Three new species of northern Australian Glycine (Fabaceae, Phaseolae), G. gracei, G. montis-douglas and G. syndetika

Pfeil, Bernard E.; Craven, Lyn A.; Brown, A. H. D.; Murray, B. G.; Doyle, Jeff J.

doi:10.1071/sb05035

Cited by 23 publications

(14 citation statements)

References 25 publications

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“…(Doyle et al 2004; Pfeil et al 2006). The two diploid species, D3 and D4, diverged approximately 2.5 Ma and hybridized to give rise to T2 within the last 100,000 years (Doyle et al 2004).…”

Section: Methodsmentioning

confidence: 99%

Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

Coate

Doyle

2010

Genome Biology and Evolution

106

129

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Evolutionary biologists are increasingly comparing gene expression patterns across species. Due to the way in which expression assays are normalized, such studies provide no direct information about expression per gene copy (dosage responses) or per cell and can give a misleading picture of genes that are differentially expressed. We describe an assay for estimating relative expression per cell. When used in conjunction with transcript profiling data, it is possible to compare the sizes of whole transcriptomes, which in turn makes it possible to compare expression per cell for each gene in the transcript profiling data set. We applied this approach, using quantitative reverse transcriptase-polymerase chain reaction and high throughput RNA sequencing, to a recently formed allopolyploid and showed that its leaf transcriptome was approximately 1.4-fold larger than either progenitor transcriptome (70% of the sum of the progenitor transcriptomes). In contrast, the allopolyploid genome is 94.3% as large as the sum of its progenitor genomes and retains ≥93.5% of the sum of its progenitor gene complements. Thus, “transcriptome downsizing” is greater than genome downsizing. Using this transcriptome size estimate, we inferred dosage responses for several thousand genes and showed that the majority exhibit partial dosage compensation. Homoeologue silencing is nonrandomly distributed across dosage responses, with genes showing extreme responses in either direction significantly more likely to have a silent homoeologue. This experimental approach will add value to transcript profiling experiments involving interspecies and interploidy comparisons by converting expression per transcriptome to expression per genome, eliminating the need for assumptions about transcriptome size.

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“…(Doyle et al 2004; Pfeil et al 2006). The two diploid species, D3 and D4, diverged approximately 2.5 Ma and hybridized to give rise to T2 within the last 100,000 years (Doyle et al 2004).…”

Section: Methodsmentioning

confidence: 99%

Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

Coate

Doyle

2010

Genome Biology and Evolution

106

129

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“…The study group consisted of the natural allopolyploid, G. dolichocarpa (2n ¼ 80; designated 'T2') and its diploid progenitors, G. tomentella (2n ¼ 40; 'D3') and G. syndetika (2n ¼ 40; 'D4'), which are perennial relatives of the cultivated soybean (G. max; Doyle et al, 2004;Pfeil et al, 2006). The two diploid species, D3 and D4, diverged approximately 3.2 MYA (Egan AN and Doyle JJ, unpublished results), and hybridized to give rise to T2 within the last 100 000 years (Doyle et al, 2004).…”

Section: Plant Materialsmentioning

confidence: 99%

Transgressive physiological and transcriptomic responses to light stress in allopolyploid Glycine dolichocarpa (Leguminosae)

et al. 2012

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Allopolyploidy is often associated with increased photosynthetic capacity as well as enhanced stress tolerance. Excess light is a ubiquitous plant stress associated with photosynthetic light harvesting. We show that under chronic excess light, the capacity for non-photochemical quenching (NPQ max ), a photoprotective mechanism, was higher in a recently formed natural allotetraploid (Glycine dolichocarpa, designated 'T2') than in its diploid progenitors (G. tomentella, 'D3'; and G. syndetika, 'D4'). This enhancement in NPQ max was due to an increase in energy-dependent quenching (qE) relative to D3, combined with an increase in zeaxanthin-dependent quenching (qZ) relative to D4. To explore the genetic basis for this phenotype, we profiled D3, D4 and T2 leaf transcriptomes and found that T2 overexpressed genes of the water-water cycle relative to both diploid progenitors, as well as genes involved in cyclic electron flow around photosystem I (CEF-PSI) and the xanthophyll cycle, relative to D4. Xanthophyll pigments have critical roles in NPQ, and the water-water cycle and CEF-PSI are non-photosynthetic electron transport pathways believed to facilitate NPQ formation. In the absence of CO 2 , T2 also exhibited greater quantum yield of photosystem II than either diploid, indicating a greater capacity for non-photosynthetic electron transport. We postulate that, relative to its diploid progenitors, T2 is able to achieve higher NPQ max due to an increase in xanthophyll pigments coupled with enhanced electron flow through the water-water cycle and CEF-PSI.

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“…1998). The largest genome group (A‐genome) includes several named species, but taxonomic boundaries are dynamic (e.g., Pfeil et al. 2006), in part due to hybridization (e.g., Brown et al.…”

Section: Characterization Of Thirteen Microsatellite Loci In Two A‐gmentioning

confidence: 99%

Isolation and characterization of thirteen polymorphic microsatellite loci in the A‐genome perennial group of the legume genus Glycine

Bronski

Straub

Bogdanowicz

et al. 2009

Molecular Ecology Resources

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Thirteen polymorphic microsatellite loci were developed for the closely related and reproductively compatible species comprising the A-genome perennial group of the legume genus Glycine. Primers developed from the widespread and isozymically differentiated G. canescens amplified successfully across G. clandestina and four other species within the complex. Species were highly polymorphic, and observed heterozygosities were extremely low for all loci, as expected for these predominantly autogamous taxa. These markers will be useful in studying genetic variation, population structure, gene flow, and polyploidy within the A-genome group.

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Three new species of northern Australian Glycine (Fabaceae, Phaseolae), G. gracei, G. montis-douglas and G. syndetika

Cited by 23 publications

References 25 publications

Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

Transgressive physiological and transcriptomic responses to light stress in allopolyploid Glycine dolichocarpa (Leguminosae)

Isolation and characterization of thirteen polymorphic microsatellite loci in the A‐genome perennial group of the legume genus Glycine

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