The Challenges of Genomics in Polyploid Spartina Species: How to Deal with Hybrid Genomes and High Redundancy?

Hybridization and genome duplication (polyploidy) are particularly well-illustrated in genus Spartina, resulting in complex genomes which exhibit several duplication events, including those dating back to the Poaceae family. The most complex genome (namely the invasive allo-dodecaploid Spartina anglica) arose recently in Europe c.a. 150 years ago, by genome duplication of the homoploid hybrid S. x townsendii resulting from an interspecifc cross between the introduced S. alterniflora (2n=6x=62) and the European native S. maritima(2n=6x=60). This well described system represents one of the rare known examples of recent allopolyploid speciation that gave rise to a highly successful new species.

In the perspective of understanding the role of reticulate evolution and whole genome duplications in the phenotypic plasticity and adaptation of the recently formed Spartina anglica, the high ploidy levels of this species (dodecaploid) and its parents (hexaploids) makes genetic and genomic studies particularly challenging. We are using massive parallel sequencing technologies to explore the genomes and transcriptomes of these species, and we have developed bioinformatic approaches and tools for detecting the different putative orthologous copies originating from the parents (duplicated homoeologs) in S. anglica.

These datasets allowed us (1) to assemble reference transcriptomes for the five species (2 hexaploid parents, 2 independently formed F1 hybrids and the allododecaploid); (2) to assemble genomic contigs for the European hexaploid S. maritima and estimate the repetitive fraction of its genome; and (3) to detect the duplicated copies within parental hexaploids and to assign their parental origin in the homoploid hybrids and allododecaploid.