Using BUSCO to Assess Insect Genomic Resources

Waterhouse, Robert M.; Seppey, Mathieu; Simão, Felipe A.; Zdobnov, Evgeny M.

doi:10.1007/978-1-4939-8775-7_6

Cited by 31 publications

(27 citation statements)

References 28 publications

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“…A corresponding protein set was created using TransDecoder [42] with the default parameters. In order to obtain a unigene set (one amino acid sequence per gene), isoforms were grouped at the gene (g) level, because grouping at the contig (c) level reduced the number of conserved, single-copy genes measured by BUSCO ( [43] ; Figure S2; Table S10). With this protein set, CD-HIT [44] was used in order to remove peptides that are entirely contained within larger proteins with default word size and sequence identity threshold of 1.0.…”

Section: Transcriptome Processing and Annotationmentioning

confidence: 99%

A transcriptomic and proteomic atlas of expression in the Nezara viridula (Heteroptera: Pentatomidae) midgut suggests the compartmentalization of xenobiotic metabolism and nutrient digestion

Denecke

Ioannidis

Buer

et al. 2019

Preprint

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Background Stink bugs are an emerging threat to crop security in many parts of the globe, but there are few genetic resources available to study their physiology at a molecular level. This is especially true for tissues such as the midgut, which forms the barrier between ingested material and the inside of the body. Results Here, we focus on the midgut of the southern green stink bug Nezara viridula and use both transcriptomic and proteomic approaches to create an atlas of expression along the four compartments of the anterior-posterior axis. Estimates of the transcriptome completeness were high, which led us to compare our predicted gene set to other related stink bugs and Hemiptera, finding a high number of species-specific genes in N. viridula. To understand midgut function, gene ontology and gene family enrichment analyses were performed for the most highly expressed and specific genes in each midgut compartment. These data suggested a role for the anterior midgut (regions M1-M3) in digestion and xenobiotic metabolism, while the most posterior compartment (M4) was enriched in transmembrane proteins. A more detailed characterization of these findings was undertaken by identifying individual members of the cytochrome P450 superfamily and nutrient transporters thought to absorb amino acids or sugars. Conclusions These findings represent an initial step to understand the compartmentalization and physiology of the N. viridula midgut at a genetic level. Future studies will be able to build on this work and explore the molecular physiology of the stink bug midgut.

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Section: Transcriptome Processing and Annotationmentioning

confidence: 99%

A transcriptomic and proteomic atlas of expression in the Nezara viridula (Heteroptera: Pentatomidae) midgut suggests the compartmentalization of xenobiotic metabolism and nutrient digestion

Denecke

Ioannidis

Buer

et al. 2019

Preprint

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“…Candidates identified in either the D. melanogaster or H. sapiens search were considered as candidate SLCs for that species. As the proteomes of some nonmodel arthropods may contain many fragmented genes, we estimated the completeness of each proteome using BUSCO ( Waterhouse et al. 2019 ).…”

Section: Methodsmentioning

confidence: 99%

The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods

Denecke

Driva

Lương

et al. 2020

Genome Biology and Evolution

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The Solute Carrier (SLC) transporter superfamily comprises an ancient and ubiquitous group of proteins capable of translocating a range of nutrients, endogenous molecules, and xenobiotics. Although the group has been the subject of intense investigation and identification in both bacteria and mammals, its systematic investigation in arthropods has not yet been undertaken. Here, we present a genome-wide identification of all 66 SLC families in 174 arthropod species. A pipeline (SLC_id) was constructed to identify and group SLCs using a combination of hidden Markov model and BLAST searches followed by filtering based on polypeptide length and the number of transmembrane domains. Comparative analysis of the number of transporters in each family across diverse arthropod lineages was accomplished using one-way analysis of variance (ANOVA) and the Computational Analysis of Family Expansion (CAFE). These results suggested that many SLC families have undergone expansions or contractions in particular evolutionary lineages. Notably, the sugar transporting SLC2 family was significantly larger in insects compared to arachnids. This difference may have been complemented by a rapid expansion of the SLC60 family in arachnids which also acts on dietary sugars. Furthermore, the SLC33 family underwent a recent and drastic expansion in aphids, although the biological relevance of this expansion was not possible to infer. Information on specific SLC transporter families across arthropod species can be accessed through an R shiny web application at http://chrysalida.imbb.forth.gr:3838/Arthropod_SLC_Database/. The present study greatly facilitates further study of the understudied and diverse group of SLC transporters in arthropods.

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“…The AalbS3 assembly more than doubled the content of transposable elements and other repetitive sequences (Table S2, File S2). The QV score (Berlin et al 2015, Solarese et al 2018 Zdobnov, 2019, Waterhouse et al, 2019) and scored a 99.0% with 98.2% of genes represented in this genome as complete and single copy and 0.8% as complete and duplicated (Table 1 and Table S3). By mapping Illumina reads from each of the parents to the AalbS3 assembly, the levels of heterozygosity were also calculated for each chromosome, which range from 0.0004 to 0.0011 (Table S4, Figure S1).…”

Section: Assembly Of the Anopheles Albimanus Genomementioning

confidence: 99%

The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere

Compton

Liang

Chen

et al. 2020

G3 Genes|Genomes|Genetics

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Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50=13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step towards the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp telomeric repeat unit (TRU) and are confirmed by analysing the termini of long reads and through both chromosomal in situ hybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step towards resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species.

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Using BUSCO to Assess Insect Genomic Resources

Cited by 31 publications

References 28 publications

A transcriptomic and proteomic atlas of expression in the Nezara viridula (Heteroptera: Pentatomidae) midgut suggests the compartmentalization of xenobiotic metabolism and nutrient digestion

A transcriptomic and proteomic atlas of expression in the Nezara viridula (Heteroptera: Pentatomidae) midgut suggests the compartmentalization of xenobiotic metabolism and nutrient digestion

The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods

The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere

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