Genome sequence of the English grain aphid,<i>Sitobion avenae</i>and its endosymbiont<i>Buchnera aphidicola</i>

Byrne, Stephen; Schughart, Maximilian; Carolan, James C.; Gaffney, Michael; Thorpe, Peter; Malloch, G.; Wilkinson, T. L.; Namara, Louise Mc

doi:10.1093/g3journal/jkab418

Cited by 7 publications

(6 citation statements)

References 56 publications

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“…(2019) to the annotated gene models increased from 78% in Simis_v1 to 83% in Simis_v2 ( Supplementary Table 2 ). Taken together, our highly complete genome assemblies and annotations of S. miscanthi, S. avenae and M. dirhodum provide a solid foundation to study grain aphid biology and compliment two other contig-level long-read genome assemblies of S. avenae (clone SA3 [Byrne et al . 2022] and SaG1 [Villarroel et al .…”

Section: Resultsmentioning

confidence: 63%

Hybridisation has shaped a recent radiation of grass-feeding aphids

Mathers

Wouters

Mugford

et al. 2022

Preprint

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Aphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, clonal aphids give birth to live apterous or winged young that are already pregnant. Together, these qualities enable rapid population growth and have facilitated the colonisation of crops globally. In several cases so-called "super clones" have come to dominate agricultural systems. However, the extent to which the sexual stage of the aphid life cycle has shaped global pest populations has remained largely unclear, as have the origins of successful lineages. Here, we used chromosome-scale genome assemblies to disentangle the evolution of two of the most significant global pests of cereals - the English (Sitobion avenae) and Indian (Sitobion miscanthi) grain aphids. We found that genome-wide divergence between S. avenae and S. miscanthi is low and that S. avenae sensu stricto is part of a larger cryptic species complex that includes multiple diverged S. miscanthi lineages. Moreover, comparison of haplotype-resolved assemblies reveals that the S. miscanthi isolate used for genome sequencing is likely a hybrid, with one of its diploid genome copies being closely related to S. avenae (~0.5% divergence) and the second being substantially more divergent (> 1%). Analyses of genotyping-by-sequencing (GBS) data of grain aphids from the UK and China revealed that S. avenae and S. miscanthi are part of a species complex with many highly differentiated lineages that predate the origins of agriculture. The complex consists of hybrid lineages that display a tangled history of hybridisation and genetic introgression. These data demonstrate that hybridisation has substantially contributed to grain aphid diversity, and hence, to the evolutionary potential of this important pest species.

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Section: Resultsmentioning

confidence: 63%

Hybridisation has shaped a recent radiation of grass-feeding aphids

Mathers

Wouters

Mugford

et al. 2022

Preprint

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“…We identified 484 single-copy genes using OrthoFinder v2.5.4 32 based on protein sequences from 15 aphid genomes, including 7 Macrosiphini species ( M. cerasi 33 , M. perisicae 5 , Sitobion avenae 34 , Metopolophium dirhodum 35 , A. pisum 9 , B. brassicae , and D. noxia 7 ), 5 Aphidini species ( Rhopalosiphum maidis 36 , Rhopalosiphum padi 33 , Aphis fabae 33 , A. gossypii 6 , Aphis glycines 33 ), one species from each subfamily of Chaitophorinae ( Sipha flava 37 ), Lachnini ( Cinara cedri 38 ), Phylloxeridae ( Daktulosphaira vitifoliae 39 ). The protein sequences of the single-copy genes were concatenated and aligned automatically by OrthoFinder and generated a multiple sequence alignment file, which was used for phylogenetic analysis.…”

Section: Methodsmentioning

confidence: 99%

A chromosome-level genome assembly of the cabbage aphidBrevicoryne brassicae

Wu,

Li,

Lin

et al. 2024

Preprint

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The cabbage aphid,Brevicoryne brassicae, is a major pest on Brassicaceae plants, and causes significant yield losses annually. However, lacking genomic resources hinders the progress in understanding this pest at the level of molecular biology. Here, a high-quality, chromosomal-level genome was assembled forB. brassicaebased on PacBio HIFI long-read sequencing and Hi-C data. The final assembled size was 429.99 Mb with a scaffold N50 of 93.31 Mb. Importantly, 96.2% of the assembled sequences were anchored to eight chromosomes. The genome recovered 98.50% of BUSCO genes and 92.30% of CEGMA genes, supporting the high level of completeness. By combining high-coverage transcriptome data, a total of 22,671 protein-coding genes and 3,594 lncRNA genes were annotated. Preliminary comparative genomic analyses were focused on genes related to host colonisation, such as chemosensory- and detoxification-related genes, as well as those encoding putative protein effectors and cross-kingdom lncRNA Ya. In summary, our study presents a contiguous and complete genome forB. brassicaethat will benefit our understanding of the biology of it and other aphids.

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“…The genome, CDS, protein, and genome annotation file of 18 aphid species, except S. avenae, were obtained from the InsectBase 2.0 (http://v2.insect-genome.com/ (accessed on 15 November 2022)) as the local database. The genome, CDS, protein, and genome annotation file of S. avenae were obtained from the figshare website (https://figshare.com/ (accessed on 13 November 2022)) [58] (Table S10). Then, using the HMMER 3.0 tool with e-value < 1 × 10 −10 , the CYP450 typical domain (PF00067) was retrieved from the PFAM database (http://pfam-legacy.xfam.org/ (accessed on 16 November 2022)) and used as the query to search against the protein database of every species of aphid.…”

Section: Genome-wide Identification Of Cyp450 Genes In 19 Aphid Speciesmentioning

confidence: 99%

Genome-Wide Comparative Analysis of the Cytochrome P450 Monooxygenase Family in 19 Aphid Species and Their Expression Analysis in 4 Cereal Crop Aphids

Wang,

Hao,

Wang

et al. 2024

IJMS

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Cytochrome P450 monooxygenases (CYP450s) play a variety of physiological roles, including pesticide resistance, plant allelochemical detoxification, and hormone metabolism catalysis. However, limited information is available on the classification and expression profiles of the CYP450 gene family in aphid species. This is the first study to identify the cytochrome P450 gene family in 19 aphid species at the whole genome level. A total of 1100 CYP450 genes were identified in 19 aphid species. Three hundred CYP450 genes belonged to six cereal crop aphid species, which were further classified into four subfamilies according to the phylogenetic relationship. The conserved motifs, exon-intron structures, and genomic organization of the same subfamilies were similar. Predictions of subcellular localization revealed that the endoplasmic reticulum harbored the majority of CYP450 proteins. In Sitobion avenae and Rhopalosiphum maidis, the increase in the CYP450 gene was primarily caused by segmental duplication events. However, only tandem duplication occurred in the CYP450 gene family of Diuraphis noxia, Rhopalosiphum padi, Schizaphis graminum, and Sitobion miscanthi. Synteny analysis found three continuous colinear CYP450 gene pairs among six cereal crop aphid species. Furthermore, we obtained the expression profiles of four cereal crop aphids, including R. padi, D. noxia, S. graminum, and S. avenae. Differential expression analysis provided growth stage specificity genes, tissue specificity genes, organ specificity genes and some detoxification metabolic genes among these four cereal crop aphids. Meanwhile, their expression patterns were showed. The related functions and pathways of CYP450s were revealed by GO and KEGG enrichment analysis. Above all, we picked the differentially expressed CYP450 genes from all of the differentially expressed genes (DEGs). These differentially expressed CYP450 genes provided some new potential candidates for aphid control and management. This work establishes the foundation for further investigations into the regulatory functions of the CYP450 gene family in aphid species and beyond.

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Genome sequence of the English grain aphid,Sitobion avenaeand its endosymbiontBuchnera aphidicola

Cited by 7 publications

References 56 publications

Hybridisation has shaped a recent radiation of grass-feeding aphids

Hybridisation has shaped a recent radiation of grass-feeding aphids

A chromosome-level genome assembly of the cabbage aphidBrevicoryne brassicae

Genome-Wide Comparative Analysis of the Cytochrome P450 Monooxygenase Family in 19 Aphid Species and Their Expression Analysis in 4 Cereal Crop Aphids

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