Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis

Jonathan Wright; Kendall Baker; Tom Barker; Leah Catchpole; Alex Durrant; Fiona Fraser; Karim Gharbi; Christian Harrison; Suzanne Henderson; Naomi Irish; Gemy Kaithakottil; Ilia J. Leitch; Jun Li; Sacha Lucchini; Paul Neve; Robyn Powell; Hannah Rees; David Swarbreck; Chris Watkins; Jonathan Wood; Seanna McTaggart; Anthony Hall; Dana MacGregor

doi:10.1038/s41597-024-04222-y

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis

Jonathan Wright, Kendall Baker, Tom Barker, Leah Catchpole, Alex Durrant, Fiona Fraser, Karim Gharbi, Christian Harrison, Suzanne Henderson, Naomi Irish, Gemy Kaithakottil, Ilia J. Leitch, Jun Li, Sacha Lucchini, Paul Neve, Robyn Powell, Hannah Rees, David Swarbreck, Chris Watkins, Jonathan WoodSeanna McTaggart, Anthony Hall, Dana MacGregor^*

^*Corresponding author for this work

Institute of Biological, Environmental & Rural Sciences (IBERS)

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

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Abstract

Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A. aequalis with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of A. aequalis is more similar to Hordeum vulgare rather than the more closely related Alopecurus myosuroides.

Original language	English
Article number	1368
Number of pages	15
Journal	Scientific data
Volume	11
Early online date	18 Dec 2024
DOIs	https://doi.org/10.1038/s41597-024-04222-y
Publication status	Published - 31 Dec 2024

Keywords

Chromosomes, Plant
Poaceae
Hordeum
Genome, Plant
Molecular Sequence Annotation

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41597-024-04222-y

ArticleFinal published version, 2.63 MBLicence: CC BY

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Wright, J., Baker, K., Barker, T., Catchpole, L., Durrant, A., Fraser, F., Gharbi, K., Harrison, C., Henderson, S., Irish, N., Kaithakottil, G., Leitch, I. J., Li, J., Lucchini, S., Neve, P., Powell, R., Rees, H., Swarbreck, D., Watkins, C., ... MacGregor, D. (2024). Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis. Scientific data, 11, Article 1368. https://doi.org/10.1038/s41597-024-04222-y

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title = "Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis",

abstract = "Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A. aequalis with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of A. aequalis is more similar to Hordeum vulgare rather than the more closely related Alopecurus myosuroides.",

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author = "Jonathan Wright and Kendall Baker and Tom Barker and Leah Catchpole and Alex Durrant and Fiona Fraser and Karim Gharbi and Christian Harrison and Suzanne Henderson and Naomi Irish and Gemy Kaithakottil and Leitch, {Ilia J.} and Jun Li and Sacha Lucchini and Paul Neve and Robyn Powell and Hannah Rees and David Swarbreck and Chris Watkins and Jonathan Wood and Seanna McTaggart and Anthony Hall and Dana MacGregor",

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doi = "10.1038/s41597-024-04222-y",

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Wright, J, Baker, K, Barker, T, Catchpole, L, Durrant, A, Fraser, F, Gharbi, K, Harrison, C, Henderson, S, Irish, N, Kaithakottil, G, Leitch, IJ, Li, J, Lucchini, S, Neve, P, Powell, R, Rees, H, Swarbreck, D, Watkins, C, Wood, J, McTaggart, S, Hall, A & MacGregor, D 2024, 'Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis', Scientific data, vol. 11, 1368. https://doi.org/10.1038/s41597-024-04222-y

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AU - Wright, Jonathan

AU - Baker, Kendall

AU - Barker, Tom

AU - Catchpole, Leah

AU - Durrant, Alex

AU - Fraser, Fiona

AU - Gharbi, Karim

AU - Harrison, Christian

AU - Henderson, Suzanne

AU - Irish, Naomi

AU - Kaithakottil, Gemy

AU - Leitch, Ilia J.

AU - Li, Jun

AU - Lucchini, Sacha

AU - Neve, Paul

AU - Powell, Robyn

AU - Rees, Hannah

AU - Swarbreck, David

AU - Watkins, Chris

AU - Wood, Jonathan

AU - McTaggart, Seanna

AU - Hall, Anthony

AU - MacGregor, Dana

PY - 2024/12/31

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AB - Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A. aequalis with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of A. aequalis is more similar to Hordeum vulgare rather than the more closely related Alopecurus myosuroides.

KW - Chromosomes, Plant

KW - Poaceae

KW - Hordeum

KW - Genome, Plant

KW - Molecular Sequence Annotation

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SN - 2052-4463

VL - 11

JO - Scientific data

JF - Scientific data

M1 - 1368

ER -

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis

Abstract

Keywords

UN SDGs

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