SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

Koehorst, Jasper J.; Dam, Jesse C. J. van; Saccenti, Edoardo; Santos, Vítor A. P. Martins dos; Suárez-Diez, María; Schaap, Peter J.

doi:10.1093/bioinformatics/btx767

Cited by 56 publications

(81 citation statements)

References 13 publications

(12 reference statements)

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“…Finally, AUGUSTUS was used to predict genes in the genome based on the extrinsic evidence. Functional annotations of the obtained gene set were conducted using Semantic Annotation Platform (SAPP) using the InterProScan module (P. Jones et al, 2014; Koehorst et al, 2018) and Blast2GO (Götz et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

Uengwetwanit

Pootakham

Nookaew

et al. 2020

Preprint

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The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

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Section: Methodsmentioning

confidence: 99%

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

Uengwetwanit

Pootakham

Nookaew

et al. 2020

Preprint

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“…Annotation was carried out with an in-house pipeline (adapted from (34)), with Prodigal v2.5 for prediction of protein coding DNA sequences (CDS) (35), InterProScan 5RC7 for protein annotation (36), tRNAscan-SE v1.3.1 for prediction of tRNAs (37) and RNAmmer v1.2 for the prediction of rRNAs (38). Additional protein function predictions were derived via BLAST searches against the UniRef50 (39) and Swissprot (40) databases (download August 2013).…”

Section: Methodsmentioning

confidence: 99%

A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle

Gerrritsen

Hornung

Ritari

et al. 2019

Preprint

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24Cultivation-independent surveys have shown that the recently described genus Romboutsia within the 25 family Peptostreptococcaceae is more diverse than previously acknowledged. The majority of 26Romboutsia-associated 16S rRNA gene sequences have an intestinal origin, but the specific roles that 27Romboutsia species play in the digestive tract are largely unknown. The complete genomes of the 28 human intestinal isolate Romboutsia hominis FRIFI T (DSM 28814) and the soil isolate Romboutsia 29 lituseburensis A25K T (DSM 797) were sequenced. An evaluation of the common traits of this recently 30 defined genus was done based on comparative genome analysis of the two strains together with the 31 previously elucidated genome of the type species Romboutsia ilealis CRIB T . These analyses showed 32 that the genus Romboutsia covers a broad range of metabolic capabilities with respect to 33 carbohydrate utilization, fermentation of single amino acids, anaerobic respiration and metabolic end 34 products. Main differences between strains were found in their abilities to utilize specific 35 carbohydrates, to synthesize vitamins and other cofactors, and their nitrogen assimilation capabilities. 36In addition, differences were found with respect to bile metabolism and motility-related gene clusters. 37 38

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“…A total of 5713 publicly available complete bacterial genomes were downloaded from the NCBI repository (November 2016) 40 . To prevent technical bias due to the use of different annotation tools and pipelines and different thresholds for assessing the significance of the inferred genetic elements, genomes were consistently structurally and functionally de-novo annotated using SAPP 22 , an annotation platform implementing a strictly defined ontology 41 .…”

Section: Genome Annotationmentioning

confidence: 99%

Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content

Koehorst

Schaap

Suárez-Diez

2018

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BackgroundThe omnipresent 16S ribosomal RNA gene (16S-rRNA) is commonly used to identify and classify bacteria though it does not take into account the distinctive functional characteristics of taxa. We explored functional domain landscapes of over 5700 complete bacterial genomes, representing a wide coverage of the bacterial tree of life, and investigated to what extent the observed protein domain diversity correlates with the expected evolutionary diversity, using 16S-rRNA as metric for evolutionary distance. Results Analysis of protein domains showed that 83% of the bacterial genes code for at least one of the 9722 domain classes identified. By comparing clade specific and global persistence scores, candidate horizontal gene transfer and signifying domains could be identified. 16S-rRNA and functional domain content distances were used to evaluate and compare species divergence and overall a sigmoid curve is observed. Already at close 16S-rRNA evolutionary distances, high levels of functional diversity can be observed. At a larger 16S-rRNA distance, functional differences accumulate at a relatively lower pace. Conclusions Analysis of 16S-rRNA sequences in the same taxa suggests that, in many cases, additional means of classification are required to obtain reliable phylogenetic relationships. Whole genome protein domain class phylogenies correlate with, and complement 16S-rRNA sequence-based phylogenies. Moreover, domain-based phylogenies can be constructed over large evolutionary distances and provide an in-depth insight of the functional diversity within and among species and enables large scale functional comparisons. The increased granularity obtained paves way for new applications to better predict the relationships between genotype, physiology and ecology. 2/15 4/15

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SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

Cited by 56 publications

References 13 publications

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle

Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content

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