Pete McQuilton and Richard Smith of Nowomics have pulled a load of information on Arabidopsis trends for us to write this fascinating guest blog post. Nowomics is a new website that fetches data from many biological databases every day and works out what’s changed, and finds genes and species names mentioned in new PubMed abstracts. This lets users (this can be anyone – it’s free!) to follow genes and gene ontology terms to create a personalised news feed of new papers and data.
Arabidopsis thaliana, the humble model organism for flowering plants, has been studied for over 140 years. Discovered by Johannes Thal (hence the name thaliana), the mouse-ear cress is a member of the mustard family (Brassicaceae), alongside such luminaries as cabbage and radish. With it’s relatively small sequenced genome (114.5mb/125Mb total), rapid life cycle (about 6 weeks from germination to mature seed), prolific seed production and many genetic tools and mutants, Arabidopsis is a wonderful model organism for basic research in genetics and molecular biology.
As part of a series of blog posts at Nowomics we have examined the publication trends in Arabidopsis-related research. We’ve extracted data on primary research papers from PubMed (excluding reviews and clinical trials) for a ten year range from 2004-2013 and have identified those that mention Arabidopsis in the title or abstract. These papers are defined as Arabidopsis papers (further details of the method are given below).
From this analysis, it is clear that the Arabidopsis community is thriving, having produced just over 3500 papers in 2013, up from 1847 in 2004. This represents a 91% increase in article number, keeping pace with the overall rise in number of journal articles published, which has grown by 95% since 2004.
From 2004 to 2011, Plant Physiology (Plant Physiol.), Plant Journal (Plant J.) and Plant Cell made up the top three journals publishing Arabidopsis research (see figure 2). Plant Signal Behaviour (Plant Signal Behav.) has risen rapidly from it’s inception in 2006 to join the top five in 2008. By far the strongest trend, however, is the rise of PLoS ONE from outside the top ten in 2010 with just 66 Arabidopsis papers, to topping the chart with 315 in 2013. That figure represents 9% of all Arabidopsis articles in 2013. The meteoric rise of PLoS ONE can be seen for other organisms, such as in Drosophila, as described in a previous blog post.
A third of all Arabidopsis articles in 2013 were published in five journals, namely, PLoS ONE, Plant Physiol., Plant Cell, Plant Signal Behav. and Plant J., indicating that researchers favour publishing in these top five journals. By comparison Drosophila research, which produces a similar number of papers each year, exhibits a greater spread of publication, with only one journal publishing more than 100 papers, unsurprisingly this was PLoS ONE with 324. However, it does seem that Arabidopsis research is becoming more broadly spread across journals. In 2004 the top ten journals accounted for 57% of all articles, with 194 journals featuring at least one Arabidopsis paper, but by 2013 the top ten journals account for only 47% of articles, with 352 journals in total.
While some journals, like PLOS ONE, are rapidly expanding their Arabidopsis portfolio, others are publishing fewer Arabidopsis papers. Examples include Plant J., publishing 163 in 2013 (5% of all Arabidopsis articles), down from 187 in 2004 (10%) and Plant Molecular Biology (Plant Mol. Biol.), which has dropped from publishing 86 papers in 2004 (4.6%) to 54 (1.5%) in 2013. In fact all journals in the top ten in 2004 have seen a drastic drop in their percentage share of Arabidopsis output with the exception of the Journal of Experimental Botany (J. Exp. Bot.) which has doubled (from 2% to 4%).
One factor that we thought may play a part in publication choice could be accessibility, and the rise of open access journals. Using the journal list at PubMed Central as a guide, only 25 of the top 100 Arabidopsis-publishing journals are open access (in PubMed Central). Interestingly, these are spread pretty evenly across the 100 journals; only two of the top ten are in PubMed Central – PLoS ONE and Frontiers in Plant Science. It appears then that accessibility may not be a major factor in Arabidopsis publishing choice.
Around the Globe
So Arabidopsis-related research is growing, but how is this growth distributed across the globe? As figure 4 shows, the main increase in Arabidopsis papers is found in China, with explosive growth from 74 papers in 2004 to 650 papers in 2013, matching the output of the USA. Other Asian countries have also experienced significant growth but not to such high volumes, such as India rising from 3 papers in 2004 to 70 in 2013 and South Korea increasing from 49 to 142. Publication levels in Germany and Japan have risen slightly, but overall have remained relatively constant over the last 10 years, as has the output from the UK. Overall, and in line with an overall increase in the number of articles published, almost all countries assessed show a modest increase in the number of publications over the last 10 years. However, with the growing activity in China many countries have seen a drop in percentage of overall Arabidopsis papers from 2004 to 2013: USA 32-19%, Japan 13-9%, and UK 7-4%.
Overall, research on the plant model organism Arabidopsis thaliana is going from strength to strength. With an increasing number of publications, and it’s own active model organism database, Arabidopsis continues to be at the forefront of agricultural, horticultural and genetic research.
If you want to keep up with the latest Arabidopsis research, you can use the Nowomics Arabidopsis news feed, showing all the abstracts of the latest and popular Arabidopsis papers, along with Arabidopsis-related curated annotation. This feed can be provided as a weekly email digest, and displays various statistics on the most updated Arabidopsis genes and top journals. You can also follow particular genes and ontology terms to build your own personalised news feed of new papers and data from many sources.
As always, do let us know if you have any questions, suggestions, or comments on this blog post, or indeed on Nowomics, by dropping us an email – firstname.lastname@example.org
The LINNAEUS software was used to identify mentions of Arabidopsis (in various formats and guises, such as A. thaliana or Arabidopsis) in titles and abstracts of records in PubMed. PubMed records were restricted to journal articles only and excluded reviews and clinical trials. For the country data we extracted country (or major city/US state) names from the affiliation listed for the first author.