Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes

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.

The highly improved genome ofIxodes scapulariswith X and Y pseudochromosomes

“…This duplication is in line with the 12,750 more predicted gene models than the previous IscaW1 genome annotation, which only contained 20,486 gene models (Table S1). The chromosome-scale arthropod genome assemblies have revealed a higher percentage of duplicated BUSCOs than less contiguous assemblies ( Hotaling et al, 2021 ; Saha et al, 2021 ), supporting that IscGN assembly is much higher quality compared with the previous assembly. Interestingly, the De et al (2023) annotation contained ∼7% more duplicated BUSCOs.…”

Diaci v3.0: Chromosome-level assembly,de novotranscriptome and manual annotation ofDiaphorina citri,insect vector of Huanglongbing

“…During the curation process, we removed 258 predicted genes that were not supported by expression data or represented false duplications. In addition to manual curation, we also generated functional annotation for OGSv3 gene models using the AgBase functional annotation pipeline [40] to assign experimentally validated GO terms, InterProScan domains and pathways based on sequence similarity.…”

“…During the curation process, we removed 258 predicted genes that were not supported by expression data or represented false duplications. In addition to manual curation, we also generated functional annotation for OGSv3 gene models using the AgBase functional annotation pipeline [40] to assign experimentally validated GO terms, InterProScan domains and pathways based on sequence similarity. 3 Legend: The Diaphorina citri Official Gene Set versions 1, v2 and v3 include automatically predicted gene models (columns "OGSv1", "OGSv2" and "OGSv3"), of which, over 1000 have been manually curated (column "Curated").…”