Polyphyly, gene-duplication and extensive allopolyploidy framed the evolution of the ephemeral Vulpia grasses and other fine-leaved Loliinae (Poaceae)

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal

“…2 and S2) reflects a close relationship of this Loretia-type species with the Festuca rubra group (Aulaxyper). This supports a recent LCNG GBSSI-based study (Díaz-Pérez et al, 2014), which recovered strong phylogenetic relationships between members of the Loretia clade and different Aulaxyper taxa, supporting recent gene flow between the two clades; this favored the occurrence of intergeneric x Festulpia hybrids and introgressed plants. The two V. alopecuros Aulaxyper-type b-amylase copies likely represent a fraction of a semi-paralogous sequence, even though the orthologous sequences of V. alopecuros, which should be nested within the Loretia clade, have not been found.…”

“…Amplified b-amylase sequences from16 Brachypodium and Loliinae samples were cloned to check for potential paralogous and heterologous copies: Brachypodium distachyon (9 clones), Festuca abyssinica (2), F. altaica (7), F. arundinacea (7), F. capillifolia (9), F. elegans (7), F. fenas (7), F. hystrix (5), F. panciciana (2), F. paniculata (10), F. rubra (5), F. scabra (5), F. scariosa (8), F. simensis (7), Micropyropsis tuberosa (2), Vulpia alopecuros (5). These taxa previously showed paralogous copies in other LCNG in Loliinae and close allies [GBSSI (Granule-Bound-Starch-Synthase I); Díaz-Pérez et al, 2014] and Brachypodium [CAL (Calmodulin-binding protein), DGAT (Diacyl Glycerol Acyl Transferase), GI (Gigantea); Catalán et al, 2012]. The origins of the plants studied, the locations of voucher specimens, and the GenBank sequence accession numbers are listed in Table S1.…”

“…For these analyses we used a matrix with only exon positions. This matrix included all Poaceae sequences sampled (142 grass species); however, to discard spurious variation from Polymerase Chain Reaction (PCR) artifacts, the cloned sequences from 16 species were collapsed into a single consensus sequence (or type) from closely related sequences following Díaz-Pérez et al (2014). All intraspecific sequences with a p-distance lower than 0.01 (base differences per site) were collapsed into a single type using the program BioEdit v7.2.5 (Hall, 1999) (Table 1, b-amylase data set 2; 146 sequences, 588 positions, exons 2-5).…”

“…Highly similar clones were grouped into consensus types according to the p-distance (<0.01) criterion (Díaz-Pérez et al, 2014). Clones from twelve out of 16 species were grouped into a single type, suggesting that they represent the same orthologous copy (Fig.…”

“…However, distinguishing paralogous copies which diverged after a duplication event from orthologs related by descent can be a challenge (Fu and Dooner, 2002;Small et al, 2004). Several publications have demonstrated paralogous copies in LCNGs such as the b-amylase (Kreis et al, 1987;Wang et al, 1997;Li et al, 2002;Mason-Gamer, 2005) and GBSSI (Díaz-Pérez et al, 2014) genes in the grasses. In our study, a single case of b-amylase semi-paralogy has been found in the fine-leaved Loliinae Vulpia alopecuros.…”