Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola

Stephen Byrne; Maximilian Schughart; James C Carolan; Michael Gaffney; Peter J Thorpe; Gaynor Malloch; Tom Wilkinson; Louise McNamara

doi:10.1093/g3journal/jkab418

Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola

Stephen Byrne^*, Maximilian Schughart, James C Carolan, Michael Gaffney, Peter J Thorpe, Gaynor Malloch, Tom Wilkinson, Louise McNamara

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of Barley Yellow Dwarf Virus (BYDV) leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein-coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.

Original language	English
Article number	jkab418
Number of pages	8
Journal	G3: Genes, Genomes, Genetics
Volume	12
Issue number	3
Early online date	8 Dec 2021
DOIs	https://doi.org/10.1093/g3journal/jkab418
Publication status	Published - 1 Mar 2022

Keywords

Aphid
PacBio HiFi
Sitobion avenae
Genome

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10.1093/g3journal/jkab418Licence: CC BY

Byrne-2021-Genome-sequence-of-G3-jkab418-CCBY
Copyright VC The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 610 KBLicence: CC BY

ISSF Funding Mar2021 - P Thorpe: ISSF Funding March 2021
Thorpe, P. J. (PI)
The Wellcome Trust
1/04/21 → 31/03/22
Project: Standard

Cite this

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title = "Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola",

abstract = "The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of Barley Yellow Dwarf Virus (BYDV) leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein-coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.",

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AU - Gaffney, Michael

AU - Thorpe, Peter J

AU - Malloch, Gaynor

AU - Wilkinson, Tom

AU - McNamara, Louise

N1 - Funding: Teagasc grant-in-aid. MS. is supported by a Teagasc Walsh Scholarship. PT: bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit (AMD3BIOINF), funded by Wellcome Trust ISSF awards 105621/Z/14/Z and XISF6P.

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N2 - The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of Barley Yellow Dwarf Virus (BYDV) leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein-coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.

AB - The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of Barley Yellow Dwarf Virus (BYDV) leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein-coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.

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Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola

Abstract

Keywords

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Projects

ISSF Funding Mar2021 - P Thorpe: ISSF Funding March 2021

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