Molecular phylogeny and reticulate origins of several American polyploid Hordeum species

Botany ◽  
2011 ◽  
Vol 89 (6) ◽  
pp. 405-415 ◽  
Author(s):  
Huan Wang ◽  
Genlou Sun
Keyword(s):  
Diploid Species ◽  
Nuclear Gene ◽  
Single Copy ◽  
Polyploid Species ◽  
Sequence Comparisons ◽  
Internal Transcribed Spacer Sequences ◽  
Hordeum Jubatum ◽  
Terminal Element ◽  
Hordeum Species ◽  
Genome Donors

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.

Origin of the H genome in StH-genomic Elymus species based on the single-copy nuclear gene DMC1

Genome ◽  
2011 ◽  
Vol 54 (8) ◽  
pp. 655-662 ◽  
Author(s):  
Genlou Sun ◽  
Xiaodi Zhang
Keyword(s):  
North American ◽  
Diploid Species ◽  
Nuclear Gene ◽  
Single Copy ◽  
Elymus Lanceolatus ◽  
Single Copy Nuclear Gene ◽  
Elymus Species ◽  
Elymus Multisetus ◽  
Elymus Hystrix ◽  
Hordeum Species

Previous studies have suggested that the H haplome in Elymus could originate from different diploid Hordeum species, however, which diploid species best represent the parental species remains unanswered. The focus of this study seeks to pinpoint the origin of the H genome in Elymus. Allopolyploid Elymus species that contain the StH genome were analyzed together with diploid Hordeum species and a broad sample of diploid genera in the tribe Triticeae using DMC1 sequences. Both parsimony and maximum likelihood analyses well separated the American Hordeum species, except Hordeum brachyantherum subsp. californicum, from the H genome of polyploid Elymus species. The Elymus H-genomic sequences were formed into different groups. Our data suggested that the American Horedeum species, except H. brachyantherum subsp. californicum, are not the H-genomic donor to the Elymus species. Hordeum brevisubulatum subsp. violaceum was the progenitor species to Elymus virescens, Elymus confusus, Elymus lanceolatus, Elymus wawawaiensis, and Elymus caninus. Furthermore, North American H. brachyantherum subsp. californicum was a progenitor of the H genome to Elymus hystrix and Elymus cordilleranus. The H genomes in Elymus canadensis, Elymus sibiricus, and Elymus multisetus were highly differentiated from the H genome in Hordeum and other Elymus species. The H genome in both North American and Eurasian Elymus species was contributed by different Hordeum species.

Genomic constitution and phylogenetic position of several New Zealand Triticeae species revealed by two single copy nuclear genes

2011 ◽  
Vol 59 (1) ◽  
pp. 1 ◽  
Author(s):  
Aimee G. Oliver ◽  
Kara Harnish ◽  
Genlou Sun
Keyword(s):  
New Zealand ◽  
North American ◽  
Diploid Species ◽  
Single Copy ◽  
Nuclear Genes ◽  
Phylogenetic Position ◽  
Genome Constitution ◽  
Elymus Species ◽  
New Zealand Flora ◽  
Hordeum Species

Three genera of Triticeae, Elymus, Stenostachys and Australopyrum, are described in the New Zealand flora. Cytological analyses suggested that five basic genomes (St, H, Y, P and W) donated by different diploid species in different combinations exist in the genera Elymus and Stenostachys, whereas Australopyrum species contain the W genome only. Morphological and cytogenetic data suggested that the genome constitution for both E. apricus and E. multiflorus is StYW. Chloroplast DNA and ITS data supported the genome constitution of these Elymus species, but the HW genome constitution was assigned to the Stenostachys species. In this study, sequences of two single copy nuclear genes, RPB2 and DMC1, were used to confirm or refute the genome constitutions of the two Stenostachys species and the two Elymus species from New Zealand, and to analyse their phylogenetic relationships with other Elymus species. Our RPB2 and DMC1 data confirmed that the genome constitution of hexaploid E. apricus is StWY, and tetraploid S. gracilis is HW. The presence of the StW genome in hexaploid E. multiflorus, and the W genome in tetraploid S. laevis is also confirmed. No obvious St genome differentiation between New Zealand and non-New Zealand species is observed. The H genomes in the S. gracilis and S. laevis are closely related to the H genome from North American species, indicating that the H genomes in these two New Zealand species might originate from North American Hordeum species.

scholarly journals Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1843-1854 ◽  
Author(s):  
Nancy N FitzSimmons ◽  
Craig Moritz ◽  
Colin J Limpus ◽  
Lisa Pope ◽  
Robert Prince
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Green Turtle ◽  
Nuclear Dna ◽  
Nuclear Gene ◽  
Chelonia Mydas ◽  
Single Copy ◽  
Microsatellite Data ◽  
Ecological Data ◽  
Infinite Allele Model

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

Molecular phylogeny of diploid Hordeum species and incongruence between chloroplast and nuclear datasets

Genome ◽  
2011 ◽  
Vol 54 (12) ◽  
pp. 986-992 ◽  
Author(s):  
Huan Wang ◽  
Dongfa Sun ◽  
Genlou Sun
Keyword(s):  
Evolutionary History ◽  
Nuclear Gene ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Genome Species ◽  
Different Types ◽  
History Of ◽  
Morphological And Molecular Data ◽  
Hordeum Species ◽  
Eurasian Species

The phylogeny of diploid Hordeum species has been studied using both chloroplast and nuclear gene sequences. However, the studies of different nuclear datasets of Hordeum species often arrived at similar conclusions, whereas the studies of different chloroplast DNA data generally resulted in inconsistent conclusions. Although the monophyly of the genus is well supported by both morphological and molecular data, the intrageneric phylogeny is still a matter of controversy. To better understand the evolutionary history of Hordeum species, two chloroplast gene loci (trnD-trnT intergenic spacer and rps16 gene) and one nuclear marker (thioreoxin-like gene (HTL)) were used to explore the phylogeny of Hordeum species. Two obviously different types of trnD-trnT sequences were observed, with an approximately 210 base pair difference between these two types: one for American species, another for Eurasian species. The trnD-trnT data generally separated the diploid Hordeum species into Eurasian and American clades, with the exception of Hordeum marinum subsp. gussoneanum. The rps16 data also grouped most American species together and suggested that Hordeum flexuosum has a different plastid type from the remaining American species. The nuclear gene HTL data clearly divided Hordeum species into two clades: the Xu + H genome clade and the Xa + I genome clade. Within clades, H genome species were well separated from the Xu species, and the I genome species were well separated from the Xa genome species. The incongruence between chloroplast and nuclear datasets was found and discussed.

scholarly journals Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)

2012 ◽  
Vol 12 (1) ◽  
pp. 70 ◽  
Author(s):  
Danying Cai ◽  
Flor Rodríguez ◽  
Yuanwen Teng ◽  
Cécile Ané ◽  
Meredith Bonierbale ◽  
...  
Keyword(s):  
Nuclear Gene ◽  
Single Copy ◽  
Gene Analysis ◽  
Single Copy Nuclear Gene ◽  
Solanum Section Petota ◽  
Section Petota ◽  
Wild Potatoes

scholarly journals Hepatica transsilvanica Fuss (Ranunculaceae) is an Allotetraploid Relict of the Tertiary Flora in Europe – Molecular Phylogenetic Evidence

2020 ◽  
Vol 89 (3) ◽  
Author(s):  
Levente Laczkó ◽  
Gábor Sramkó
Keyword(s):  
Parental Species ◽  
Gene Tree ◽  
Diploid Species ◽  
Nuclear Gene ◽  
Hybrid Origin ◽  
Distribution Area ◽  
Recent Common Ancestor ◽  
Term Survival ◽  
Quaternary Glaciation ◽  
Eastern Carpathians

The <em>Hepatica </em>section <em>Angulosa </em>consists of mainly tetraploid (2<em>n </em>= 28) species that are distributed disjunctly throughout Eurasia. Karyological evidence proves the hybrid origin of the polyploid species of this section. <em>Hepatica transsilvanica </em>is a member of this species group with a conspicuous distribution restricted to the Eastern Carpathians. Based on genome size and cytotypes, the paternal parent of <em>H. transsilvanica </em>is described to be the only diploid species in section <em>Angulosa</em>, <em>H. falconeri</em>. The maternal species is hypothesized to be <em>H. nobilis</em>, a European species with entirely lobed leaves and a wider distribution area. Although the hybrid origin of <em>H. transsilvanica </em>is well documented by karyological evidence, the time of hybridization has never been studied. By using sequences of both the nuclear and plastid genome, we reconstructed the phylogenetic relationships and divergence times of <em>H. transsilvanica </em>and its parental species. The identity of the parental species is corroborated by discordant gene tree topologies of the nrITS and plastid sequences. Moreover, both gene copies of the parental species could be identified with the low-copy nuclear gene, <em>MLH1</em>. Divergence dating analysis using Bayesian phylogenetic methods strongly supported the long-term survival of <em>H. transsilvanica </em>in the Southeastern Carpathians, as the most recent common ancestor of the hybrid and parent species existed not later than the beginning of the Pleistocene, ca. 3 million years ago. These results not only highlight the biogeographic importance of the Southeastern Carpathians in the Quaternary glaciation periods, but also emphasize that Tertiary lineages could have survived in a Central European cryptic refugium.

Generating single-copy nuclear gene data for a recent adaptive radiation

2006 ◽  
Vol 39 (1) ◽  
pp. 124-134 ◽  
Author(s):  
Justen B. Whittall ◽  
Andrew Medina-Marino ◽  
Elizabeth A. Zimmer ◽  
Scott A. Hodges
Keyword(s):  
Adaptive Radiation ◽  
Nuclear Gene ◽  
Single Copy ◽  
Single Copy Nuclear Gene ◽  
Gene Data

Evidence for genetic suppression of heterogenetic chromosome pairing in polyploidy species of Solanum, sect. Petota

1983 ◽  
Vol 25 (5) ◽  
pp. 530-539 ◽  
Author(s):  
Jan Dvořák
Keyword(s):  
Chromosome Pairing ◽  
Interspecific Hybrids ◽  
Diploid Species ◽  
Diploid Hybrid ◽  
Polyploid Species ◽  
Chromosome Differentiation ◽  
Genetic Suppression ◽  
Solanum Sect ◽  
Paradoxical Results

Data on chromosome pairing in haploids and interspecific hybrids of Solanum, sect. Petota reported in the literature were used to determine whether the diploidlike chromosome pairing that occurs in some of the polyploid species of the section is regulated by the genotype or brought about by some other mechanism. The following trends emerged from these data. Most of the polyploid × polyploid hybrids had high numbers of univalents, which seemed to indicate that the polyploid species were constructed from diverse genomes. Haploids, except for those derived from S. tuberosum, had incomplete chromosome pairing. All hybrids from diploid × diploid crosses had more or less regular chromosome pairing, which suggested that all investigated diploid species have the same genome. Likewise, hybrids from polyploid × diploid crosses had high levels of chromosome pairing. These paradoxical results are best explained if it is assumed that (i) the genotypes of most polyploid species, but not those of the diploid species, suppress heterogenetic pairing, (ii) that nonstructural chromosome differentiation is present among the genomes of both diploid and polyploid species, and (iii) the presence of the genome of a diploid species in a polyploid × diploid hybrid results in promotion of heterogenetic pairing. It is, therefore, concluded that heterogenetic pairing in most of the polyploid species is genetically suppressed.

Phylogeny in the genus Hordeum based on nucleotide sequences closely linked to the vrs1 locus (row number of spikelets)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 973-981 ◽  
Author(s):  
Takao Komatsuda ◽  
Ken-ichi Tanno ◽  
Björn Salomon ◽  
Tomas Bryngelsson ◽  
Roland von Bothmer
Keyword(s):  
Nuclear Dna ◽  
Sister Group ◽  
Single Copy ◽  
Nucleotide Sequences ◽  
Restriction Maps ◽  
Deletion Event ◽  
Single Base ◽  
Genome Group ◽  
The Difference ◽  
Hordeum Species

The phylogenetic relationship between four basic genomes designated H, I, Xa, and Xu in the genus Hordeum was studied using a nuclear DNA sequence. The sequence, cMWG699, is single copy in the H. vulgare genome, and tightly linked to the vrs1 locus which controls two- and six-rowed spikes. DNA fragments homologous to cMWG699 were amplified from diploid Hordeum species and the nucleotide sequences were determined. A phylogeny based on both base substitutions and an insertion-deletion event showed that the H- and Xa-genome groups are positioned in one monophyletic group indicating that the Xa-genome taxa should be included in the H-genome group. The large H-genome group is highly homogeneous. The I and Xu genomes are distinctly separated from H and Xa, and form sister groups. Another phylogeny pattern based on data excluding the insertion-deletion gave a result that the Xa genome forms a sister group to the H-genome group. The difference between the H and Xa genomes was affected only by a single base insertion-deletion event, thus the H and Xa genomes are likely to be closely related. The I and Xu genomes were again distinctly separated from the H and Xa genomes.Key words: genome DNA, molecular markers, restriction maps, barley, Psathyrostachys.

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