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Authors de Carvalho, JF; Boutte, J; Bourdaud, P; Chelaifa, H; Ainouche, K; Salmon, A; Ainouche, M
Author Full Name de Carvalho, Julie Ferreira; Boutte, Julien; Bourdaud, Pierre; Chelaifa, Houda; Ainouche, Kader; Salmon, Armel; Ainouche, Malika
Title Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)
Source PLANT SYSTEMATICS AND EVOLUTION
Language English
Document Type Article
Author Keywords Allopolyploidy; Gene expression; Haplotype detection; Hybridization; Quantitative PCR; Spartina
Keywords Plus TRAGOPOGON-MISCELLUS ASTERACEAE; ALLOPOLYPLOID COFFEA-ARABICA; ENCODING CYTOCHROME-C; SALT STRESS; HOMOEOLOGOUS RECOMBINATION; MARITIMA POACEAE; LEVEL DOMINANCE; GENOMIC CHANGES; BRASSICA-NAPUS; X-TOWNSENDII
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. x townsendii and S. x 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.
Author Address [de Carvalho, Julie Ferreira] Netherland Inst Ecol NIOO KNAW, Dept Terr Ecol, Droevendaalsesteeg 10, NL-6708 PB Wageningen, Netherlands; [Boutte, Julien; Bourdaud, Pierre; Chelaifa, Houda; Ainouche, Kader; Salmon, Armel; Ainouche, Malika] Univ Rennes 1, OSUR, UMR CNRS ECOBIO 6553, Bat 14A Campus Sci Beaulieu, F-35042 Rennes, France
Reprint Address Ainouche, M (corresponding author), Univ Rennes 1, OSUR, UMR CNRS ECOBIO 6553, Bat 14A Campus Sci Beaulieu, F-35042 Rennes, France.
E-mail Address malika.ainouche@univ-rennes1.fr
ResearcherID Number de Carvalho, Julie Ferreira/ABD-8098-2020; KNAW, NIOO-KNAW/A-4320-2012
ORCID Number de Carvalho, Julie Ferreira/0000-0001-6200-3344; KNAW, NIOO-KNAW/0000-0002-3835-159X
Funding Agency and Grant Number International Associated Laboratory
Funding Text This work was supported by the International Associated Laboratory
Times Cited 6
Total Times Cited Count (WoS, BCI, and CSCD) 6
Publisher SPRINGER WIEN
Publisher City WIEN
Publisher Address SACHSENPLATZ 4-6, PO BOX 89, A-1201 WIEN, AUSTRIA
ISSN 0378-2697
29-Character Source Abbreviation PLANT SYST EVOL
ISO Source Abbreviation Plant Syst. Evol.
Publication Date OCT
Year Published 2017
Volume 303
Issue 8
Beginning Page 1061
Ending Page 1079
Digital Object Identifier (DOI) 10.1007/s00606-017-1446-3
Page Count 19
Web of Science Category Plant Sciences; Evolutionary Biology
Subject Category Plant Sciences; Evolutionary Biology
Document Delivery Number FJ7YL
Unique Article Identifier WOS:000412976200007
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