<scp>EnTAP</scp>: Bringing faster and smarter functional annotation to non‐model eukaryotic transcriptomes

Hart, Alexander; Ginzburg, Samuel; Xu, Muyang; Fisher, Cera R; Rahmatpour, Nasim; Mitton, Jeffry B.; Paul, R.; Wegrzyn, Jill L.

doi:10.1111/1755-0998.13106

Cited by 167 publications

(136 citation statements)

References 28 publications

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“…On average, the Illumina isoforms (7,220 bp) were longer than the PacBio isoforms (6,044 bp). By running the EnTAP functional annotation pipeline with the entire NCBI RefSeq plant database (Hart et al 2018), we observed that 672 isoforms were annotated with a plant protein, while the remaining 486 transcript isoforms were not identified in the previous walnut gene annotation.…”

Section: Resultsmentioning

confidence: 99%

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High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Marrano

Britton

Zaini

et al. 2019

Preprint

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27The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements 28 in the characterization of walnut genetic and functional variation. However, it is highly 29 fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to 30 fully elucidate walnut biological processes. Here we report the new chromosome-scale assembly 31 of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-32 read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the 33 previous reference genome, the new assembly features an 84.4-fold increase in N50 size, and the 34 full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences 35 at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 36 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of 37 the new protein-coding genes (90%) are full-length, which represents a significant improvement 38 compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new 39 chromosome-level genome on different areas of walnut research. By studying the proteome 40 changes occurring during catkin development, we observed that the virtual proteome obtained 41 from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the 42 identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale 43 genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously 44 undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic 45 regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler 46 v2.0 is a valuable resource to understand and explore walnut biology better.47 48Persian walnut (Juglans regia L.) is among the top three most-consumed nuts in the world, and 50 over the last ten years, its global production increased by 37% (International Nut and Dried Fruit 51

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Section: Resultsmentioning

confidence: 99%

“…The percent identity and coverage of each J. regia transcript compared to proteins in the NCBI plant RefSeq database was also determined by running the EnTAP pipeline v.0.9.0 (Hart et al 2018).…”

Section: Methodsmentioning

confidence: 99%

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Marrano

Britton

Zaini

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…The EnTAP functional annotation package was employed to remove unlikely gene models and provide provisional functional information (Hart et al , ). Multi‐exonic and mono‐exonic gene models were subjected to different functional filtering pipelines that each utilized EnTAP.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomics of six Juglans species reveals disease‐associated gene family contractions

et al. 2020

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† These authors are joint first authors. SUMMARYJuglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 27 000 and 44 000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high-quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance-related wall-associated kinase (WAK), Catharanthus roseus receptor-like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole-genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.

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“…The EnTAP functional annotation package was employed to remove unlikely gene models and provide provisional functional information (Hart et al 2018). Multi-exonic and mono-exonic gene models were subjected to different functional filtering pipelines that each utilized EnTAP.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics of Six Juglans Species Reveals Patterns of Disease-associated Gene Family Contractions

Trouern-Trend

Falk

Zaman

et al. 2019

Preprint

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Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae) represents most of the family’s commercially valuable fruit and wood-producing trees and includes several species used as rootstock in agriculture for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional in-house developed tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multiexonic and monoexonic putative genes to yield between 27,000 and 44,000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 89.6%. We utilized these high quality annotations to assess gene family evolution within Juglans and among Juglans and selected Eurosid species, which revealed significant contractions in several gene families in J. hindsii including disease resistance-related Wall-associated Kinase (WAK) and Catharanthus roseus Receptor-like Kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.SIGNIFICANCEHigh-quality full genome annotations for six species of walnut (Juglans) and a wingnut (Pterocarya) outgroup were constructed using semi-unsupervised gene prediction followed by gene model filtering and functional characterization. These annotations represent the most comprehensive set for any hardwood genus to date. Comparative analyses based on the gene models uncovered rapid evolution in multiple gene families related to disease-response and a whole genome duplication in a Juglandaceae common ancestor.

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EnTAP: Bringing faster and smarter functional annotation to non‐model eukaryotic transcriptomes

Cited by 167 publications

References 28 publications

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Comparative genomics of six Juglans species reveals disease‐associated gene family contractions

Comparative Genomics of Six Juglans Species Reveals Patterns of Disease-associated Gene Family Contractions

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