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Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis

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Abstract

Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91 % of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67 %). Non-LTR retrotransposons represent 0.75 %, DNA transposons 0.99 %, whereas small RNA, simple repeats and low-complexity sequences account for 1.38 % of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1 % of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6 % of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family.

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Acknowledgements

This work was supported by CNRS INEE and University of Rennes 1, the Partner University Funds and by the Genoscope (GENOSPART Project). The analyses benefited from the Genouest (Bioinformatics) Plateform facilities. J. Ferreira de Carvalho benefited from a Ph.D. Grant (ARED EVOSPART) from the Regional Council of Brittany.

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  1. UMR CNRS 6553 ECOBIO, OSUR, University of Rennes 1, Bât 14A Campus Scientifique de Beaulieu, 35042, Rennes Cedex, France

    J. Ferreira de Carvalho, H. Chelaifa, J. Boutte, A. Salmon & M. Ainouche

  2. Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France

    J. Poulain, A. Couloux & P. Wincker

  3. Centre National de Ressources génomiques végétales-INRA, 24 Chemin de Borde Rouge, CS 52627, 31326, Castanet Tolosan Cedex, France

    A. Bellec, J. Fourment & H. Bergès

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  1. J. Ferreira de Carvalho
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Ferreira de Carvalho, J., Chelaifa, H., Boutte, J. et al. Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis. Plant Mol Biol 83, 591–606 (2013). https://doi.org/10.1007/s11103-013-0111-7

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