Molecular phylogeny of the genus Hordeum using three chloroplast DNA sequences

Abstract

The genus Hordeum consists of three cytotypes (2x, 4x, and 6x). Its reproductive isolation has been incomplete between closely related species and hence the genetic relationship is reticulate and complex. We used 32 taxa of Hordeum and three chloroplast DNA sequences, matK, atpB-rbcL, and trnL-trnF in the current study. Molecular phylogenetic analysis based on sequence data of the three chloroplast DNA regions clearly demonstrated genetic relationships among taxa and origin of polypoids. The formation of H. secalinum likely involved hybridization between Hordeum marinum subsp. marinum and a Eurasian diploid possessing the H genome. The formation of hexaploid Hordeum brachyantherum involved hybridization between tetraploid H. brachyantherum and diploid H. marinum subsp. gussoneanum. The formation of three tetraploids, H. brachyantherum, Hordeum jubatum, and Hordeum guatemalense, probably involved hybridization between H. brachyantherum subsp. californicum and an altered H genome diploid. The formation of Hordeum arizonicum involved the two taxa Hordeum pusillum and H. jubatum.

Progress in phylogenetic analysis and a new infrageneric classification of the barley genus Hordeum (Poaceae: Triticeae)

“…Analyses of loci of the chloroplast genome consistently showed taxa of the sea barley complex (H. marinum and H. gussoneanum) polyphyletic (Doebley et al 1992, Provan et al 1999, Nishikawa et al 2002, Petersen and Seberg 2003, Jakob and Blattner 2006, which contradicts traditional taxonomy and results derived from nuclear markers (Komatsuda et al 2001, Blattner 2004, Petersen and Seberg 2004, Jakob et al 2007. Moreover, the affiliation of diploid species from Central Asia were partly unclear, being either monophyletic (Doebley et al 1992, Nishikawa et al 2002 or being polyphyletic and grouping with species from the New World and from the Mediterranean (Petersen and Seberg 2003).…”

“…Particularly DNA sequencing resulted in fast advances in molecular phylogenetics of the genus during the last decade (Komatsuda et al 1999, Nishikawa et al 2002, Petersen and Seberg 2003, Blattner 2004, 2006, Jakob and Blattner 2006, Kakeda et al 2009, Sun et al 2009). …”

“…Taking into account the importance of barley, surprisingly few phylogenetic studies of Hordeum with a complete or at least representative taxon sample were conducted. Studies with higher species numbers or including at least most diploid species have been published by Jørgensen (1986), Doebley et al (1992), Komatsuda et al (1999), Provan et al (1999), Nishikawa et al (2002), Seberg (2003, 2004), Blattner (2004Blattner ( , 2006, Jakob and Blattner (2006), Kakeda et al (2009), andSun et al (2009). The results were partly contradictory, due to (i) inconsistencies between chloroplast and nuclear phylogenies, (ii) differences in taxon sampling, (iii) incongruence among specific loci, and (iv) different analysis methods.…”

“…Moreover, the affiliation of diploid species from Central Asia were partly unclear, being either monophyletic (Doebley et al 1992, Nishikawa et al 2002 or being polyphyletic and grouping with species from the New World and from the Mediterranean (Petersen and Seberg 2003). Chloroplast data generally agree on monophyly of H. vulgare and H. bulbosum, and the H. murinum complex, respectively.…”

In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

“…It is possible because of the maternal inheritance of the chloroplast genomes (plastomes), whereas nuclear genomes have biparental inheritance and polyploidy that may cause difficulties for phylogenetic analyses (Nishikawa et al 2002). The plastome is an important source of genetic markers for phylogenetic analysis; population-level studies, genotyping and mapping that can be used for genomic characterization and interspecific comparison (Raubeson et al 2007).…”