Dataset Information

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

ABSTRACT: Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE) provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecular study of rapid Al tolerance evolution at the PGE. We examined the Al content of Anthoxanthum tissues and conducted RNA-sequencing of root tips, the primary site of Al induced damage. We found that despite its high tolerance Anthoxanthum is not an Al accumulating species. Genes similar to those involved in organic acid exudation (TaALMT1, ZmMATE), cell wall modification (OsSTAR1), and internal Al detoxification (OsNRAT1) in cultivated grasses were responsive to Al exposure. Expression of a large suite of novel loci was also triggered by early exposure to Al stress in roots. Three-hundred forty five transcripts were significantly more up- or down-regulated in tolerant vs. sensitive Anthoxanthum genotypes, providing important targets for future study of rapid evolution at the PGE.

SUBMITTER: Gould B

PROVIDER: S-EPMC4493143 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

Gould Billie B McCouch Susan S Geber Monica M

PloS one 20150706 7

Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE) provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecu ...[more]

PMID: 26148203

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Project description:We compared the results of a long-term (65 years) experiment in a South African grassland with the world's longest-running ecological experiment, the Park Grass study at Rothamsted, U.K. The climate is warm and humid in South Africa and cool and temperate in England. The African grassland has been fertilized with two forms of nitrogen applied at four levels, phosphorus and lime in a crossed design in 96 plots. In 1951, about 84% of plant cover consisted of Themeda triandra, Tristachya leucothrix and Setaria nigrirostris. Currently, the dominant species are Panicum maximum, Setaria sphacelata and Eragrostis curvula, making up 71% of total biomass. As in the Park Grass experiment, we found a significant (additive) interaction effect on ANPP of nitrogen and phosphorus, and a (marginally significant) negative correlation between ANPP and species richness. Unlike the Park Grass experiment, there was no correlation between ANPP and species richness when pH was included as a covariate. There was also a significant negative effect of nitrogen amount and nitrogen form and a positive effect of lime on species richness and species diversity. Soil pH had an important effect on species richness. Liming was insufficient to balance the negative effects on species richness of nitrogen fertilization. There was a significant effect of pH on biomass of three abundant species. There were also significant effects of light on the biomass of four species, with only Panicum maximum having a negative response to light. In all of the abundant species, adding total species richness and ANPP to the model increased the amount of variance explained. The biomass of Eragrostis curvula and P. maximum were negatively correlated with species richness while three other abundant species increased with species richness, suggesting that competition and facilitation were active. Consistent with the results from the Park Grass and other long-term fertilization experiments of grasslands, we found a positive effect of soil pH and a negative effect of nitrogen amount on species richness, a more acutely negative effect on species richness of acidic ammonium sulphate fertilizer than limestone ammonium nitrate, a negative relationship between species richness and biomass, and a positive effect on species richness of lime interacting with nitrogen.

Project description:The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus.

Dataset Information

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

Publications

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

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