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U.S. Department of Agriculture
  1. Publication
  2. Workflows For Rapid Functional Annotation of Diverse Arthropod Genomes.

Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes.

Summary
Publication Type
Journal Article
Abstract

Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide the foundational information required to apply 'omics technologies to a more diverse set of species. However, biologists require genome annotation to use these genomes and derive a better understanding of complex biological systems. Genome annotation incorporates two related, but distinct, processes: Demarcating genes and other elements present in genome sequences (structural annotation); and associating a function with genetic elements (functional annotation). While there are well-established and freely available workflows for structural annotation of gene identification in newly assembled genomes, workflows for providing the functional annotation required to support functional genomics studies are less well understood. Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.). A first-pass genome-wide functional annotation effort can rapidly identify under-represented gene sets for focused community annotation efforts. We present an open-source, open access, and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to various arthropod species. We show that the performance of the predictions is consistent across a set of arthropod genomes with varying assembly and annotation quality.
Citation
Saha S, Cooksey AM, Childers AK, Poelchau MF, McCarthy FM. Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes.. Insects. 2021 Aug 19; 12(8).
Publication Date
2021 Aug 19
DOI
10.3390/insects12080748
Authors
Saha S, Cooksey AM, Childers AK, Poelchau MF, McCarthy FM
Cross Reference
Database Accession
PMID 34442314
Analyses
Name Program
Functional annotation of Heliothis virescens annotations OGS 1.1 AgBase functional annotation pipeline
Functional annotation of NCBI Helicoverpa zea Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Plodia interpunctella Annotation Release GCF_027563975.2-RS_2024_04 AgBase functional annotation pipeline
Functional annotation of NCBI Anabrus simplex Annotation Release GCF_040414725.1-RS_2024_09 AgBase functional annotation pipeline
Functional annotation of NCBI Tribolium castaneum Annotation Release GCF_031307605.1-RS_2024_04 AgBase functional annotation pipeline
Functional annotation of Heliothis virescens annotations GCA_002382865.1_K63_refined_pacbio_genomic 1 AgBase functional annotation pipeline
Functional annotation of NCBI Bactrocera dorsalis Annotation Release 103 AgBase functional annotation pipeline
Functional annotation of Drosophila eugracilis Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Drosophila kikkawai Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of Drosophila elegans Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of Lucilia sericata Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Rhipicephalus microplus Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of Annotation v0.5.3 of the Homalodisca vitripennis assembly using MAKER (Baylor College of Medicine) AgBase functional annotation pipeline
Functional annotation of Photinus pyralis Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of BCM annotation of the Eurytemora affinis assembly using Maker and additional analyses AgBase functional annotation pipeline
Functional annotation of Oncopeltus fasciatus Official Gene Set v1.2 AgBase functional annotation pipeline
Functional annotation of Annotation v0.5.3 of the Latrodectus hesperus assembly using MAKER AgBase functional annotation pipeline
Functional annotation of Annotation v0.5.3 of the Agrilus planipennis assembly using MAKER (Baylor College of Medicine) AgBase functional annotation pipeline
Functional annotation of NCBI Drosophila takahashii Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Schistocerca americana Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Neodiprion lecontei Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Schistocerca gregaria Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Amyelois transitella Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Bemisia tabaci Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Bombus terrestris Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Contarinia nasturtii Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Diachasma alloeum Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Tribolium madens Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of Apis mellifera annotations amel_OGSv3.3 AgBase functional annotation pipeline
Functional annotation of NCBI Varroa jacobsoni Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of Hyalella azteca hyaazt OGSv1.2 AgBase functional annotation pipeline
Functional annotation of NCBI Bactrocera oleae Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Cephus cinctus Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Drosophila ficusphila Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Habropoda laboriosa Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Leptinotarsa decemlineata Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Odontomachus brunneus Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Neodiprion lecontei Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Nicrophorus vespilloides Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Galleria mellonella Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of Onthophagus taurus BCM version 0.5.3 AgBase functional annotation pipeline
Functional annotation of Pachypsylla venusta BCM version 0.5.3 AgBase functional annotation pipeline
Functional annotation of Medauroidea extradentata Mext OGS v1.0 AgBase functional annotation pipeline
Functional annotation of Parasteatoda tepidariorum Augustus gene set Primary Gene Set AgBase functional annotation pipeline
Functional annotation of Loxosceles reclusa BCM version 0.5.3 AgBase functional annotation pipeline
Functional annotation of Locusta migratoria JAMg OGSv1 AgBase functional annotation pipeline
Functional annotation of Laodelphax striatellus laostr OGSv1.2 AgBase functional annotation pipeline
Functional annotation of Manduca sexta Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of Halyomorpha halys halhal OGSv1.2 AgBase functional annotation pipeline
Functional annotation of Tribolium castaneum annotations TCAS_OGSv3.1 AgBase functional annotation pipeline
Functional annotation of Gerris buenoi gerbue OGSv1.1 AgBase functional annotation pipeline
Functional annotation of Frankliniella occidentalis fraocc OGSv1.1 AgBase functional annotation pipeline
Functional annotation of Euglossa dilemma GeneSet v1-0 AgBase functional annotation pipeline
Functional annotation of Catajapyx aquilonaris BCM version 0.5.3 AgBase functional annotation pipeline
Functional annotation of Blattella germanica blager OGS v1.0 AgBase functional annotation pipeline
Functional annotation of Anoplophora glabripennis OGS v1 2 AgBase functional annotation pipeline
Functional annotation of Centruroides sculpturatus BCM version 0.5.3 AgBase functional annotation pipeline
Functional annotation of NCBI Dufourea novaeangliae Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Schistocerca nitens Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of Tigriopus californicus TCALIF_v1.0 AgBase functional annotation pipeline
Functional annotation of Clitarchus hookeri AgBase functional annotation pipeline
Functional annotation of NCBI Bombus huntii Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Pectinophora gossypiella Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Bombus affinis Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Aethina tumida Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of BCM annotation of the Athalia rosae assembly using Maker and additional analyses AgBase functional annotation pipeline
Functional annotation of NCBI Bactrocera dorsalis Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Zeugodacus cucurbitae Annotation Release GCF_028554725.1-RS_2023_03 AgBase functional annotation pipeline
Functional annotation of NCBI Chelonus insularis Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Diaphorina citri Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Drosophila biarmipes Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Drosophila bipectinata Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Drosophila rhopaloa Annotation Release 102 AgBase functional annotation pipeline
Functional annotation of NCBI Fopius arisanus Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Microplitis demolitor Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Nylanderia fulva Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Osmia lignaria Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of Orussus abietinus oruabi OGS v1.0 AgBase functional annotation pipeline
Functional annotation of Mayetiola destructor OGS1.0 AgBase functional annotation pipeline
Functional annotation of Lasioglossum albipes Lalb OGSv5.42 AgBase functional annotation pipeline
Functional annotation of Melipona quadrifasciata ASM127656v1 GenBank annotations AgBase functional annotation pipeline
Functional annotation of Ladona fulva Official Gene Set ladful_OGS_v1.0 AgBase functional annotation pipeline
Functional annotation of Ephemera danica ephdan OGSv1.0 AgBase functional annotation pipeline
Functional annotation of NCBI Dermacentor andersoni Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Neodiprion pinetum Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Neodiprion fabricii Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Neodiprion virginiana Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Diprion similis Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of Trichogramma pretiosum BCM version 0.5.3 AgBase functional annotation pipeline
Functional annotation of Tribolium castaneum annotations TCAS_OGSv3 AgBase functional annotation pipeline
Functional annotation of NCBI Schistocerca serialis cubense Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Megachile rotundata Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of Cimex lectularius Official Gene Set v1.2 AgBase functional annotation pipeline
Functional annotation of NCBI Anthonomus grandis grandis Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Venturia canescens Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Bradysia coprophila Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of Annotation v0.5.3 of the Limnephilus lunatus assembly using MAKER (Baylor College of Medicine) AgBase functional annotation pipeline
Functional annotation of NCBI Bombus impatiens Annotation Release 103 AgBase functional annotation pipeline
Functional annotation of NCBI Aethina tumida Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Varroa destructor Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Schistocerca piceifrons Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Plodia interpunctella Annotation Release GCF_027563975.1-RS_2023_02 AgBase functional annotation pipeline
Functional annotation of NCBI Schistocerca cancellata Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of Annotation (v0.5.3) of the Copidosoma floridanum assembly using MAKER (Baylor College of Medicine) AgBase functional annotation pipeline
Functional annotation of NCBI Bactrocera oleae Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Ornithodoros turicata Annotation Release GCF_037126465.1-RS_2024_04 AgBase functional annotation pipeline
Functional annotation of NCBI Anastrepha obliqua Annotation Release GCF_027943255.1-RS_2023_03 AgBase functional annotation pipeline
Functional annotation of NCBI Anastrepha ludens Annotation Release GCF_028408465.1-RS_2023_03 AgBase functional annotation pipeline
Functional annotation of NCBI Zeugodacus cucurbitae Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Vespa mandarinia Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Hylaeus anthracinus Annotation Release GCF_026225885.1-RS_2023_03 AgBase functional annotation pipeline
Functional annotation of NCBI Hylaeus volcanicus Annotation Release GCF_026283585.1-RS_2023_03 AgBase functional annotation pipeline
Functional annotation of NCBI Diorhabda carinulata Annotation Release GCF_026250575.1-RS_2023_06 AgBase functional annotation pipeline
Functional annotation of NCBI Microplitis mediator Annotation Release GCF_029852145.1-RS_2023_06 AgBase functional annotation pipeline
Functional annotation of NCBI Microplitis demolitor Annotation Release GCF_026212275.2-RS_2023_02 AgBase functional annotation pipeline
Functional annotation of NCBI Diorhabda sublineata Annotation Release GCF_026230105.1-RS_2023_05 AgBase functional annotation pipeline
Functional annotation of NCBI Bombus terrestris Annotation Release 103 AgBase functional annotation pipeline
Functional annotation of NCBI Agrilus planipennis Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Galleria mellonella Annotation Release GCF_026898425.1-RS_2022_12 AgBase functional annotation pipeline
Functional annotation of NCBI Hyalella azteca Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Centruroides sculpturatus Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Cylas formicarius Annotation Release GCF_029955315.1-RS_2023_10 AgBase functional annotation pipeline
Functional annotation of NCBI Anoplophora glabripennis Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Cydia pomonella Annotation Release GCF_033807575.1-RS_2023_12 AgBase functional annotation pipeline
Functional annotation of NCBI Orussus abietinus Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Onthophagus taurus Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Copidosoma floridanum Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Trichogramma pretiosum Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Amyelois transitella Annotation Release GCF_032362555.1-RS_2023_11 AgBase functional annotation pipeline
Functional annotation of NCBI Leguminivora glycinivorella Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Drosophila biarmipes Annotation Release 103 AgBase functional annotation pipeline
Functional annotation of NCBI Eufriesea mexicana Annotation Release 100 AgBase functional annotation pipeline
Functional annotation of NCBI Athalia rosae Annotation Release 103 AgBase functional annotation pipeline
Functional annotation of NCBI Frankliniella occidentalis Annotation Release 101 AgBase functional annotation pipeline
Functional annotation of NCBI Tigriopus californicus Annotation Release GCF_007210705.1-RS_2023_08 AgBase functional annotation pipeline
Functional annotation of NCBI Apis mellifera Annotation Release 104 AgBase functional annotation pipeline
Functional annotation of NCBI Diachasmimorpha longicaudata Annotation Release GCF_034640455.1-RS_2024_03 AgBase functional annotation pipeline
Functional annotation of NCBI Vanessa tameamea Annotation Release GCF_037043105.1-RS_2024_03 AgBase functional annotation pipeline
Functional annotation of Lifted BCM annotation of the Catajapyx aquilonaris assembly using Maker and additional analyses AgBase functional annotation pipeline
Functional annotation of Ceratitis capitata Official Gene Set OGSv1 AgBase functional annotation pipeline
Functional annotation of NCBI Ceratitis capitata Annotation Release 103 AgBase functional annotation pipeline
Functional annotation of Holacanthella duospinosa annotations Holacanthella_duospinosa_annotation 1.0 AgBase functional annotation pipeline