InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

Östlund, Gabriel; Schmitt, Thomas; Forslund, Kristoffer; Köstler, Tina; Messina, David N.; Roopra, Sanjit; Frings, Oliver; Sonnhammer, Erik L. L.

doi:10.1093/nar/gkp931

Cited by 573 publications

(520 citation statements)

References 37 publications

Supporting

Mentioning

512

Contrasting

Unclassified

Order By: Relevance

“…Protein-coding loci were identified using homology-based FgenesH and GenomeScan predictions and ,260,000 PASA 37 EST assemblies from E. grandis and sister species. Gene family clustering was performed with the Inparanoid algorithm 38,39 and peptide sequences analysed with Interproscan 40 , SignalP 41 , Predotar 42 , TMHMM 43 and orthology-based projections from Arabidopsis. We performed maximum-likelihood-based phylogenetic reconstruction 44 of the green plant phylogeny based on 174,020 peptides encoded by single copy orthologous genes from 17 plant genomes.…”

Section: Methods Summarymentioning

confidence: 99%

See 1 more Smart Citation

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

710

750

View full text Add to dashboard Cite

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

show abstract

Section: Methods Summarymentioning

confidence: 99%

“…Gene family cluster and gene ontology analysis. The Inparanoid algorithm 38,39 was used to identify orthologous and paralogous genes that arose through duplication events. Clusters were determined using a reciprocal best pair match and then an algorithm for adding in-paralogues was applied.…”

Section: Research Article Methodsmentioning

confidence: 99%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

710

750

View full text Add to dashboard Cite

show abstract

“…A pairwise BLAST was conducted between every two proteomes (whole protein sets) with InParanoid 4.1 (Östlund et al., 2010), and all pairwise orthologs were combined into orthologous groups using MultiParanoid (Alexeyenko, Tamas, Liu, & Sonnhammer, 2006). All one‐to‐one orthologous groups were assigned a cluster ID for further analysis.…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids

Wang

Lamer

Gaughan

et al. 2016

Ecology and Evolution

View full text Add to dashboard Cite

Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor‐joining distance tree constructed using over 2,500 one‐to‐one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression.

show abstract

“…Para ello, se hizo una búsqueda de proteínas ortólogas con la herramienta OrthoMCL (18) de la base de datos TriTrypDB (versión 4.2) (19) y la base de datos InParanoid 7 (20). Posteriormente, se hizo una DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST) (21) de las secuencias representantes de cada gen y, en la base de datos de proteínas humanas, se compararon los parámetros y se identificaron las proteínas con menor similitud y nivel de identidad.…”

Section: Análisis De Similitud Con Las Proteínas De La Vía Del Fosfatunclassified