The University of Southampton
University of Southampton Institutional Repository

Characterization of the poplar pan-genome by genome-wide identification of structural variation

Characterization of the poplar pan-genome by genome-wide identification of structural variation
Characterization of the poplar pan-genome by genome-wide identification of structural variation
Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.

With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2?Mb and 62.9?Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.

Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.

Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.
2706-2719
Pinosio, S.
e76abb69-1698-4e04-8894-1dda3d5bc005
Giacomello, S.
5f91fdc6-a7d7-48cc-aa93-97617861de74
Faivre-Rampant, P.
5cd7c2cf-3b0b-4e7c-8257-4a793bf05322
Taylor, G.
f3851db9-d37c-4c36-8663-e5c2cb03e171
Jorge, V.
d5e6a90f-d319-4243-a026-2ae9411cdb32
Le Paslier, M.C.
00473cbb-4c20-4777-8ae4-81544b0b6829
Zaina, G.
97af61de-3068-4e93-a790-10cfb1156c78
Bastien, C.
224ff58a-cec9-4507-9882-9f8fe0ee5c24
Cattonaro, F.
38a4acf1-aded-4413-9c09-35bb8d7f0e8b
Marroni, F.
d50e3f71-6411-461c-bf64-66a597e005f9
Morgante, M.
9bc7fa99-3c2b-4071-bcb5-1cee212d0ecf
Pinosio, S.
e76abb69-1698-4e04-8894-1dda3d5bc005
Giacomello, S.
5f91fdc6-a7d7-48cc-aa93-97617861de74
Faivre-Rampant, P.
5cd7c2cf-3b0b-4e7c-8257-4a793bf05322
Taylor, G.
f3851db9-d37c-4c36-8663-e5c2cb03e171
Jorge, V.
d5e6a90f-d319-4243-a026-2ae9411cdb32
Le Paslier, M.C.
00473cbb-4c20-4777-8ae4-81544b0b6829
Zaina, G.
97af61de-3068-4e93-a790-10cfb1156c78
Bastien, C.
224ff58a-cec9-4507-9882-9f8fe0ee5c24
Cattonaro, F.
38a4acf1-aded-4413-9c09-35bb8d7f0e8b
Marroni, F.
d50e3f71-6411-461c-bf64-66a597e005f9
Morgante, M.
9bc7fa99-3c2b-4071-bcb5-1cee212d0ecf

Pinosio, S., Giacomello, S., Faivre-Rampant, P., Taylor, G., Jorge, V., Le Paslier, M.C., Zaina, G., Bastien, C., Cattonaro, F., Marroni, F. and Morgante, M. (2016) Characterization of the poplar pan-genome by genome-wide identification of structural variation. Molecular Biology and Evolution, 33 (10), 2706-2719. (doi:10.1093/molbev/msw161).

Record type: Article

Abstract

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.

With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2?Mb and 62.9?Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.

Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.

Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.

Text
Characterization of the poplar pan-genome by genome-wide identification of structural variation.pdf - Accepted Manuscript
Available under License Creative Commons Attribution.
Download (783kB)
Text
Mol Biol Evol-2016-Pinosio-2706-19.pdf - Version of Record
Available under License Creative Commons Attribution.
Download (632kB)

More information

Accepted/In Press date: 30 July 2016
e-pub ahead of print date: 7 August 2016
Published date: October 2016
Organisations: Centre for Biological Sciences

Identifiers

Local EPrints ID: 404632
URI: http://eprints.soton.ac.uk/id/eprint/404632
PURE UUID: b1879080-fb75-49f8-85ef-cac9e5b7c98c
ORCID for G. Taylor: ORCID iD orcid.org/0000-0001-8470-6390

Catalogue record

Date deposited: 13 Jan 2017 15:03
Last modified: 17 Dec 2019 01:54

Export record

Altmetrics

Contributors

Author: S. Pinosio
Author: S. Giacomello
Author: P. Faivre-Rampant
Author: G. Taylor ORCID iD
Author: V. Jorge
Author: M.C. Le Paslier
Author: G. Zaina
Author: C. Bastien
Author: F. Cattonaro
Author: F. Marroni
Author: M. Morgante

University divisions

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×