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Publication Type J
Authors de Carvalho, J. F., J. Poulain, C. Da Silva, P. Wincker, S. Michon-Coudouel, A. Dheilly, D. Naquin, J. Boutte, A. Salmon and M. Ainouche
Title Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)
Source Heredity
Author Keywords transcriptome assembly polyploidy invasive species Spartina chloridoideae allopolyploid tragopogon-miscellus gene-expression root transcriptome snp discovery comparative genomics apoplastic proteins cordgrass spartina hubbard poaceae anglica stress
Abstract Spartina species have a critical ecological role in salt marshes and represent an excellent system to investigate recurrent polyploid speciation. Using the 454 GS-FLX pyrosequencer, we assembled and annotated the first reference transcriptome (from roots and leaves) for two related hexaploid Spartina species that hybridize in Western Europe, the East American invasive Spartina alterniflora and the Euro-African S. maritima. The de novo read assembly generated 38 478 consensus sequences and 99% found an annotation using Poaceae databases, representing a total of 16 753 non-redundant genes. Spartina expressed sequence tags were mapped onto the Sorghum bicolor genome, where they were distributed among the subtelomeric arms of the 10 S. bicolor chromosomes, with high gene density correlation. Normalization of the complementary DNA library improved the number of annotated genes. Ecologically relevant genes were identified among GO biological function categories in salt and heavy metal stress response, C4 photosynthesis and in lignin and cellulose metabolism. Expression of some of these genes had been found to be altered by hybridization and genome duplication in a previous microarray-based study in Spartina. As these species are hexaploid, up to three duplicated homoeologs may be expected per locus. When analyzing sequence polymorphism at four different loci in S. maritima and S. alterniflora, we found up to four haplotypes per locus, suggesting the presence of two expressed homoeologous sequences with one or two allelic variants each. This reference transcriptome will allow analysis of specific Spartina genes of ecological or evolutionary interest, estimation of homoeologous gene expression variation using RNA-seq and further gene expression evolution analyses in natural populations. Heredity (2013) 110, 181-193; doi:10.1038/hdy.2012.76; published online 14 November 2012
Author Address [de Carvalho, J. Ferreira; Boutte, J.; Salmon, A.; Ainouche, M.] Univ Rennes 1, UMR CNRS Ecobio 6553, F-35042 Rennes, France. [Poulain, J.; Da Silva, C.; Wincker, P.] Genoscope, Evry, France. [Michon-Coudouel, S.; Dheilly, A.; Naquin, D.] Environm Genom Platform Biogenouest, Rennes, France. Ainouche, M (reprint author), Univ Rennes 1, UMR CNRS Ecobio 6553, Bat 14A Campus Sci Beaulieu, F-35042 Rennes, France. malika.ainouche@univ-rennes1.fr
ISSN 0018-067X
ISBN 0018-067X
Publication Date Feb
Year Published 2013
Volume 110
Issue 2
Beginning Page 181-193
Digital Object Identifier (DOI) 10.1038/hdy.2012.76
Unique Article Identifier WOS:000313836500012
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