ArticlePDF Available

Abstract

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 devel-opment, 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 research-ers 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. The Plant Ontology (PO, www.plantontology.org) is a structured vocabulary and database resource that links plant anatomy and development to gene expression and phenotypic datasets from all areas of plant biology (Jaiswal et al.
IAWA Journal, Vol. 33 (2), 2012: 113–117
AN EXTENSION OF THE PLANT ONTOLOGY PROJECT
SUPPORTING WOOD ANATOMY AND DEVELOPMENT RESEARCH
Frederic Lens1*, Laurel Cooper2, Maria Alejandra Gandolfo3,
Andrew Groover4, Pankaj Jaiswal2, Barbara Lachenbruch5, Rachel Spicer6,
Margaret E. Staton7, Dennis W. Stevenson8, Ramona L. Walls8 and
Jill Wegrzyn9
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 devel-
opment, evolution, ecology, and physiological function of plant anatomical attributes.
Integrating anatomical and molecular data sets is of major importance to the eld 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, denitions, identication 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 dened, allowing a wide array of research-
ers to (1) use terms consistently in scientic 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.
The Plant Ontology (PO, www.plantontology.org) is a structured vocabulary and
database resource that links plant anatomy and development to gene expression and
phenotypic datasets from all areas of plant biology (Jaiswal et al. 2005; Avraham
et al. 2008). The Wood Ontology project (http://wiki.plantontology.org/index.php/
Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda), which was recently
initiated during the Wood Ontology Workshop at the New York Botanical Garden on
1) Netherlands Centre for Biodiversity Naturalis, P.O. Box 9514, 2300 RA Leiden, The Netherlands.
2) Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
3) L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA.
4) Institute of Forest Genetics, US Forest Service, Davis, CA 95618, USA.
5) Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR 97331, USA.
6) Department of Botany, Connecticut College, New London, CT O6320, USA.
7) Clemson University Genomics Institute, Clemson University, 51 New Cherry Street, Clemson,
SC 29634, USA.
8) New York Botanical Garden, Bronx, New York 10458, USA.
9) Department of Plant Sciences, Davis, CA 95616, USA.
*) Corresponding author: Frederic Lens [E-mail: lens@nhn.leidenuniv.nl].
IAWA Journal, Vol. 33 (2), 2012
114
Figure 1. A simple ontology diagram showing a subset of wood anatomy terms from the Plant
Ontology. This diagram illustrates the two most important relationships in the ontology (is_a
and part_of) and shows how data annotations are associated with ontology terms. For example, a
tracheid (PO:0000301) is_a type of tracheary element (PO:0000290) and all tracheary elements
are part_of some xylem tissue (PO:0005352). Using the relationships specied in this ontology,
a computer or human could infer that any tracheid is part_of some xylem tissue. Similarly, it
can be inferred that a tracheid is a plant cell (PO:0009002), that xylem is a type of plant tissue,
and that both are plant structures (PO:0009011).
The ontology also facilitates genomics studies through data annotations, such as genes expressed
in plant structures represented by terms in the Plant Ontology. For example, px1, a class III
peroxidase-encoding gene from Picea abies, is associated to tracheid via its effect on lignin
biosynthesis during tracheid development (Marjamaa et al. 2006). Since a tracheid is part_of
xylem, xylem also exhibits the phenotypic qualities of px1. Similarly, PgMYB2, a transcription
factor that acts as regulator of lignin and phenylpropanoid metabolism during wood forma-
tion in Picea glauca, is associated to the general term xylem, since the experiment did not
specify the exact cell type it was expressed in (Bedon et al. 2007). If a user searches the Plant
Ontology for annotations on xylem and its subtypes, both px1 and PgMYB2 will be retrieved.
If the homologs of these genes are known for other tree species, a researcher can query the mutant
and gene expression data for those species to look for genes regulating wood quality and devel-
opment.
115
Lens et al.The Wood Ontology project
February 5 to 7th, 2012, is a subset of the Plant Ontology with the goal of providing a
uniform vocabulary and set of logical relations for wood anatomical characters, stages
of wood development, and wood qualities. This wood-related vocabulary should be
particularly useful for annotating molecular and genomic datasets for wood formation
(e.g., Schrader et al. 2004; Tuskan et al. 2006; Melzer et al. 2008; Dharmawardhana
et al. 2010; Agusti et al. 2011) and establishing a semantic framework for compara-
tive queries across data sets from various species. The Wood Ontology is thus being
developed in collaboration with genomic resources for trees, such as TreeGenes (http://
dendrome.ucdavis.edu/treegenes) and the Hardwood Genomics Project (http://www.
hardwoodgenomics.org).
In the Plant Ontology, the terms are each assigned a unique identier (PO:xxxxxxx)
and are connected by dened relationships. For example, the is_a relation species
that one term (e.g., a structure or development stage) is a subtype of another term.
Similarly, the part_of relation describes how one term is a part of another term. For
example, Figure 1 shows that every tracheid (PO:0000301) is_a tracheary element
(PO:0000290), which is_a plant cell (PO:0009002), and every tracheary element is
part_of some xylem tissue (PO:0005352), which is_a vascular tissue (PO:0009015).
The network of terms in an ontology allows a user or a computer to interpret and ana-
lyze the relationships consistently. For example, using the relationships in Figure 1,
a computer asked to retrieve data associated with the query term xylem” would also
return any data associated with tracheary element, and all of its subtypes, including,
amongst others, tracheid.
Why is it important to develop such a resource for our IAWA community? Increasingly,
wood scientists from different disciplines (anatomy, archeology, dendrology, genom-
ics, mechanics, physiology, technology) are carrying out multidisciplinary research
using terminology that may or may not be consistently applied. This often happens
because two different communities either use similar terms to describe different enti-
ties or use different terms to describe the same entity, such as the words for juvenile,
crown-formed, and core wood (Amarasekara & Denne 2002). The wood anatomical
community has played a leading role in establishing a controlled glossary (IAWA
Committee 1964) and lists of anatomical features useful for wood identication (IAWA
Committee 1989, 2004) and bark identication (Trockenbrodt 1990). However, our
efforts are an exception rather than the rule in the broader eld of plant science, and
the current glossary of terms is not interpreted in a relational context. By incorporat-
ing the IAWA glossary and feature lists into the PO, these vocabularies will not only
be accessible to a wider audience, but will also be accessible to computer algorithms
to perform complex database queries. For example, it would be possible to retrieve a
list of genes involved in cell wall metabolism that are expressed in all of the cell types
(or any given cell type) found in xylem. Thus, the Wood Ontology will be the means
by which new genomic and molecular data are integrated with wood anatomical data.
Finally, by expanding the PO to include a comprehensive set of terms associated with
wood anatomy, we will forge new links between research on secondary growth and
that of the larger plant biology community.
IAWA Journal, Vol. 33 (2), 2012
116
The Wood Ontology project will provide a structured vocabulary and database resource
that will be valuable for all scientists, including the IAWA community. To maximize
the utility of the resource and analyses it empowers, it is important for researchers to
adopt the use of the ontology terms in the collection and dissemination of their data.
The PO website (www.plantontology.org) is the main portal for the Plant Ontology,
and presents the current version. Researchers can contribute to the Wood Ontology by
suggesting terms or commenting on existing denitions using the SourceForge tracker
site (http://sourceforge.net/tracker/?group_id=76834&atid=835555) after register-
ing and logging in. Specic questions can also be sent via e-mail to the PO project
by lling out the web based feedback form (http://plantontology.org/db/feedback/
send_feedback?refer_to=/index.html), which can be reached via the “Feedback” link
from the PO home page.
ACKNOWLEDGMENTS
The authors wish to thank Barry Smith (University at Buffalo, NY, USA) for advice on ontology build-
ing during the workshop. This work is supported by the National Science Foundation - IOS #0822201
(PI: P Jaiswal, co-PIs: MA Gandolfo, DW Stevenson).
REFERENCES:
Agusti, J., R. Lichtenberger, M. Schwarz, L. Nehlin & T. Greb. 2011. Characterization of tran-
scriptome remodeling during cambium formation identies MOL1 and RUL1 as opposing
regulators of secondary growth. PLoS Genet. 7: e1001312.
Amarasekara, H. & M. P. Denne. 2002. Effects of crown size on wood characteristics of Cor-
sican pine in relation to denitions of juvenile wood, crown formed wood and core wood.
Forestry 75: 51–61.
Ashburner, M., C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolins-
ki, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis,
J.C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin & G. Sherlock. 2000. Gene ontology:
tool for the unication of biology. The Gene Ontology Consortium. Nat. Genet. 25: 25–29.
Avraham, S., C.-W. Tung, K. Ilic, P. Jaiswal, E. A. Kellogg, S. McCouch, A. Pujar, L. Reiser,
S.Y. Rhee, M.M. Sachs, M. Schaeffer, L. Stein, P. Stevens, L. Vincent, F. Zapata & D. Ware.
2008. The Plant Ontology Database: a community resource for plant structure and devel-
opmental stages controlled vocabulary and annotations. Nucleic Acids Res. 36, Database
issue D449–D454.
Bedon, F., J. Grima-Pettenati & J. Mackay. 2007. Conifer R2R3-MYB transcription factors:
sequence analyses and gene expression in wood-forming tissues of white spruce (Picea
glauca). BMC Plant Biol. 7: 17.
Dharmawardhana, P., A.M. Brunner & S.H. Strauss. 2010. Genome-wide transcriptome anal-
ysis of the transition from primary to secondary stem development in Populus trichocarpa.
BMC Genom. 11: 150.
IAWA Committee on Nomenclature. 1964. Multilingual glossary of terms used in wood anatomy.
Konkordia, Winterthur, Switzerland. 185 pp.
IAWA Committee. 1989. IAWA list of microscopic features for hardwood identication. IAWA
Bull. n.s. 10: 219–332.
IAWA Committee. 2004. IAWA list of microscopic features for softwood identication. IAWA
J. 25: 1–70.
117
Lens et al.The Wood Ontology project
Jaiswal, P., S. Avraham, K. Ilic, E.A. Kellogg, S. McCouch, A. Pujar, L. Reiser, S.Y. Rhee,
M.M. Sachs, M. Schaeffer, L. Stein, P. Stevens, L. Vincent, D. Ware & F. Zapata. 2005.
Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp.
Funct. Genom. 6: 388–397.
Marjamaa, K., K. Hildén, E. Kukkola, M. Lehtonen, H. Holkeri, P. Haapaniemi, S. Koutaniemi,
T.H. Teeri, K. Fagerstedt & T. Lundell. 2006. Cloning, characterization and localization of
three novel class III peroxidases in lignifying xylem of Norway spruce (Picea abies). Plant
Mol. Biol. 61: 719–732.
Melzer, S., F. Lens, J. Gennen, S. Vanneste, A. Rhode & T. Beeckman. 2008. Flowering-time
genes modulate meristem determinacy and growth form in Arabidopsis. Nat. Genet. 40:
1489–1492.
Schrader, J., J. Nilsson, E. Mellerowicz, A. Berglund, P. Nilsson, M. Hertzberg & G. Sandberg.
2004. A high-resolution transcript prole across the wood-forming meristem of poplar identi-
es potential regulators of cambial stem cell identity. The Plant Cell 16: 2278–2292.
Smith, B., M. Ashburner, C. Rosse, J. Bard, W. Bug, W. Ceusters, L. J. Goldberg, K. Eilbeck,
A. Ireland, C.J. Mungall, The OBI Consortium, N. Leontis, P. Rocca-Serra, A. Ruttenberg,
S.-A. Sanone, R. H. Scheuermann N. Shah, P.L. Whetzel & S. Lewis. 2007. The OBO
Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat.
Biotech. 25: 1251–1255.
Trockenbrodt, M. 1990. Survey and discussion of the terminology used in bark anatomy. IAWA
Bull. n.s. 11: 141–166.
Tuskan, G. A., S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph,
S. Rombauts, A. Salamov, J. Schein, L. Sterck, A. Aerts, R.R. Bhalerao, R. P. Bhalerao,
D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot,
J. Chapman, G.-L. Chen, D. Cooper, P.M. Coutinho, J. Couturier, S. Covert, Q. Cronk,
R. Cunningham, J. Davis, S. Degroeve, A. Déjardin, C. dePamphilis, J. Detter, B. Dirks,
I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov,
J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat,
D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jorgensen,
C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler,
U. Kalluri, F. Larimer, J. Leebens-Mack, J.-C. Leplé , P. Locascio,Y. Lou, S. Lucas, F. Martin,
B. Montanini, C. Napoli, D.R. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda,
G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi,
K. Ritland, P. Rouzé, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui,
F. Sterky, A. Terry, C.-J. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler,
G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. Van de Peer & D. Rokhsar. 2006.
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:
1596–1604.
... To study such innovations in habits and growth forms, researchers have typically taken a three-pronged approach. They have (1) generated a detailed understanding of plant anatomy through extensive descriptive work (Carlquist, 1996, among many others) and ensured corresponding terminology was used consistently throughout their collaborative efforts (IAWA, 1964), allowing the development of a comprehensive plant trait ontology (Lens et al., 2012); (2) built and maintained extensive tissue collections, even though those collections often require nonstandard preservation techniques (e.g., spirit collections and wood samples housed separately from herbarium sheets); and (3) employed up-to-date methods in comparative analyses to better understand the intersection of evolution and development in the context of phylogenies (Pace et al., 2009;Chery et al., 2020). ...
Article
Full-text available
Herbaceous plants collectively known as geophytes, which regrow from belowground buds, are distributed around the globe and throughout the land plant tree of life. The geophytic habit is an evolutionarily and ecologically important growth form in plants, permitting novel life history strategies, enabling the occupation of more seasonal climates, mediating interactions between plants and their water and nutrient resources, and influencing macroevolutionary patterns by enabling differential diversification and adaptation. These taxa are excellent study systems for understanding how convergence on a similar growth habit (i.e., geophytism) can occur via different morphological and developmental mechanisms. Despite the importance of belowground organs for characterizing whole‐plant morphological diversity, the morphology and evolution of these organs have been vastly understudied with most research focusing on only a few crop systems. Here, we clarify the terminology commonly used (and sometimes misused) to describe geophytes and their underground organs and highlight key evolutionary patterns of the belowground morphology of geophytic plants. Additionally, we advocate for increasing resources for geophyte research and implementing standardized ontological definitions of geophytic organs to improve our understanding of the factors controlling, promoting, and maintaining geophyte diversity.
... Variations in these traits underlie differences between key morphological features with evolutionary and ecological importance, e.g., imbricate vs. tunicate bulbs (see Tribble et al., 2021, in this issue), and demonstrate the need to further develop the Plant Ontology. In addition to capturing morphological diversity of particular taxa, ontologies can focus on specific traits such as wood anatomy (Lens et al., 2012). For example, a tracheary element is a plant cell and part of the xylem, which can be further designated as primary or secondary xylem. ...
... Two independent efforts have brought tree biologists and computational teams to the same table to curate traits and structures. A wood anatomy and development working group contributed to PO through the partial conversion of established vocabularies in the Glossary of Terms used in Wood Anatomy (Lens et al. 2012). While this glossary is known to the research community, the term definitions lose meaning when adopted in other disciplines classifying the same structures. ...
Article
Full-text available
Sequencing technologies and bioinformatic approaches are now available to resolve the challenges associated with complex and heterozygous genomes. Increased access to less expensive and more effective instrumentation will contribute to a wealth of high‐quality plant genomes in the next few years. In the meantime, more than 370 tree species are associated with public projects in primary repositories that are interrogating expression profiles, identifying variants, or analyzing targeted capture without a high‐quality reference genome. Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes. This data contributes to forest tree biology but the associated sequence remains trapped in supplemental files that are poorly integrated in plant community databases and comparative genomics platforms. Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non‐model plant species. Unique to forest trees with large populations that are long lived, outcrossing, and genetically diverse, the phenotypic and environmental metrics associated with georeferenced populations are just as important as the genomic data sampled for each individual. To address questions related to forest health and productivity, cyberinfrastructure must keep pace with the magnitude of genomic and phenomic sampling of larger populations. This review examines the current landscape of cyberinfrastructure, with an emphasis on best practices to align community data with the Findable, Accessible, Interoperable, and Reusable (FAIR) guidelines. This article is protected by copyright. All rights reserved.
... The ability to provide this, and cross-site query, relies heavily on the curation of ontologies to describe data housed in these frameworks. Initiatives that curate woody plant ontologies, to describe plant structures and measured traits, are critical components of forest tree database cross-talk (Jaiswal et al., 2005;Lens et al., 2012;Cooper et al., 2018). When these terms are provided within the framework of recommended standards for data collection, such as the Minimal Information About a Plant Phenotyping Experiment (MIAPPE), opportunities for analytical pipelines to evaluate complex data becomes a reality (Krajewski et al., 2015). ...
Article
Full-text available
Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.
... For example, classes for seed trichome development stages were added at the request of scientists describing gene expression in cotton, but because these stages have been described generically, they can be used for any plant with seed trichomes. PO curators continue to work with experts from different communities to incorporate new development stage terms, such as those for secondary xylem (wood) development stages (Lens et al., 2012). Work is ongoing to add new terms for flagellate plants, through a collaboration with the biodiversity community (Endara et al., 2018). ...
Article
Full-text available
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database (http://www.planteome.org) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.
... However, variation in the dimensions and the arrangement of these cells provide a challenge to anyone who aims to describe and understand quantitative and qualitative differences between wood samples. The challenge lies not only in the consistent application and interpretation of terms (Lens et al., 2012), but also in how we deal with a dynamic continuum (i.e., fuzzy morphology sensu Agnes Arber and Rolf Sattler) that includes intergradations, intermediate forms, analogous and homologous features (Sattler and Rutishauser, 1997). ...
Thesis
Full-text available
Parenchyma represents an important interconnected three-dimensional living tissue in secondary xylem of woody seed plants, with functions ranging from transport and storage to defence and biomechanics, along with less understood functions, such as in long-distance water transport. We lack a large-scale analysis of ecological traits associated with ray parenchyma (RP) and axial parenchyma (AP). Here, we explore global trends in the AP and RP fraction per cross-sectional wood area based on literature data, including 1,727 entries from three major biomes (temperate, subtropical and tropical). We found a 29-fold variation in RAP fraction, where temperature was found to be the biggest driver of RAP (RP+AP) levels, followed by precipitation, with the latter showing a significant but negative relationship with RAP, demonstrating an increase in RAP towards drier sites. RAP fractions were higher in tropical than temperate angiosperm trees (21.1 vs 36.2 %), respectively, where AP was found to be the most versatile parenchyma type resulting in the sharp rise of RAP in the tropics, while RP remained relatively constant. Succulents (including pachycauls) and lianas were found to have higher RAP fractions than non-succulent angiosperm trees and conifers, with the latter having the lowest RAP fractions, as expected. The observed trends were interpreted with respect to the various functions of RAP in plants. We tested one of the hypotheses arising from the global analysis, and found RAP or/and ‘living’ fibres levels in a range of temperate species to be the uppermost limit for NSC storage, demonstrating that species with higher RAP and/or living fibre fractions in the selected species have a greater capacity for carbon storage: the same trend was not found for lowland tropical species. Also, starch accumulation was equally distributed across both RP and AP (including contact cells) in most of the temperate species analysed at the onset of winter, a trend not observed in the tropical species, where, although evident, the distribution was far sparser, with the exception of Brosimum sp. In summary, our results form a strong basis in which to better understand the functional implications of the great anatomical variability in wood parenchyma.
... However, variation in the dimensions and the arrangement of these cells provide a challenge to anyone who aims to describe and understand quantitative and qualitative differences between wood samples. The challenge lies not only in the consistent application and interpretation of terms (Lens et al. 2012), but also in how we deal with a dynamic continuum (i.e., fuzzy morphology sensu Agnes Arber & Rolf Sattler) that includes intergradations, intermediate forms, analogous and homologous features (Sattler & Rutishauser 1997). ...
... The PO SourceForge tracker (http://sourceforge.net/tracker/?group_id=76834&atid=8355 55) is the main avenue for new term requests and/or modifications and collaborations for larger scale projects. Outreach workshops and presentations have been held at national and international conferences, and in-house workshops are held with specific groups of domain experts such as wood anatomists (Lens et al. 2012). For more information, see the PO outreach page (http://wiki.plantontology.org/index.php/POC_ ...
Article
The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
... Compared to plant anatomical entities, ontologies for plant qualities may be still significantly under-developed for systematic descriptions of plant characters, as is shown by a review of existing glossaries and ontologies (Cui, 2010a). PO curators are working with members of the scientific community, including FNA and PATO curators, members of the International Association of Wood Anatomists (IAWA; Lens et al., 2012), and the databases that contribute to the PO, to enrich the list of quality descriptors for plants. A number of terms for plant qualities already exist in PATO, along with many terms relating to generally applicable qualities such as shape, size, or texture, and the ability to construct meaningful EQ statements for systematic work using PATO and other existing ontologies has already been clearly demonstrated (Dahdul et al., 2010). ...
Article
Full-text available
Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.
Article
Full-text available
Capsicum is a genus of flowering plants in the Solanaceae family in which the members are well known to have a high economic value. The Capsicum fruits, which are popularly known as peppers or chili, have been widely used by people worldwide. It serves as a spice and raw material for many products such as sauce, food coloring, and medicine. For many years, scientists have studied this plant to optimize its production. A tremendous amount of knowledge has been obtained and shared, as reflected in multiple knowledge-based systems, databases, or information systems. An approach to knowledge-sharing is through the adoption of a common ontology to eliminate knowledge understanding discrepancy. Unfortunately, most of the knowledge-sharing solutions are intended for scientists who are familiar with the subject. On the other hand, there are groups of potential users that could benefit from such systems but have minimal knowledge of the subject. For these non-expert users, finding relevant information from a less familiar knowledge base would be daunting. More than that, users have various degrees of understanding of the available content in the knowledge base. This understanding discrepancy raises a personalization problem. In this paper, we introduce a solution to overcome this challenge. First, we developed an ontology to facilitate knowledge-sharing about Capsicum to non-expert users. Second, we developed a personalized faceted search algorithm that provides multiple structured ways to explore the knowledge base. The algorithm addresses the personalization problem by identifying the degree of understanding about the subject from each user. In this way, non-expert users could explore a knowledge base of Capsicum efficiently. Our solution characterized users into four groups. As a result, our faceted search algorithm defines four types of matching mechanisms, including three ranking mechanisms as the core of our solution. In order to evaluate the proposed method, we measured the predictability degree of produced list of facets. Our findings indicated that the proposed matching mechanisms could tolerate various query types, and a high degree of predictability can be achieved by combining multiple ranking mechanisms. Furthermore, it demonstrates that our approach has a high potential contribution to biodiversity science in general, where many knowledge-based systems have been developed with limited access to users outside of the domain.
Article
Full-text available
With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal region of the developing shoot provides a steep developmental gradient from primary to secondary growth that facilitates identification of genes that play specialized functions during each of these phases of growth. Using a genomic microarray representing the majority of the transcriptome, we profiled gene expression in stem segments that spanned primary to secondary growth. We found 3,016 genes that were differentially expressed during stem development (Q-value </= 0.05; >2-fold expression variation), and 15% of these genes encode proteins with no significant identities to known genes. We identified all gene family members putatively involved in secondary growth for carbohydrate active enzymes, tubulins, actins, actin depolymerizing factors, fasciclin-like AGPs, and vascular development-associated transcription factors. Almost 70% of expressed transcription factors were upregulated during the transition to secondary growth. The primary shoot elongation region of the stem contained specific carbohydrate active enzyme and expansin family members that are likely to function in primary cell wall synthesis and modification. Genes involved in plant defense and protective functions were also dominant in the primary growth region. Our results describe the global patterns of gene expression that occur during the transition from primary to secondary stem growth. We were able to identify three major patterns of gene expression and over-represented gene ontology categories during stem development. The new regulatory factors and cell wall biogenesis genes that we identified provide candidate genes for further functional characterization, as well as new tools for molecular breeding and biotechnology aimed at improvement of tree growth rate, crown form, and wood quality.
Article
Full-text available
Current use of the terms 'juvenile wood', 'crown formed wood' and 'core wood' is confusing: some authors have used the terms synonymously, while others have used each term in a more restricted sense to imply the region of a log where wood structure and properties are influenced by ring number from the pith (or distance from it), or by crown size. The present work was designed to clarify the use of these terms, since their definition is relevant to interpretation of the influence of silvicultural management on the wood quality of a log. Wood production and properties were studied in 23-year-old suppressed, co-dominant and dominant Corsican pine (Pinus nigra var. maritima) trees, in relation to crown size as determined by leaf dry weight profiles. At comparable ring number from the pith, differences in crown size from suppressed to dominant tree class resulted in a substantial increase in average ring width, decrease in mean percentage latewood, MOR, MOE and maximum compression strength, inconclusive differences in mean specific gravity, and negligible differences in tracheid length. From these trends, it is here suggested that 'juvenile wood' should be defined as the region around the pith in which there are inherent changes in structural characteristics associated with cambial age, independent of crown influences. The term 'crown formed' wood should be used to describe fluctuations in wood structure associated with the size of the crown, which are superimposed upon the inherent trends due to cambial age. The term 'core wood' should be retained for use in a more generalized sense, indicating the central region of the log where structure and properties are variable and differ from those of the outer wood.
Article
Full-text available
The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved.
Article
Full-text available
Several members of the R2R3-MYB family of transcription factors act as regulators of lignin and phenylpropanoid metabolism during wood formation in angiosperm and gymnosperm plants. The angiosperm Arabidopsis has over one hundred R2R3-MYBs genes; however, only a few members of this family have been discovered in gymnosperms. We isolated and characterised full-length cDNAs encoding R2R3-MYB genes from the gymnosperms white spruce, Picea glauca (13 sequences), and loblolly pine, Pinus taeda L. (five sequences). Sequence similarities and phylogenetic analyses placed the spruce and pine sequences in diverse subgroups of the large R2R3-MYB family, although several of the sequences clustered closely together. We searched the highly variable C-terminal region of diverse plant MYBs for conserved amino acid sequences and identified 20 motifs in the spruce MYBs, nine of which have not previously been reported and three of which are specific to conifers. The number and length of the introns in spruce MYB genes varied significantly, but their positions were well conserved relative to angiosperm MYB genes. Quantitative RTPCR of MYB genes transcript abundance in root and stem tissues revealed diverse expression patterns; three MYB genes were preferentially expressed in secondary xylem, whereas others were preferentially expressed in phloem or were ubiquitous. The MYB genes expressed in xylem, and three others, were up-regulated in the compression wood of leaning trees within 76 hours of induction. Our survey of 18 conifer R2R3-MYB genes clearly showed a gene family structure similar to that of Arabidopsis. Three of the sequences are likely to play a role in lignin metabolism and/or wood formation in gymnosperm trees, including a close homolog of the loblolly pine PtMYB4, shown to regulate lignin biosynthesis in transgenic tobacco.
Article
Full-text available
Cell-to-cell communication is crucial for the development of multicellular organisms, especially during the generation of new tissues and organs. Secondary growth--the lateral expansion of plant growth axes--is a highly dynamic process that depends on the activity of the cambium. The cambium is a stem cell-like tissue whose activity is responsible for wood production and, thus, for the establishment of extended shoot and root systems. Attempts to study cambium regulation at the molecular level have been hampered by the limitations of performing genetic analyses in trees and by the difficulty of accessing this tissue in model systems such as Arabidopsis thaliana. Here, we describe the roles of two receptor-like kinases, REDUCED IN LATERAL GROWTH1 (RUL1) and MORE LATERAL GROWTH1 (MOL1), as opposing regulators of cambium activity. Their identification was facilitated by a novel in vitro system in which cambium formation is induced in isolated Arabidopsis stem fragments. By combining this system with laser capture microdissection, we characterized transcriptome remodeling in a tissue- and stage-specific manner and identified series of genes induced during different phases of cambium formation. In summary, we provide a means for investigating cambium regulation in unprecedented depth and present two signaling components that control a process responsible for the accumulation of a large proportion of terrestrial biomass.
Article
Full-text available
Plants have evolved annual and perennial life forms as alternative strategies to adapt reproduction and survival to environmental constraints. In isolated situations, such as islands, woody perennials have evolved repeatedly from annual ancestors. Although the molecular basis of the rapid evolution of insular woodiness is unknown, the molecular difference between perennials and annuals might be rather small, and a change between these life strategies might not require major genetic innovations. Developmental regulators can strongly affect evolutionary variation and genes involved in meristem transitions are good candidates for a switch in growth habit. We found that the MADS box proteins SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FRUITFULL (FUL) not only control flowering time, but also affect determinacy of all meristems. In addition, downregulation of both proteins established phenotypes common to the lifestyle of perennial plants, suggesting their involvement in the prevention of secondary growth and longevity in annual life forms.