Introduction to the Plant DNA C-values database

Introduction

Estimating DNA C-values
The need for C-value data
The need for reference lists

The need for an electronic database

The first electronic database for DNA C-values in angiosperms
Updating the Angiosperm DNA C-values database
The Pteridophyte DNA C-values database

The Plant DNA C-values database

Release 1.0, September 2001
Release 2.0, January 2003
Release 3.0 December 2004
Release 4.0 December 2005

References

INTRODUCTION

Nuclear DNA C-value and genome size are important biodiversity characters with fundamental biological significance and many uses (Bennett and Leitch, 1995; Bennett et al., 2000). The DNA C-value of an organism is the amount of nuclear DNA in its unreplicated gametic nucleus  (Swift 1950), irrespective of the ploidy level of the taxon. (For a recent paper discussing the terms 'genome size' and 'C-value' see Greilhuber et al., 2005.)

Estimating DNA C-values (genome sizes)
The first C-values estimated for a few plants were made in the 1950s using tedious chemical extraction methods.  The subsequent development of other techniques including Feulgen microdensitometry, flow cytometry and more recently DNA image cytometry, have made estimating DNA amount both easier and faster, such that C-value data are now available for almost 5,000 plant species.

The need for C-value data
Information about C-values is used in a wide range of biological fields (e.g. see Bennett et al., 2000). Interest in such data, judging by the numbers of new estimates published, has remained high in recent years. Moreover, several authors have noted a need for additional C-value data for more plant species in order to extend their comparative studies. Thus, specific needs were noted for more grass taxa (Jasienski and Bazzaz, 1995), and for more higher order taxa among angiosperms and other land plant groups (Obermayer et al., 2002; Leitch et al., 2005).

The need for reference lists
Information on DNA amounts in different plant taxa is often hard to locate as published data are widely scattered in a diverse range of journals, whilst a significant proportion are unpublished and unavailable.
 

• Angiosperms

By 1976 Bennett had decided to start compiling lists of DNA C-values in angiosperms and to publish them. Eight extensive collected lists are now  published in hard copy form, primarily for reference purposes (Bennett and Smith, 1976; Bennett et al., 1982; Bennett and Smith, 1991; Bennett and Leitch, 1995, 1997, 2005; Bennett et al., 2000; Zonneveld et al. 2005).  Together these list C-values for over 4,400 species, cited from 466 original references, and represent c. 1.7% of the global angiosperm flora.
 
• Gymnosperms

Work on C-values in other plant groups lagged behind that in angiosperms. This issue was addressed in September 1997 when the Angiosperm Genome size workshop and discussion meeting was held at the Royal Botanic Gardens, Kew.  A key aim of the workshop was to identify major gaps in our knowledge of plant DNA C-values and to recommend targets and priorities for new work to fill them by international collaboration.  At the workshop Murray reviewed our knowledge of C-values in non-angiosperm groups and produced the first list of DNA amounts in gymnosperms (Murray 1998). The list contained C-value estimates for 117 species (corresponding to 16% of all gymnosperm species), cited from 24 original references. Since this list, C-value estimates in a further 12 original references have been published and these include data for 90 species not previously reported, but no new compiled list in hard copy has been published.
 
• Pteridophytes and bryophytes

In 1997 Murray also reviewed data for pteridophytes and bryophytes and noted that the situation was much worse with estimates for only c. 0.42% of pteridophytes and c. 0.1% for bryophytes. He also noted that locating the C-value data had been very difficult.  There was clearly a need to collate DNA amount data in these  groups and to make them easily accessible.

For pteridophytes, estimates of DNA amounts were pooled into one user-friendly reference list by Bennett and Leitch (2001).  This contained DNA C-values for just 48 pteridophyte species from eight original references and highlighted the ongoing need for work to increase knowledge in this area. Later, Obermayer et al. (2002) reported new C-values for thirty species. Nine estimates from Grime et al. (1988) have also been located, together with estimates for five species in Hanson and Leitch (2002).  However, no further compiled list has been published in hard copy.

In bryophytes there is still no equivalent pooled list of C-values published in hard copy.  C-value data are available but scattered in the literature. The largest source of data comes from Voglmayr (2000) who estimated C-values in 138 moss taxa in a carefully targeted study whose aim was to cover a representative spectrum of moss taxa. Voglmayr's paper also reviewed C-value estimates made by previous workers and is thus the closest approximation to a single reference source for C-values in bryophytes currently available in hard copy.
 

• Algae

The 1997 Angiosperm Genome Size workshop did not assess knowledge of C-values in algae.  This was not because they were seen as unimportant, but the gaps identified for several other groups seemed daunting enough.  However, once first compilations of DNA C-values for gymnosperms (Murray, 1998), pteridophytes (Obermayer et al., 2002) and bryophytes (Voglmayr, 2000) were available, the lack of readily accessible C-value data in algae became more apparent.  This major gap has now been addressed as Kapraun (2005) has published the first compilation of genome size estimates for 247 species of red (Rhodophyta), green (Chlorophyta) and brown (Phaeophyta) algae. In his paper he also reviews the considerable diversity in this character and its possible evolutionary significance.

THE NEED FOR AN ELECTRONIC DATABASE

From the above, it became clear that there was a growing need to combine available C-value estimates for different plant groups into a single, easily accessible, electronic database.

The first electronic database of DNA C-values in angiosperms (release 1.0, April 1997)
The collected lists of angiosperm DNA amounts were produced to make data more accessible for both reference and analysis purposes. However, as the number of such lists rose, finding whether an estimate for a particular species was listed, and if so, its reported size, took longer. To overcome this, in 1997 we decided to pool all the data from collected lists that had been published into one combined database for about 2,800 angiosperm species, and to make this available in an electronic form. A first version of the electronic Angiosperm DNA C-values database (release 1.0) went live in April 1997. This contained C-value data but lacked many associated details and explanatory footnotes (e.g. chromosome number, ploidy level, life cycle type, and calibration standard and techniques used) given in the original published lists.
Updating the Angiosperm DNA C-values database
Release 2.0, October 1998: On 31st October 1998 an updated version of the Angiosperm DNA C-values database (release 2.0) was released. A new user-friendly format made it possible to search and query the database for the first time.

Release 3.0, December 2000: Following publication of a sixth list of DNA amounts (Bennett et al., 2000) which included first DNA C-value estimates for 691 species not included in any of the previous five lists, it became necessary to update the database again.   Release 3.0 went live in December 2000. Not only did it contain C-value data for an additional 691species, but it also gave 1C DNA amounts expressed in megabase pairs (Mb) for the first time. (The factor used to convert picograms to Mb was 1 pg = 980 Mb (Cavalier-Smith, 1985; Bennett et al., 2000).)

Further releases : Since 2000 further releases have gone live. In release 4.0 (January 2003) new systematic and reference data were added, whereas in release 5.0 and 6.0 additional C-value data were added for over 1200 species including 939 new to the database. Data for releases 5.0 and 6.0 were taken from Bennett and Leitch (2005) and Zonneveld et al. (2005) respectively.
 

The Pteridophyte DNA C-values database (release 1.0, December 2000)
To compliment the growing Angiosperm DNA C-values database, the first electronic database for a non-angiosperm group - the pteridophytes, was release in December 2000. This contained C-value estimates for 48 species given in Bennett and Leitch (2001).  Additional information on spore type (i.e. homosporous or heterosporous), sperm flagella number (i.e. biflagellate or multiflagellate), sporangial type (i.e. eusporangiate or leptosporangiate), chromosome number and ploidy level was also given where known.

THE PLANT DNA C-VALUES DATABASE

Key recommendation 2  of the Angiosperm Genome Size workshop (1997) identified a clear need 'To improve accessibility to plant C-value data by making them readily available for reference purposes as published reference lists and/or on the internet in one plant DNA C-values database'.

Release 1.0,  September 2001

Release 1.0 of the Plant DNA C-values database contributed significantly to fulfilling this recommendation.  By incorporating C-value data for all embryophyte plant groups (i.e. angiosperms, pteridophytes, gymnosperms and bryophytes) into the Plant DNA C-values database, a single compilation of C-value data for land plants was available for the first time.

Release 2.0, January 2003

Following Release 1.0, work continued to develop and extend the Plant DNA C-values database and a second release went live in January 2003 with four major improvments.

1.  C-value estimates for additional pteridophytes and gymnosperms were made available
2.  Additional C-value estimates for a species could be viewed
3.  The original reference sources for C-value estimates could be viewed
4.  In angiosperms, a new systematic option using the APG families for searching the database was made available

Release 3.0, December 2004

As further C-value data became available this was added to the database and release 3.0 went live in December 2004.

1. New data for angiosperms, gymnosperms, pteridophytes and bryophytes were added
For angiosperms, C-values for 804 species (628 of which were new to the database) were collated from 88 original references into a sixth supplementary list of DNA amounts (Bennett and Leitch 2005).  These were added to the database.

For gymnosperms, pteridophytes and bryophytes no new compiled lists have been published, but new data from individual research papers and communications were added to the database.

2. Algal C-values now available online
Release 3.0 also included 253 algal DNA C-values for the first time.  Following the publication of a compiled list of 247 algal species by Kapraun (2005) these values, together with six additional species were entered into the database and made available online.


Release 4.0, October 2005

Following the publication of Zonneveld et al. (2005), C-values for a further 411 species (308 of which are new to the database) have been added.

In summary, the Plant DNA C-values database (release 4.0, Oct. 2005) contains C-values for 5150 species comprising:

               Angiosperm DNA C-values (4427 species)
               Gymnosperm DNA C-values (207 species)
               Pteridophyte DNA C-values (87 species)
               Bryophyte DNA C-values (176 species)

     Algal DNA C-values: 253 species comprising:
                 Chlorophyta (green algae) - 91 species
                 Phaeophyta (brown algae) - 44 species
                 Rhodphyta (red algae) - 118 species


For full details of these updates go to Updates and releases

Users can choose between analysing C-value data across different groups of plants (using the Plant DNA C-values database), or searching just part of the database (e.g. angiosperms) by selecting the specific plant group of interest (i.e. angiosperms, gymnosperms, pteridophytes, bryophytes or algae) from the Plant DNA C-values homepage.

Searching a particular plant group (e.g. selecting just the angiosperms) also gives the option of quering on the following additional fields.
 
 
 

Angiosperm C-values	Angiosperm group (i.e. monocots, eudicot or basal angiosperm) Life cycle type Family (traditional or APG)

 

Gymnosperm C-values	Gymnosperm group (i.e. Cycadales, Ginkgoales, Gnetales, Pinaceae, or Coniferales II (all conifers excluding Pinaceae) Sperm flagella number (i.e. multiflagellate or none)

 

Pteridophyte C-values	Pteridophyte group (i.e. Lycopodiophyta, Equisetophyta, Psilotaceae, or Polypodiophyta) Spore type (i.e. homosporous or heterosporous) Sporangium type (i.e. eusporangiate or leptosporangiate) Sperm flagella number (i.e. biflagellate or multiflagellate)

 

Bryophyte C-values	Bryophyte  group (i.e. hornwort, liverworts, mosses)


 

Algal C-values	Algal group (i.e. Chlorophyta, Phaeophyta, Rhodophyta)


 
 
For help with searching and quering the database please go to the page: How to search the Plant DNA C-values database.

REFERENCES

APG. 1998. An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden 85: 531-553.

APG II. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants. Botanical Journal of the Linnean Society 141: 399-436.

Bennett MD, Smith JB. 1976. Nuclear DNA amounts in angiosperms. Philosophical Transactions of the Royal Society of London, B 274: 227-274.

Bennett MD, Smith JB. 1991. Nuclear DNA amounts in angiosperms. Philosophical Transactions of the Royal Society of London, B 334: 309-345.

Bennett MD, Smith JB, Heslop-Harrison JS. 1982. Nuclear DNA amounts in angiosperms. Proceedings of the Royal Society of London, B 16:179-199.

Bennett MD, Leitch IJ. 1995. Nuclear DNA amounts in angiosperms. Annals of Botany, 76: 113-176.

Bennett MD, Leitch IJ.1997. Nuclear DNA amounts in angiosperms - 583 new estimates. Annals of Botany, 80: 169-196.

Bennett MD, Leitch IJ.  2001. Nuclear DNA amounts in pteridophytes. Annals of Botany, 87: 335-345.

Bennett MD, Leitch IJ. 2005. Nuclear DNA amounts in angiosperms - progress, problems and prospects. Annals of Botany 95: 45-90.

Bennett MD, Bhandol P, Leitch IJ.  2000. Nuclear DNA amounts in angiosperms and their modern Uses 807 new estimates. Annals of Botany 86:859-909.

Cavalier-Smith T.  1985.  The evolution of genome size. Chichester: John Wiley and Sons.

Greilhuber J, Dolezel J, Lysak MA, Bennett MD. 2005. The origin, evolution and proposed stabilization of the terms 'Genome Size' and 'C-Value' to describe nuclear DNA contents. Annals of Botany 95: 255-260.

Grime JP, Hodgson JG, Hunt R. 1988. Comparative plant ecology: a functional approach to common British species. London: Unwin Hyman.

Hanson L, Leitch IJ. 2002. DNA amounts for five pteridophyte species fill phylogenetic gaps in C-value data. Botanical Journal of the Linnean Society 140: 169-173.

Jasienski M, Bazzaz FA. 1995. Genome size and high CO₂. Nature 376:559-560.

Kapraun DF. 2005. Nuclear DNA content estimates in multicellular eukaryotic green, red and brown algae: phylogenetic considerations. Annals of Botany 95: 7-44.

Leitch IJ, Chase MW, Bennett MD.  1998. Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. Annals of Botany 82 (Supplement A): 85-94.

Leitch IJ, Hanson L, Winfield M, Parker J, Bennett MD.  2001. Nuclear DNA C-values complete familial representation in Gymnosperms. Annals of Botany 88: 843-849.

Leitch IJ, Soltis DE, Soltis PS, Bennett MD. 2005. Evolution of DNA amounts across land plants (Embryophyta). Annals of Botany 95: 207-217.

Murray BG. 1998. Nuclear DNA amounts in gymnosperms. Annals of Botany 82 (Supplement A): 3-15.

Obermayer R, Leitch IJ, Hanson L, Bennett MD. 2002. Nuclear DNA C-values in 30 species double the familial representation in pteridophytes. Annals of Botany 90: 209-217.

Swift H. 1950. The constancy of deoxyribose nucleic acid in plant nuclei. Proceedings of the National Academy of Sciences 36: 643-654.

Voglmayr  H. 2000. Nuclear DNA amounts in mosses (Musci). Annals of Botany 85: 531-546.

Zonneveld BJM, Leitch IJ, Bennett MD. 2005. First nuclear DNA amounts in more than 300 angiosperms. Annals of Botany 96: 229-244.