Molecular phylogeny and reticulate origins of the polyploid Bromus species from section Genea (Poaceae)

Abstract

The origin of polyploid Bromus species of section Genea was investigated using molecular data. This group of annual species native from the Old-World is composed of three diploids, two tetraploids, one hexaploid, and one octoploid. Molecular cloning, sequencing, and phylogenetic analyses were performed on several accessions per species. We used the low copy nuclear gene Waxy, repeated rDNA spacers ITS1 and ITS2 and chloroplast spacers trnT-trnL and trnL-trnF. Our analyses revealed four different lineages involved in the parentage of the polyploids and confirmed their reticulate origin. Three of these lineages are closely related to the diploid species B. sterilis, B. tectorum, and B. fasciculatus. The fourth lineage could not be related to any diploid according to the available data. Our data gave insights on the origin of all the polyploids of section Genea, and chloroplast data allowed us to identify the maternal lineages. The Waxy gene was the most informative regarding origin of the polyploids. The Waxy copies duplicated by polyploidy appear selectively maintained in the polyploid species. No sequence heterogeneity was encountered in the ITS region, where concerted evolution seems to have occurred toward either maternal or paternal repeats. These results provide new information about the origin and molecular evolution of these polyploids and will allow a more accurate taxonomic treatment of the concerned species, based on their evolutionary history.

Velvet bentgrass (Agrostis canina L.) is the likely ancestral diploid maternal parent of allotetraploid creeping bentgrass (Agrostis stolonifera L.)

“…Alternatively, in some Gossypium, Aegilops, Nicotiana and Bromus allotetraploid species concerted evolution has also occurred between homoeologous loci and has resulted in homogenization of the ITS regions to one of the parental types (Wendel et al 1995;Wang et al 2000;Kovarik et al 2004;Fortune et al 2008). Our data on allotetraploid creeping and The single most parsimonious phylogenetic tree recovered from an exhaustive search of the nuclear conserved orthologous set gene sequences.…”

Hybridization and polyploidy of an aquatic plant,Ruppia(Ruppiaceae), inferred from plastid and nuclear DNA phylogenies

“…The alternative scenario, though it seems less likely, is the possibility of gene losses following the duplication of the PHYB locus, which occurs singly in genomes of grasses ( Mathews and Sharrock, 1996 ), except in maize ( Childs et al, 1997 ;Sheehan et al, 2004 ). If this is the case, however, the resultant tree may be expected to have two clear lineages, as is the case of GB-SSI-1 and -2 in family Rosaceae ( Evans et al, 2000 ), Adh1 and Adh2 in Paeonia ( Sang et al, 2004 ), and WaxyA and WaxyB in Spartina ( Fortune et al, 2008 ). That is apparently not the case in the present study; the plastid and nuclear trees are otherwise mostly congruent.…”

Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae)

“…By individually sequencing these homoeologs in allopolyploids, using either specific primers, single-molecule (sm) polymerase chain reaction (PCR) (see Kraytsberg and Khrapko 2005), or in vivo cloning (reviewed in Brysting et al 2011), reticulate organism phylogenies can be untangled (e.g., Popp and Oxelman 2001; Sang 2002; Smedmark et al 2003; Howarth and Baum 2005; Popp et al 2005; Huber et al 2006; Brysting et al 2007; Popp and Oxelman 2007; Fortune et al 2008; Kim et al 2008; Mason-Gamer 2008; Mandáková et al 2010; Marcussen et al 2011; Brysting et al 2011). The raw data are a set of multilabeled trees (or MUL trees), i.e., gene trees that contain more than one sequence for some of their included species as a result of gene duplication (paralogy) and/or polyploidy (homoeology), and these are then transformed into a species network.…”