Announcing rhizobial genomes
In my last post, I highlighted the great job that Wayne Reeve has been doing in getting rhizobial genomes sequenced and published. I listed 18 papers that he has published since the start of 2013 – each describing a genome. This is a very impressive effort! There may have been an incentive for this quick-fire rate of publication: the reports were all in a journal called Standards in Genomic Sciences (Impact Factor 2.0), which has recently been taken over by BMC, who are now imposing a hefty publication charge of £865 (about US$1450 or €1050) for each genome announcement.
SIGS is an unusual journal, specialising in bacterial and archaeal genome announcements in a short format that meets the Minimum Information about a Genome Sequence (MIGS) specification. Providing important information in a standard format is very sensible, though all the articles seem also to include a photo of the organism. I can see the attraction of this if the genome belongs to an endangered orchid or a cuddly mammal, but the genomes are all bacterial, and there is limited interest in a succession of pictures of grey sausages.
When the first bacterial genomes were sequenced, each one was a prodigious effort that merited a high profile publication. The first rhizobial genome was announced with characteristic Japanese understatement (Kaneko et al. 2000), but the second managed to garner a paper in Science and three papers in PNAS (see Downie and Young 2001). These days, bacterial genome sequences come off the production lines so fast that many never get a publication at all, and most of the rest only merit a relatively brief announcement. Besides SIGS, many bacterial genome announcements have appeared in Journal of Bacteriology, but the publishers, the American Society for Microbiology, have recently started a special journal called Genome Announcements (no impact factor yet). These announcements are limited to 500 words, and cost the authors US$500 (€360, £300), which works out at a dollar a word. ASM members get a reduced rate of US$330.
Of course, many people would like to write more than 500 words about their favourite genome, and if there is substantial biological interest that can be developed into a full paper, there are many journals that might publish it. An Open Access example would be BMC Genomics (IF 4.4). Publishing there will cost you a substantial £1325/$2215/€1600, though.
If you want to write more than 500 words, and Open Access appeals to you (it does increase visibility and citations, and many funders now require it), then I can offer you a less expensive alternative. I happen to be the editor of a relatively new journal called Genes, and we are keen to publish more bacterial genomes. We have already published the genome of the type strain of Bradyrhizobium japonicum (Kaneko et al. 2011), as well as several other bacterial genomes. We have recently been added to PubMed and PMC, so readers will be able to click straight through from GenBank entries to the linked articles. We do not have an Impact Factor yet, but we are aiming to get one. The cost of publication is a modest 500 Swiss Francs (about £340/$565/€410), and your article can be as long as you like (within reason!). I look forward to seeing your genome manuscripts!
Kaneko, T., Nakamura, Y., Sato, S., Asamizu, E., Kato, T., Sasamoto, S., … & Tabata, S. (2000). Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Research, 7(6), 331-338.
Downie, J. A., & Young, J. P. W. (2001). Genome sequencing: the ABC of symbiosis. Nature, 412(6847), 597-598.
Kaneko, T., Maita, H., Hirakawa, H., Uchiike, N., Minamisawa, K., Watanabe, A., & Sato, S. (2011). Complete genome sequence of the soybean symbiont Bradyrhizobium japonicum strain USDA6T. Genes, 2(4), 763-787.