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Plant Systematics and Evolution

, Volume 303, Issue 8, pp 1061–1079 | Cite as

Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)

  • Julie Ferreira de Carvalho
  • Julien Boutte
  • Pierre Bourdaud
  • Houda Chelaifa
  • Kader Ainouche
  • Armel Salmon
  • Malika Ainouche
Original Article
Part of the following topical collections:
  1. Polyploidy in Shallow and Deep Evolutionary Times

Abstract

Allopolyploidy is a peculiar process entailing the cohabitation of two (or more) divergent genomes. Consequences on plant genomes are varied and can utlimately alter gene expression and regulatory interactions. Most studies have explored polyploid expression evolution in experimental controlled conditions. Here, we analyzed global gene expression variation in natural populations of the Spartina polyploid complex including hexaploid parental species (S. maritima and S. alterniflora), two F1 hybrids (S. × townsendii and S. × neyrautii) and the allododecaploid S. anglica. In situ sampling and quantitative PCR were performed for comparing global expression of candidate genes involved in responses to abiotic stresses, lignin and cellulose metabolisms between five Spartina taxa. Illumina sequencing datasets and dedicated bioinformatic pipelines were employed to explore sequence heterogeneity in these highly duplicated genomes. Levels of gene expression were significantly higher in S. alterniflora (compared to the other hexaploid parent S. maritima) for seven of the analyzed genes. Effects of both hybridization and polyploidization are detected and consistent with previous global transcriptome analyses performed on Spartina plants grown in controlled conditions. Duplicated copies present in the hybrids and the allododecaploid were successfully assigned to either one of the parental genomes. Phylogenetic analyses identified for each of the parental hexaploid species, the presence of two distinct clades including two or more expressed copies. We provide here a comprehensive gene expression study based on individuals sampled in their natural habitat and detected the superimposed effect of environmental heterogeneity, hybridization and allopolyploidy.

Keywords

Allopolyploidy Gene expression Haplotype detection Hybridization Quantitative PCR Spartina 

Notes

Acknowledgements

This work was supported by the International Associated Laboratory “Ecological Genomics of Polyploidy” supported by CNRS (INEE, UMR CNRS 6553 Ecobio), University of Rennes 1, Iowa State University (Ames, USA), and the Partner University Funds (to M. A., A. S.). The analyses benefited from the Molecular Ecology (UMR CNRS 6553 Ecobio) and Genouest (Bioinformatics) facilities. Authors J. Ferreira de Carvalho benefited from a PhD grant (ARED EVOSPART) from the Regional Council of Brittany and J. Boutte from a PhD scholarship from the University of Rennes 1. We thank two anonymous reviewers for helpful comments and suggestions on the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

This research does not involve human participants or animals.

Supplementary material

606_2017_1446_MOESM1_ESM.pdf (108 kb)
Online Resource 1 Primer sequences of the 13 target genes and three housekeeping genes used for quantitative PCR and cloning of the Metal tolerance protein gene (PDF 107 kb)
606_2017_1446_MOESM2_ESM.pdf (102 kb)
Online Resource 2 Functions, annotations and number of loci in Sorghum bicolor for the candidate genes studied in Spartina natural populations (PDF 102 kb)
606_2017_1446_MOESM3_ESM.fasta (5 kb)
Online Resource 3 Alignment matrix of nucleotide sequences cloned and sequenced in S. maritima from the transcript coding a Metal tolerance protein (FASTA 4 kb)
606_2017_1446_MOESM4_ESM.fasta (4 kb)
Online Resource 4 Alignment matrix of haplotype sequences found in S. alterniflora, S. maritima and S. x townsendii for the Transcriptional adapter ADA2 gene (FASTA 3 kb)
606_2017_1446_MOESM5_ESM.fasta (11 kb)
Online Resource 5 Alignment matrix of haplotype sequences found in S. alterniflora, S. maritima and orthologous sequences in Setaria italica, Zea mays and Sorghum bicolor for the hexokinase 5 gene (FASTA 10 kb)

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Copyright information

© Springer-Verlag GmbH Austria 2017

Authors and Affiliations

  • Julie Ferreira de Carvalho
    • 1
  • Julien Boutte
    • 2
  • Pierre Bourdaud
    • 2
  • Houda Chelaifa
    • 2
  • Kader Ainouche
    • 2
  • Armel Salmon
    • 2
  • Malika Ainouche
    • 2
  1. 1.Department of Terrestrial EcologyNetherland Institute of Ecology NIOO-KNAWWageningenThe Netherlands
  2. 2.UMR CNRS 6553 ECOBIO, OSURUniversity of Rennes 1Rennes CedexFrance

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