacillus thuringiensis (Bt) toxins in the 1990s 8 and has developed resistance to all classes of insecticide, making it increasingly difficult to control 9,10 . P. xylostella provides an exceptional system for understanding the genetic and molecular bases of how insect herbivores cope with the broad range of plant defenses and chemicals encountered in the environment (Supplementary Fig. 2).We used a P. xylostella strain (Fuzhou-S) collected from a field in Fuzhou in southeastern China (26.08 °N, 119.28 °E) for sequencing ( Supplementary Fig. 1). Whole-genome shotgun-based Illumina sequencing of single individuals (Supplementary Table 1), even after ten generations of laboratory inbreeding, resulted in a poor initial assembly (N50 = 2.4 kb, representing the size above which 50% of the total length of the sequences is included), owing to high levels of heterozygosity ( Supplementary Figs. 3 and 4 and Supplementary Table 2). Subsequently, we sequenced 100,800 fosmid clones (comprising ~10× the genome length) to a depth of 200× ( Supplementary Fig. 5 and Supplementary Tables 3-5), assembling the resulting sequence data into 1,819 scaffolds, with an N50 of 737 kb, spanning ~394 Mb of the genome sequence (version 1; Supplementary Fig. 6 and Supplementary Table 6). The assembly covered 85.5% of a set of protein-coding ESTs (Supplementary Tables 7 and 8) generated by transcriptome sequencing 11 . Alignment of a subject scaffold against a 126-kb BAC (GenBank GU058050) from an altern...

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“…The Saccharomyces Genome Database (SGD) is annotated by InterProScan, which is a resource from the European Bioinformatics Institute (Hinxton, UK). InterProScan incorporates all of Pfam, SuperFamily, Gene3D and many other profile‐sequence tools 45, 46. For PH‐like domains in yeast, InterPro provides useful data, but its output is not close to 100% sensitive, only including 61 of 73 domains (Table S2) 47, 48.…”

Section: Profile‐sequence Tools Currently Used To Define Domainsmentioning

confidence: 99%

Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains

Fidler¹,

Murphy²,

Courtis³

et al. 2016

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Advances in membrane cell biology are hampered by the relatively high proportion of proteins with no known function. Such proteins are largely or entirely devoid of structurally significant domain annotations. Structural bioinformaticians have developed profile‐profile tools such as HHsearch (online version called HHpred), which can detect remote homologies that are missed by tools used to annotate databases. Here we have applied HHsearch to study a single structural fold in a single model organism as proof of principle. In the entire clan of protein domains sharing the pleckstrin homology domain fold in yeast, systematic application of HHsearch accurately identified known PH‐like domains. It also predicted 16 new domains in 13 yeast proteins many of which are implicated in intracellular traffic. One of these was Vps13p, where we confirmed the functional importance of the predicted PH‐like domain. Even though such predictions require considerable work to be corroborated, they are useful first steps. HHsearch should be applied more widely, particularly across entire proteomes of model organisms, to significantly improve database annotations.

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InterPro: the integrative protein signature database

Cited by 1,790 publications

References 26 publications

The genome of Eucalyptus grandis

The genome of Eucalyptus grandis

A heterozygous moth genome provides insights into herbivory and detoxification

Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains

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