The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

Childers, Anna K.; Geib, Scott M.; Sim, Sheina B.; Poelchau, Monica F.; Coates, Brad S.; Simmonds, Tyler J.; Scully, Erin D.; Smith, Timothy P. L.; Childers, Christopher P.; Corpuz, Renée L.; Hackett, Kevin J.; Scheffler, Brian E.

doi:10.3390/insects12070626

Cited by 43 publications

(37 citation statements)

References 57 publications

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“…Long reads, including those generated by third-generation sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT), have revolutionized genome assembly (Childers et al, 2021; Hotaling et al, 2021; Rhie et al, 2021). However, until recent advances (Hon et al, 2020; Wang et al, 2021), long-read sequencing technologies have had high error rates (5-15%), especially among indels (Watson & Warr, 2019).…”

Section: Mainmentioning

confidence: 99%

“polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies”

Chang

Stahlke

Chudalayandi

et al. 2022

Preprint

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Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) Continuous Long Reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.

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Section: Mainmentioning

confidence: 99%

“polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies”

Chang

Stahlke

Chudalayandi

et al. 2022

Preprint

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“…Many high-quality arthropod genomes are being generated, in particular by largescale genome projects, such as the USDA-Agricultural Research Service's Ag100Pest Initiative [13,14], and others under the Earth BioGenome Project umbrella [15]. These new genomes serve as community resources and provide the foundational information required to apply 'omics technologies to a more diverse set of species.…”

Section: Motivationmentioning

confidence: 99%

Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes

Saha

Cooksey

Childers

et al. 2021

Insects

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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.

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“…The more accurate quantification provided by the Diaci_v3 genome may reduce the need to validate transcriptomic changes using reverse transcription (RT)-PCR. We urge arthropod genome communities and funding bodies to continue to invest funds on genome improvement projects such as i5k [57] and Ag100Pest [58]. These investments can help save expenditures elsewhere by reanalyzing previously generated and yielding higher confidence in the results after using a quality genome backbone.…”

Section: Potential Implicationsmentioning

confidence: 99%

Quantification of new and archived Diaphorina citri transcriptome data using a chromosomal length D. citri genome assembly reveals the vector’s tissue-specific transcriptional response to citrus greening disease

Mann

Saha

Cicero

et al. 2021

Preprint

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Background Huanglongbing (HLB) is the most serious disease of citrus. HLB is caused by the obligate, intracellular bacterium Candidatus Liberibacter asiaticus (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid. Development of transmission blocking strategies to manage HLB relies on knowledge of CLas-D. citri interactions at the molecular level. Prior transcriptome analyses of CLas-infected and un-infected D. citri point to changes in psyllid biology due to CLas-infection. These studies relied on incomplete versions of the D. citri genome, lacked proper host plant controls, and/or were analyzed using different statistical approaches. Therefore, we used standardized experimental and computational approaches to identify differentially expressed genes in both CLas (+) and CLas (-) D. citri. The comparative analysis utilized the newest chromosomal length D. citri genome assembly Diaci_v3. In this work, we present a quantitative transcriptome analysis of excised heads, salivary glands, midguts and bacteriomes from CLas (+) and CLas (-) insects. Results Each organ had unique transcriptome profiles and responses to CLas infection. Though most psyllids were infected with CLas, CLas-derived transcripts were not detected in all organs. By analyzing the midgut dataset using both the Diaci_v1.1 and v3.0 D. citri genomes, we showed that improved genome assembly led to significant and quantifiable differences in RNAseq data interpretation. Conclusions Our results support the hypothesis that future transcriptome studies on circulative, vector-borne pathogens should be conducted at the tissue specific level using complete, chromosomal-length genome assemblies for the most accurate understanding of pathogen-induced changes in vector gene expression.

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The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

Cited by 43 publications

References 57 publications

“polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies”

“polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies”

Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes

Quantification of new and archived Diaphorina citri transcriptome data using a chromosomal length D. citri genome assembly reveals the vector’s tissue-specific transcriptional response to citrus greening disease

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