Phototroph genomics ten years on.
The onset of the genome era means different things to different people, but it is clear that this new age brings with it paradigm shifts that will forever affect biological research. Less clear is just how these shifts are changing the scope and scale of research. Are gigabases of raw data more useful than a single well-understood gene? Do we really need a full genome to understand the physiology of a single organism? The photosynthetic field is poised at the periphery of the bulk of genome sequencing work--understandably skewed toward health-related disciplines--and, as such, is subject to different motivations, limitations, and primary focus for each new genome. To understand some of these differences, we focus here on various indicators of the impact that genomics has had on the photosynthetic community, now a full decade since the publication of the first photosynthetic genome. Many useful indicators are indexed in public databases, providing pre- and post-genome sequence snapshots of changes in factors such as publication rate, number of proteins characterized, and sequenced genome coverage versus known diversity. As more genomes are sequenced and metagenomic projects begin to pour out billions of bases, it becomes crucial to understand how to harness this data in order to accumulate possible benefits and avoid possible pitfalls, especially as resources become increasingly directed toward natural environments governed by photosynthetic activity, ranging from hot springs to tropical forest ecosystems to the open ocean.
Raymond
Jason
J
School of Natural Sciences, University of California, Merced, Merced, CA, USA. jason.raymond@ucmerced.edu
Swingley
Wesley D
WD
D000818:Animals; D001483:Base Sequence; D016678:Genome / Q000235:genetics; D023281:Genomics; D006801:Humans; D010788:Photosynthesis / Q000235:genetics*; D010802:Phylogeny; D013997:Time Factors