First steps in studying the origins of secondary woodiness in Begonia (Begoniaceae): Combining anatomy, phylogenetics, and stem transcriptomics

Since Darwin’s observation that secondary woodiness is common on islands, the evolution of woody plants fromherbaceous ancestors has been documented in numerous angiosperm groups. However, the evolutionary processesthat give rise to this phenomenon are poorly understood. To begin addressing this we have used a range ofapproaches to study the anatomical and genetic changes associated with the evolution and development ofsecondary woodiness in a tractable group. Begonia is a large, mainly herbaceous, pantropical genus that showsmultiple shifts towards secondarily woody species inhabiting mainly tropical montane areas throughout the world.Molecular phylogenies, including only a sample of the woody species in Begonia, indicated at least eight instancesof a herbaceous–woody transition within the genus. Wood anatomical observations of the five woody speciesstudied revealed protracted juvenilism that further support the secondary derived origin of wood within Begonia.To identify potential genes involved in shifts towards secondary woodiness, stem transcriptomes of wooddevelopment in B. burbidgei were analysed and compared with available transcriptome datasets for the non-woodyB. venustra, B. conchifolia, and Arabidopsis, and with transcriptome datasets for wood development in Populus.Results identified a number of potential regulatory genes as well as variation in expression of key biosyntheticenzymes. </div

Temporal and palaeoclimatic context of the evolution of insular woodiness in the Canary Islands

Insular woodiness (IW), referring to the evolutionary transition from herbaceousness toward woodiness on islands, has arisen more than 30 times on the Canary Islands (Atlantic Ocean). One of the IW hypotheses suggests that drought has been a major driver of wood formation, but we do not know in which palaeoclimatic conditions the insular woody lineages originated. Therefore, we provided an updated review on the presence of IW on the Canaries, reviewed the palaeoclimate, and estimated the timing of origin of woodiness of 24 insular woody lineages that represent a large majority of the insular woody species diversity on the Canaries. Our single, broad‐scale dating analysis shows that woodiness in 60%–65% of the insular woody lineages studied originated within the last 3.2 Myr, during which Mediterranean seasonality (yearly summer droughts) became established on the Canaries. Consequently, our results are consistent with palaeoclimatic aridification as a potential driver of woodiness in a considerable proportion of the insular woody Canary Island lineages. However, the observed pattern between insular woodiness and palaeodrought during the last couple of million years could potentially have emerged as a result of the typically young age of the native insular flora, characterized by a high turnover

Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants

Many plant genes are known to be involved in the development of cambium and wood, but how the expression and functional interaction of these genes determine the unique biology of wood remains largely unknown. We used the soc1ful loss of function mutant – the woodiest genotype known in the otherwise herbaceous model plant Arabidopsis – to investigate the expression and interactions of genes involved in secondary growth (wood formation). Detailed anatomical observations of the stem in combination with mRNA sequencing were used to assess transcriptome remodeling during xylogenesis in wild-type and woody soc1ful plants. To interpret the transcriptome changes, we constructed functional gene association networks of differentially expressed genes using the STRING database. This analysis revealed functionally enriched gene association hubs that are differentially expressed in herbaceous and woody tissues. In particular, we observed the differential expression of genes related to mechanical stress and jasmonate biosynthesis/ signaling during wood formation in soc1ful plants that may be an effect of greater tension within woody tissues. Our results suggest that habit shifts from herbaceous to woody life forms observed in many angiosperm lineages could have evolved convergently by genetic changes that modulate the gene expression and interaction network, and thereby redeploy the conserved wood developmental program.The Naturalis Biodiversity Center (FES 017/202), the Alberta Mennega Stichting, the Genome Canada Large-Scale Applied Research Program (POPCAN, project 168BIO), USDA National Institute of Food and Agriculture and AgBioResearch to PPE, a NSERC (Canada) Discovery Grant to CJD and NWO (Netherlands Science Foundation) VIDI and Ecogenomics grants to MES.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-313Xhb2016Genetic

An Extension of the Plant Ontology Project Supporting Wood Anatomy and Development Research

A wealth of information on plant anatomy and morphology is available in the current and historical literature, and molecular biologists are producing massive amounts of transcriptome and genome data that can be used to gain better insights into the development, evolution, ecology, and physiological function of plant anatomical attributes. Integrating anatomical and molecular data sets is of major importance to the field of wood science, but this is often hampered by the lack of a standardized, controlled vocabulary that allows for cross-referencing among disparate data types. One approach to overcome this obstacle is through the annotation of data using a common controlled vocabulary or “ontology” (Ashburner et al. 2000; Smith et al. 2007). An ontology is a way of representing knowledge in a given domain that includes a set of terms to describe the classes in that domain, as well as the relationships among terms. Each term can be associated with an array of data such as names, definitions, identification numbers, and genes involved. Ontologies are fundamental for unifying diverse terminologies and are increasingly used by scientists, philosophers, the military and online web search engines. In an ontology, terms are carefully defined, allowing a wide array of researchers to (1) use terms consistently in scientific publications or standardized handbooks on quality/trait evaluations, and (2) search for and integrate data linked to these terms in anatomical, genetic, genomic, and other types of biological databases.This is the publisher’s final pdf. The published article is copyrighted by the International Association of Wood Anatomists and can be found at: http://science.naturalis.nl/media/337871/lens%20et%20al-2012%20iawa%20j%20plant%20ontology.pdf)

Weak tradeoff between xylem safety and xylem-specific hydraulic efficiency across the world\u27s woody plant species.

The evolution of lignified xylem allowed for the efficient transport of water under tension, but also exposed the vascular network to the risk of gas emboli and the spread of gas between xylem conduits, thus impeding sap transport to the leaves. A well-known hypothesis proposes that the safety of xylem (its ability to resist embolism formation and spread) should trade off against xylem efficiency (its capacity to transport water). We tested this safety-efficiency hypothesis in branch xylem across 335 angiosperm and 89 gymnosperm species. Safety was considered at three levels: the xylem water potentials where 12%, 50% and 88% of maximal conductivity are lost. Although correlations between safety and efficiency were weak (r(2) \u3c 0.086), no species had high efficiency and high safety, supporting the idea for a safety-efficiency tradeoff. However, many species had low efficiency and low safety. Species with low efficiency and low safety were weakly associated (r(2) \u3c 0.02 in most cases) with higher wood density, lower leaf- to sapwood-area and shorter stature. There appears to be no persuasive explanation for the considerable number of species with both low efficiency and low safety. These species represent a real challenge for understanding the evolution of xylem

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Systematic significance of wood anatomical characters in Ericales.

Systematic significance of wood anatomial characters in Ericales I General introduction II Material and Methods III Systematic and ecological wood anatomy of Ericales IV Phylogenetic analysis of Ericales V Samenvatting VI Literature cited VII Appendix VIII Reference to published manuscriptsstatus: publishe

A comparison of paraffin and resin-based techniques used in bark anatomy

Bark anatomy is an unappreciated discipline in plant systematics, despite its great potential to reveal systematically informative features. In this paper, main reasons for the lack of detailed bark anatomical data in many plant families are identified, including problems with sectioning, terminological issues, and difficulties in observation of dilated stems. We deal with these problems by focusing on two aspects: (1) compare, discuss and improve existing sectioning and maceration techniques using two species with soft and hard bark tissues; and (2) discuss the best way to collect stem bark samples. We hope that this paper will stimulate inclusion of bark anatomical data in future systematic studies

A comparison of paraffin and resin-based techniques used in bark anatomy

Bark anatomy is an unappreciated discipline in plant systematics, despite its great potential to reveal systematically informative features. In this paper, main reasons for the lack of detailed bark anatomical data in many plant families are identified, including problems with sectioning, terminological issues, and difficulties in observation of dilated stems. We deal with these problems by focusing on two aspects: (1) compare, discuss and improve existing sectioning and maceration techniques using two species with soft and hard bark tissues; and (2) discuss the best way to collect stem bark samples. We hope that this paper will stimulate inclusion of bark anatomical data in future systematic studies.status: publishe