Polyploidy and the evolution of flax

Paleopolyploidy in the flax genus, Linum

Paleopolyploidy in the flax genus, Linum

Polyploidy, the duplication of whole genomes, is an important evolutionary force that is especially prevalent in plants. Recent study has revealed that all angiosperms have undergone at least two rounds of ancient whole-genome duplication in addition to several younger, lineage-specific events. These events are thought to have been very important in the evolutionary diversification of flowering plants.

Cultivated flax (Linum usitatissimum) is known to have undergone a whole-genome duplication around 5–9 million years ago. The aim of a recent study in Annals of Botany was to investigate whether other whole-genome duplication events have occurred in the evolutionary history of cultivated flax. Knowledge of such whole-genome duplications will be important in understanding the biology and genomics of cultivated flax.

 

Sveinsson, S., McDill, J., Wong, G. K., Li, J., Li, X., Deyholos, M. K., & Cronk, Q. C. (2014) Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics. Annals of Botany, 113(5), 753-761. doi: 10.1093/aob/mct306
Transcriptomes of 11 Linum species were sequenced using the Illumina platform. The short reads were assembled de novo and the DupPipe pipeline was used to look for signatures of polyploidy events from the age distribution of paralogues. In addition, phylogenies of all paralogues were assembled within an estimated age window of interest. These phylogenies were assessed for evidence of a paleopolyploidy event within the genus Linum.
A previously unknown paleopolyploidy event that occurred 20–40 million years ago was discovered and shown to be specific to a clade within Linum containing cultivated flax (L. usitatissimum) and other mainly blue-flowered species. The finding was supported by two lines of evidence. First, a significant change of slope (peak) was shown in the age distribution of paralogues that was phylogenetically restricted to, and ubiquitous in, this clade. Second, a large number of paralogue phylogenies were retrieved that are consistent with a polyploidy event occurring within that clade.
The results show the utility of multi-species transcriptomics for detecting whole-genome duplication events and demonstrate that that multiple rounds of polyploidy have been important in shaping the evolutionary history of flax. Understanding and characterizing these whole-genome duplication events will be important for future Linum research.

 

Plant community feedbacks and long-term ecosystem responses to multi-factored global change

14057R1If you add CO2 or nitrogen to a single plant it will likely grow more, but the amount by which each resource stimulates growth differs widely across species. When you add either resource to a whole ecosystem, total plant growth will likely also increase, but there will be winners and losers, causing a change in the relative abundance of plant species, and therefore altering the way the whole ecosystem responds to the added resource, a “community feedback”. Recent studies have shown that (1) shifts in plant community structure cannot be reliably predicted from short-term plant physiological response to global change and (2) the ecosystem response to multi-factored change is commonly less than the sum of its parts. In a new review published in AoB PLANTS, Langley and Hungate survey the results from long-term field manipulation to examine the role community shifts may play in explaining these common findings. They use a simple model to examine the potential importance of community shifts in governing ecosystem response and show that community dynamics can have a large impact on ecosystem response to any single factor. Understanding tradeoffs in the ability of plants to respond positively to, or to tolerate, different global change drivers may help identify generalizable patterns of covariance in responses to different drivers of change across plant taxa.

How rice germinates under water

ADH1 and carbohydrate metabolism in seeds of rice

ADH1 and carbohydrate metabolism in seeds of rice

Rice (Oryza sativa) has the rare ability to germinate and elongate a coleoptile under oxygen-deficient conditions, which include both hypoxia and anoxia. It has previously been shown that Alcohol Dehydrogenase 1 (ADH1) is required for cell division and cell elongation in the coleoptile of submerged rice seedlings by means of studies using a rice ADH1-deficient mutant, reduced adh activity (rad).

A recent paper in Annals of Botany aims to understand how low ADH1 in rice affects carbohydrate metabolism in the embryo and endosperm, and lactate and alanine synthesis in the embryo during germination and subsequent coleoptile growth in submerged seedlings.

Even in a submerged environment containing substantial amounts of dissolved oxygen, a reduction in ADH (as brought about by an ADH1 mutation) reduces seedling viability, changes the balance between the end-products of glycolysis and decreases sugar concentrations in the endosperm and embryo. Exogenous sugar did not improve the growth or survival of the ADH1 mutant, indicating that sugar processing in the embryo was probably the limiting factor. However, how low ADH activity affects the endosperm deserves further experimental attention. The endosperm is well suited for investigations of sugar production and transport because of its simple composition and metabolism.

 

Takahashi, H., Greenway, H., Matsumura, H., Tsutsumi, N., & Nakazono, M. (2014) Rice alcohol dehydrogenase 1 promotes survival and has a major impact on carbohydrate metabolism in the embryo and endosperm when seeds are germinated in partially oxygenated water. Annals of Botany, 113 (5): 851-859. doi: 10.1093/aob/mct305

 

Sugar versus Auxin: which is dominant?

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Of the plethora of aspects of plant growth and development that the hormone (OK, plant growth regulator…) auxin is implicated in/involved with (e.g. embryo development, leaf formation, phototropism, gravitropism, fruit development, abscission, root initiation and development…), surely one of the most enduring is apical dominance.

Apical dominance is the phenomenon whereby the outgrowth of buds on the side of a shoot is suppressed in favour of growth by the apical bud (hence its name…). Maintenance of this suppression has long been assumed to be due to the production of auxin by the apical bud and its transport down the stem, which effectively keeps the lateral buds in check. Understandably, outgrowth of lateral buds upon removal of the apical bud – and its associated auxin-production and outflow – is a key bit of evidence for the role of auxin in this phenomenon.

Just as you should never (ever…) take anything for granted in science (or anything else), it’s rather satisfying to note that work by Michael Mason et al. – and rather pleasingly from ‘down under’ – has seemingly burst that little bubble of plant physiological certainty.  The primarily Australia-based team show that bud outgrowth following apical bud removal takes place >24 hours before changes in auxin content in the adjacent stem, i.e. ‘initiation of bud growth after shoot tip loss cannot be dependent on apical auxin supply’. However, upon removal of the shoot tip, sugars not only accumulate in axillary buds, but do so within a timeframe that correlates with bud release. Rather than auxin being the main lateral-growth suppressant, the team conclude that enhancement in sugar supply is both necessary and sufficient for suppressed buds to be released from apical dominance. Ah, the sweet smell of success? G’day BrucesSheilas… and ‘possums’ everywhere!

[And if this item has initiated a craving for more sugar-based botanical items, may I recommend Winnie Lin et al.’s Letter investigating nectar secretion and the role of the sugar transporter, aptly named SWEET9? – Ed.]

Developmental robustness and species diversity: A special issue of Annals of Botany open for submissions

Magnolia flowers

Flowers from the same Magnolia tree have different numbers of perianth organs, indicative of a low degree of robustness in perianth organ number determination.
Photos by Susanne Schilling.

J.B.S. Haldane is often quoted to have said that ‘God has an inordinate fondness for beetles’. Arguably, Haldane himself would not have accepted this as an explanation for the enormous number of beetle species – they make up some 25 – 30 % of all described animals. However, Haldane’s statement demonstrates that we still lack a satisfying explanation for an oddity in the tree of life: it is only a few taxa that contribute disproportionately strongly to species diversity, whereas other taxa contain relatively few species. This observation is by no means restricted to the animal kingdom; if Haldane would have been a botanist, he may have said that god (like most of us humans) has an inordinate fondness for flowering plants – these make up some 85 – 90 % of all described plant species. The question is obvious: Why are there so many flowering plant species but so few gymnosperm species? Likewise, one may ask: Why are there so many orchid, daisy and grass but so few early diverging angiosperm species? A number of explanations have been suggested over the years: the age of clades, evolutionary innovations and co-evolution may all well have contributed to the success (in terms of species number) of some taxa over others. But as obvious as some of these explanations might be for certain groups – for example, co-evolution with pollinators may well have accelerated the radiation of orchids – they fail to explain other cases of species diversity: co-evolution with pollinators can hardly explain why there are more than 10,000 species of mainly wind-pollinated grasses, for example.

However, one striking observation is that successful taxa appear to be morphologically rather uniform: all orchid flowers share a basic floral bauplan, the same applies to grasses or daisies (and also beetles have a highly standardized body plan). Highly standardized or uniform structures may be an indication for a high degree of developmental robustness. Thus, in contrast to what one may intuitively assume, robust developmental processes might facilitate rather than prevent the evolution of species diversity.

We started exploring the relationship between species diversity and developmental robustness on a symposium at the Euro Evo Devo 2014 conference in Vienna that was supported by the Annals of Botany. However, we are still far from understanding the relevance of robustness for species diversity. On account of this, a Special Issue on that topic will appear in the Annals of Botany. Authors already committed to contribute to this Special Issue are Peter Endress (Zürich), Angela Hay (Cologne), Matthew Wills (Bath), Koichi Fujimoto (Osaka), and Veronica Grieneisen (Norwich).

This is an open call for submission of manuscripts on developmental robustness, biodiversity and the relationship between the two for consideration for the Special Issue. We intend to have a mixture of papers treating the topic from the perspective of developmental genetics, evolutionary biology, plant morphology, paleobiology and systems biology. If you have a manuscript that you would like us to consider, please send an outline (Title, Authors and 250 to 500 words) until the end of 2014 to annalsbotany@le.ac.uk. If agreed, the full paper would need to be submitted by 31 March 2015, in order to enter the full review process.

Regulation of a Solanum Double-B box gene

Regulation of a Solanum Double-B box gene

Regulation of a Solanum Double-B box gene

Double B-box zinc finger (DBB) proteins are recently identified plant transcriptional regulators that participate in the response to NaCl-induced stress in arabidopsis. Kiełbowicz-Matuk et al.investigate variations in a Solanum DBB protein, SsBBX24, in S. tuberosum and S. sogarandinum and find evidence of trafficking from the nucleus to the cytosol during the light period. SsBBX24 gene expression exhibits circadian cycling under control conditions, with the highest and lowest abundances of both transcript and protein occurring 8 h and 18 h after dawn, respectively. Low temperature, salinity and polyethylene glycol disturb the circadian regulation of SsBBX24 gene expression at the protein level, and the time of the day modulates the magnitude of SsBBX24 expression in response to high salt concentration. They propose that stress-dependent, post-transcriptional mechanisms alter the regulation by the circadian clock of the amount of SsBBX24 in Solanum.

Patchy radial increment in the mangrove Avicennia

Patchy radial increment in the mangrove Avicennia

Patchy radial increment in the mangrove Avicennia

In the mangrove genus Avicennia successive vascular cambia are organized in patches, creating stems with non-concentric xylem tissue surrounded by internal phloem tissue. Robert et al. monitor stem variations in A. marina trees in a natural mangrove forest over the course of one year, and find that patchiness occurs in both the radial growth and the shrinkage and swelling patterns of the stems. Radial increment is affected by fresh water availability rather than tidal inundation. They conclude that the ability to develop successive cambia in a patchy way enables Avicennia trees to adapt to changes in the prevailing environmental conditions, enhancing its survival in the highly dynamic mangrove environment.

Genome downsizing and karyotype constancy in diploid and polyploid congeners: a model of genome size-variation

DCIM100MEDIADCIM100MEDIAIn several genera evolutionary chromosome change involves variation in DNA amount in diploids and genome downsizing in polyploids. In a new study in AoB PLANTS, Poggio et al. analysed the genome size and karyotypical parameters of Hippeastrum species with different ploidy levels.The constancy of bimodal karyotypes, even with changes in ploidy level, and DNA content per basic genome indicate that the distribution of DNA within the complement is not random and suggest the presence of mechanisms selecting for constancy, or against change, in the karyotype morphology.DCIM100MEDIA

Combining FISH and chromosome modelling in Typhonium

Combining FISH and chromosome modelling in Typhonium

Combining FISH and chromosome modelling in Typhonium

Since the advent of molecular phylogenetics, attempts have been made to infer the evolutionary trajectories of chromosome numbers on DNA phylogenies. Sousa et al.combine cytogenetics, using fluorescent in situ hybridization (FISH), and modelling of changing chromosome numbers in a maximum-likelihood framework to study Typhonium, a genus of Araceae with 2n = 24 and 2n = 8, the lowest known count in the family. A combination of a densely sampled phylogeny, ancestral state modelling and FISH reveals that the species with n = 4 is highly derived, with the FISH data pointing to a Robertsonian fusion-like chromosome rearrangement in the ancestor of this species.

Dodgy photos dog phytology

Image: Wikimedia Commons.

Image: Wikimedia Commons.

It has oft been claimed that a picture is worth a thousand words. In the case of certain images in Klementina Kakar et al.’s study entitled ‘CLASP-mediated cortical microtubule organization guides PIN polarization axis’ it seems quite clear that many more than a thousand words have been written about them. Why? The normally genteel world of botanical research has been shaken, stirred and shocked to its very core by a retraction of that paper – which purported to identify the molecular machinery that connects the organisation of microtubules to the regulation of the axis of polarisation of auxin-transporting PIN proteins (which membrane-sited molecules are needed for transport of the plant hormone auxin across plasma membranes and thereby help to maintain polarity of growth and development within the plant). Relating as it does to fundamental aspects of plant growth and development and such phenomena as gravitropism, this is an important finding and understandably published in a very high-impact and influential journal. So what’s gone awry? A retraction is, after all, a very serious state of affairs. Well, and in the words of the same four authors of the original paper, ‘after re-examination of this Letter [this is how Nature articles are formally described], concerns with some of the reported data were raised. It was found that two confocal images were near-identical in panels of Figure 3 and two confocal images were re-used in panels of Figure 4, and that some gel images were inappropriately generated by cutting and pasting of non-adjacent bands. Therefore, we feel that the most responsible action is to retract the paper. We sincerely apologize for any adverse consequences that may have resulted from the paper’s publication’. For more on this, visit the various items at the Retraction Watch* website. Fortunately – for those unaware of this from media reports, etc, but who might otherwise come across the article in their literature searches, the PubMed entry for the original Nature paper does make mention of its subsequent retraction, and provides a link to the retraction notice. Although I don’t know if the paper’s retracted status is indicated on all search engines… However, in the scrabble to find appropriate literature to cite in one’s work, one might overlook that notification. Is this therefore a weakness in the otherwise laudable retraction process/system whereby subsequent readers of those papers may not be aware of their retraction? Maybe we need a form of historical revisionism reminiscent of the rewriting of history in George Orwell’s classic novel Nineteen Eighty-Four to expunge such items from the record totally so that they’re never ever found…? Hmm, what would historians of science make of that? Do let us know!

* Retraction Watch is a blog that reports on retractions of scientific papers. Launched in August 2010 it is produced by science writers Ivan Oransky (executive editor of Reuters Health) and Adam Marcus (managing editor of Anesthesiology News).

[For more on the costs associated with retractions, check out Tracy Vence's commentary at The Scientist.  And with such sobering news, if you are concerned that retractions can unduly affect one’s career, Virginia Gewin has some words of comfort. But, if you want more retraction stories, why not check out last year’s ‘Top 10’? – Ed.]