Molecular phylogeny and reticulate origins of several American polyploid Hordeum species

Abstract

The phylogeny of diploid species in the genus Hordeum has been studied intensively. Although the origin of American polyploid species has been analyzed using multiple-copy internal transcribed spacer sequences, the origins of these species in Hordeum remain unclear. The objectives of our study were to elucidate the origins of American polyploid species and to explore phylogenetic relationships of these polyploids to diploid Hordeum and other diploid species in Triticeae using a single copy of a nuclear gene, disrupted meiotic cDNA1 (DMC1). DMC1 sequences from nine Hordeum polyploid species were analyzed. Sequence comparisons revealed that one copy of sequences from polyploid species Hordeum fuegianum, Hordeum jubatum, and Hordeum tetraploidum showed a 82 bp miniature inverted-repeat terminal element (MITE) (Stowaway) insertion, which was also detected in the Triticeae diploid species Australopyrum species (W genome) and Taeniatherum caput-medusae (Ta genome). Maximum parsimony and Bayesian analysis suggested that diploid Hordeum brachyantherum subsp. californicum is one ancestor of polyploids Hordeum arizonicum, H. brachyantherum subsp. brachyantherum, Hordeum depressum, and Hordeum procerum. The other ancestor of tetraploid H. depressum is probably Hordeum euclaston. Hordeum cordobense was suggested to be one of the genome donors to hexaploid H. procerum. The diploid Hordeum flexuosum and tetraploid H. tetraploidum were suggested as the parents to hexaploid species Hordeum parodii. The result is that one sequence from each of three Hordeum tetrapolyploids, including H. fuegianum, H. jubatum, and H. tetraploidum, and one from Hordeum hexaploid H. arizonicum fall outside the Hordeum clade of the DMC1 phylogenetic tree, therefore representing another example of complex evolutionary history. Our data may shed light on future phylogenetic studies in Triticeae, especially for the polyploids, by broadening the scope of investigations through sampling more genome types in Poaceae, not only from the tribe Triticeae. Résumé : La phylogénie d'espèces diploïdes, au sein du genre Hordeum, a été étudiée intensivement. Bien que l'origine des espèces polyploïdes d'Amérique ait été analysée en utilisant les séquences de l'espaceur interne transcrit en copies multiples, les origines des espèces d' Hordeum demeurent floues. Cette étude a pour objectifs d'élucider les origines d'espèces polyploïdes d'Amérique et d'explorer les relations phylogénétiques entre ces polyploïdes les Hordeum diploïdes ainsi que d'autres espèces diploïdes chez les Triticeae, en utilisant un gène nucléaire en simple copie, le cADN1 méiotique perturbé (C1MP). Les séquences C1MP provenant de neuf espèces d'Hordeum polyploïdes ont été analysées. Les comparaisons de séquence ont révélé qu'une copie des séquences provenant des espèces polyploïdes H. fuegianum, H. jubatum, et H. tetraploidum montrait l'insertion d'un élément terminal inversé-répété miniature (ETMI) (stowaway) de 82 pb, lequel a aussi été détecté chez les espèces de Triticeae diploïdes Australopy...

Untangling Nucleotide Diversity and Evolution of the H Genome in Polyploid Hordeum and Elymus Species Based on the Single Copy of Nuclear Gene DMC1

“…One sequences from E. confusus (PI 598463k) showed a 23 bp deletion at position 352. An 82 bp insertion was found in the sequences from polyploid species H. fuegianum , H. jubatum , and H. tetraploidum , and diploid Australopyrum velutinum and Taeniatherum caput-medusae as reported by Wang and Sun [35], and Petersen and Seberg [31], respectively. The sequence from E. trachycaulus (PI 537323L) showed a 30 bp insertion at position 1054.…”

“…californicum might be one diploid genome donor of H. arizonicum , and the second genome donor of H. arizonicum might be the common ancestor of H. brachyantherum subsp. brachyantherum , and showed that one copy of DMC1 sequences of H. arizonicum fall outside the Hordeum clade of the tree [35]. DMC1 data here suggested if the St genome was not the donor species to one copy of genome in H. arizonicum , gene flow has occurred between H. arizonicum and some Elymus StH genome species during evolutionary process.…”

“…californicum (Syn: H. californicum Covas & Stebbins), is the possible H- genome donor to Elymus species [29], which also indicated that H genome in Elymus species originated from limited Hordeum diploid. However, the published data indicated that many Hordeum diploid species have contributed to the origin of polyploids in this genus, more than 10 diploid species were suggested to be the potential donors to polyploids in Hordeum [22], [35], [46]. Taken these together, it can be concluded that the H genomes in Elymus species have originated from limited gene pool, while H genomes in Hordeum polyploids have originated from broad gene pools.…”

“…DMC1 sequence data also showed a reticulate relationship of American polyploid species and diploid Hordeum [35]. However, the relationship of the H genome in polyploid Hordeum and Elymus was not previously explored.…”

“…The single copy nuclear gene disrupted meiotic cDNA (DMC1) has been applied to phylogenetic analyses in Triticeae species. The DMC1 sequences used in this study were collected from previously published sources [21], [30]–[35].…”