Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

David Roy Smith

doi:10.1093/bfgp/elw026

Abstract

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers—peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal.

Highlights

Four decades ago, Sanger et al [1] decoded, for the first time, the entire DNA sequence of a genome, that of the bacteriophage UX174
Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science
With respect to genomes . . . we feel the scientific community would be best served by the immediate launch of a central repository of short, highly structured ‘Genome Notes’ that must be standards compliant. This could be done in the context of an existing journal, but we suggest the more radical solution of launching a new journal. [35]

Summary

Birth of the genome paper

Sanger et al [1] decoded, for the first time, the entire DNA sequence of a genome, that of the bacteriophage UX174 This historic achievement marked the inception of a new genre of scientific article: the genome paper. It would take another 4 years before scientists sequenced and published a human chromosome—our mitochondrial genome [2]—and an additional 15 years for the arrival of a nuclear genome paper (yeast) [3]. The simultaneously published articles describing the human genome [5, 6] topped Thomson Reuters’ Science Watch list of ‘hot papers’ in biology of 2001 [7] These same articles were widely covered by scientific and popular news media, which has become a recurring theme for genome papers of all stripes. This flood of genome sequence information has greatly improved our understanding of genetics and provided an inexhaustible reservoir of data for comparative studies, but it has deflated the importance of genome papers

Genome paper overkill

Rise of the genome report

Yes Yes Yes No

The pros and cons of genome reports

Conclusion