Phylogenetic relationships between Hystrix and its closely related genera (Triticeae; Poaceae) based on nuclear Acc1, DMC1 and chloroplast trnL-F sequences

Li, Sha; Fan, Xing; Yang, Ruiwu; Kang, Houyang; Ding, Chunbang; Zhang, Li; Zheng, Yu; Zhou, Yong‐Hong

doi:10.1016/j.ympev.2009.05.005

Cited by 52 publications

(61 citation statements)

References 44 publications

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“…ACCase data supported the presence of the StH genome in E. hystrix and suggested high intraspecific genetic diversity in this species (Fan et al 2007). A previous DMC1 tree showed that the H genome in E. hystrix was sister to E. wawawauensis and E. caninus (Sha et al 2010). Both ours and published data (Sha et al 2010) indicated that the DMC1 gene in the H genome from E. hystrix is differentiated from the H genome in Eurasian and North American tetraploid Elymus species.…”

Section: The H Genome In Sth-genomic Elymus Speciessupporting

confidence: 77%

“…A previous DMC1 tree showed that the H genome in E. hystrix was sister to E. wawawauensis and E. caninus (Sha et al 2010). Both ours and published data (Sha et al 2010) indicated that the DMC1 gene in the H genome from E. hystrix is differentiated from the H genome in Eurasian and North American tetraploid Elymus species. Another South American E. gayanus H genome was sister to the H-genomic sequences in the MP tree (Fig.…”

Section: The H Genome In Sth-genomic Elymus Speciessupporting

confidence: 65%

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

SunGenlou

ZhangXiaodi

2011

Genome

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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.

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Section: The H Genome In Sth-genomic Elymus Speciessupporting

confidence: 77%

Section: The H Genome In Sth-genomic Elymus Speciessupporting

confidence: 65%

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

SunGenlou

ZhangXiaodi

2011

Genome

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“…Szarvasi-1, E. hispidus, and A. cristatum -were newly determined. The phylogenetic relationships inferred from molecular data of both the rpoA gene and ITS regions supported the separation of the studied Elymus taxa from A. cristatum -formerly Sha et al (2010). Interestingly, the Hungarian A. cristatum is located far from the Danish accession of the species on the rpoA based phylogenetic tree.…”

Section: Genus Species Synonymssupporting

confidence: 53%

Tall Wheatgrass Cultivar Szarvasi-1 (Elymus elongatus subsp. ponticus cv. Szarvasi-1) as a Potential Energy Crop for Semi-Arid Lands of Eastern Europe

Csete¹,

Stranczinger²,

Szalontai³

et al. 2011

Sustainable Growth and Applications in Renewable Energy Sources

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“…Trn H- psb A inversions have been reported for other angiosperm families [51-54] but not for grasses, probably because trn L- trn F and other loci are more widely used as phylogenetic markers in the grass family [55-57]. Also, grass phylogenies that have used this marker but only included one individual per species or genus [58,59] would necessarily fail to observe intra-taxon variation.…”

Section: Discussionmentioning

confidence: 99%

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

2011

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BackgroundPolyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems.ResultsUsing 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability.We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at <100 km with chloroplast but not nuclear markers, which may be a result of restricted seed flow and long-distance pollen flow in this wind-pollinated group.ConclusionsOur results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among species, as well as to investigate phylogeographic hypotheses. This next-generation sequencing method is more affordable than and at least as reliable as bacterial cloning. It could be applied to any experiment involving sequencing of amplicon mixtures.

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Phylogenetic relationships between Hystrix and its closely related genera (Triticeae; Poaceae) based on nuclear Acc1, DMC1 and chloroplast trnL-F sequences

Cited by 52 publications

References 44 publications

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

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

Tall Wheatgrass Cultivar Szarvasi-1 (Elymus elongatus subsp. ponticus cv. Szarvasi-1) as a Potential Energy Crop for Semi-Arid Lands of Eastern Europe

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

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