De Novo Whole-Genome Assembly of the Swede Midge (<i>Contarinia nasturtii</i>), a Specialist of Brassicaceae, Using Linked-Read Sequencing

Mori, Boyd A.; Coutu, Cathy; Chen, Yolanda H.; Campbell, Erin O.; Dupuis, Julian R.; Erlandson, Martin A.; Hegedus, Dwayne D.

doi:10.1093/gbe/evab036

Cited by 6 publications

(10 citation statements)

References 53 publications

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“…Here, we report the serendipitous discovery of a full-length cdtB sequence in the genome of the gall midge Contarinia nasturtii (Diptera: Cecidomyiidae) ( supplementary table S1 , Supplementary Material online ) ( Mori et al 2021 ), which is also called the “swede” midge. The Cecidomyiidae (Diptera: Nematocera) contains over 6,600 fly species with diverse life histories, behaviors, and host use patterns ( Yukawa and Rohfritsch 2005 ; Dorchin et al 2019 ; O’Connor et al 2019 ; Mori et al 2021 ). Many cecidomyiids are herbivorous and create destructive galls on crops ( Hall et al 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes

Verster

Tarnopol

Akalu

et al. 2021

Genome Biology and Evolution

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A growing body of evidence has underscored the role of horizontal gene transfer (HGT) in animal evolution. Previously, we discovered the horizontal transfer of the gene encoding the eukaryotic genotoxin cytolethal distending toxin B (cdtB) from the pea aphid Acyrthosiphon pisum secondary endosymbiont (APSE) phages to drosophilid and aphid nuclear genomes. Here, we report cdtB in the nuclear genome of the gall-forming ‘swede midge’ Contarinia nasturtii (Diptera: Cecidomyiidae) via HGT. We searched all available gall midge genome sequences for evidence of APSE-to-insect HGT events and found five toxin genes (aip56, cdtB, lysozyme, rhs, and sltxB) transferred horizontally to cecidomyiid nuclear genomes. Surprisingly, phylogenetic analyses of HGT candidates indicated APSE phages were often not the ancestral donor lineage of the toxin gene to cecidomyiids. We used a phylogenetic signal statistic to test a transfer-by-proximity hypothesis for animal HGT, which suggested that microbe-to-insect HGT was more likely between taxa that share environments than those from different environments. Many of the toxins we found in midge genomes target eukaryotic cells, and catalytic residues important for toxin function are conserved in insect copies. This class of horizontally transferred, eukaryotic cell-targeting genes is potentially important in insect adaptation.

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Section: Introductionmentioning

confidence: 99%

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes

Verster

Tarnopol

Akalu

et al. 2021

Genome Biology and Evolution

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Section: Resultsmentioning

confidence: 99%

“…We were unable to annotate tRNA Glu in R. maxima, despite multiple attempts in MITOS2. This is potentially due to the unusually truncated tRNA genes observed in other Cecidomyiid midges (Mori et al, 2021). We compared R. maxima mitochondrial gene order to the closest relative for which a complete mitogenome is available, Orseolia oryzae.…”

Section: Mitochondrial Structure and Phylogenymentioning

confidence: 99%

The Genome of the Soybean Gall Midge (Resseliella maxima)

Melotto¹,

Jones²,

Bosley³

et al. 2023

Preprint

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The cecidomyiid fly, soybean gall midge,Resseliella maximaGagn, is a recently discovered insect that feeds on soybean plants in the Midwest US.Resseliella maximalarvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble aR. maximareference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. TheR. maximagenome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated thatR. maximaassembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge,Orseolia oryzae(Wood-Mason). TheR. maximagenome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

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“…1 ) and was similar to C . nasturtii ( Mori et al 2021 ) and M. destructor ( Zhao et al 2015 ). For the S .…”

Section: Resultsmentioning

confidence: 99%

“…The TEs represented 21.09% of the whole S. mosellana genome. Similarly, TEs occupied approximately 16% of the M. destructor genome ( Ben Amara et al 2021 ) and 13.9% of the C. nasturtii genome ( Mori et al 2021 ). TE content varies greatly among the insects and differs even between species belonging the same order.…”

Section: Resultsmentioning

confidence: 99%

A chromosome-level genome assembly of the orange wheat blossom midge,Sitodiplosis mosellanaGéhin (Diptera: Cecidomyiidae) provides insights into the evolution of a detoxification system

Jin

Duan

et al. 2022

G3 Genes|Genomes|Genetics

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The orange wheat blossom midge Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae), an economically important pest, has caused serious yield losses in most wheat-growing areas worldwide in the past half-century. A high-quality chromosome-level genome for S. mosellana was assembled using PacBio long-read, Illumina short-read, and Hi-C sequencing technologies. The final genome assembly was 180.69 Mb, with contig and scaffold N50 sizes of 998.71 Kb and 44.56 Mb, respectively. Hi-C scaffolding reliably anchored four pseudochromosomes, accounting for 99.67% of the assembled genome. In total, 12,269 protein-coding genes were predicted, of which 91% were functionally annotated. Phylogenetic analysis indicated that S. mosellana and its close relative, the swede midge Contarinia nasturtii, diverged about 32.7 million years ago. The S. mosellana genome showed high chromosomal synteny with the genome of Drosophila melanogaster and Anopheles gambiae. The key gene families involved in the detoxification of plant secondary chemistry were analyzed. The high-quality S. mosellana genome data will provide an invaluable resource for research in a broad range of areas, including the biology, ecology, genetics, and evolution of midges, as well as insect–plant interactions and coevolution.

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De Novo Whole-Genome Assembly of the Swede Midge (Contarinia nasturtii), a Specialist of Brassicaceae, Using Linked-Read Sequencing

Cited by 6 publications

References 53 publications

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes

The Genome of the Soybean Gall Midge (Resseliella maxima)

A chromosome-level genome assembly of the orange wheat blossom midge,Sitodiplosis mosellanaGéhin (Diptera: Cecidomyiidae) provides insights into the evolution of a detoxification system

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