Environmental genomics
Date: 19.10.2015
The majority of Earth’s biodiversity is microscopic and cannot be kept in permanent cultures. However, our knowledge of life is based on extensive exploitation of few either macroscopic (Arabidopsis, Oryza, Drosophila, Caenorhabditis, rat or Xenopus…) or cultivable unicellular (Saccharomyces, Neurospora, Chlamydomonas…) models representing only a small fraction of true diversity. Laboratory of environmental genomics (LEG) was founded in March 2013 and its main goal is to characterize diversity, ecological role and metabolic potential of important/interesting unicellular eukaryotes not available from cultures using the power of the next-generation sequencing and bioinformatics.
At present, the main attention is focused on the planktonic diplonemids. These obscure marine protozoans related to kinetoplastid parasites (Trypanosoma, Leishmania) and/or ubiquitous euglenids, were found to be the sixth most abundant and third most species-rich component of eukaryotic plankton of sun-lit oceans as revealed by global Tara Oceans dataset. Our analyses suggest they are even more abundant in oceanic depths and where they dominate eukaryotic communities of some localities and are probably parasites. All this suggests planktonic diplonemids are one of the key players of the ecosystem and their detailed knowledge is crucial for our better understanding of the oceans.
Our ultimate goal is to bring these organisms into the culture and turn (at least) one strain into a genetically tractable system. Cooperation: Tara consortium, namely Colomban de Vargas Station Biologique de Roscoff (France) and Chris Bowler, ENS Paris (France).
Author: Aleš Horák PhD.
We acknowledge the use of research infrastructure that has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 316304.
This issue is processed eg. in:
Woo Y, Ansari H, Otto TD, Klinger CM, Kolísko M, Michálek J, SaxenaS, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast F, Miranda-Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings ND, Padron-Regalado E, Ramaprasad A, Samad N, Tomčala A, Wilkes J, Neafsey DE, Doerig D, Bowler C, Keeling PJ, Roos DS, Dacks JB, Templeton TJ, Waller RF, Lukeš J, Oborník M, Pain A. (2015) Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. e-Life (re-submitted)
Lukeš J., Flegontova O. & Horák A. (2015) Diplonemids. Curr. Biol. (in press)
Sample P., Kořený L., Paris Z., Gaston K.W., Rubio M.A., Fleming I.M., Hinger S., Horáková E., Limbach P.A., Lukeš J. & Alfonzo J.D. (2015) A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria. Nucl. Acids Res. (in press).
de Vargas C., Audic S., Henry N., Decelle J., Mahé F., Logares R., Lara E., Berney C., Le Bescot N., Probert I., Carmichael M., Poulain J., Romac S., Colin S., Aury J.-M., Bittner L., Chaffron S., Dunthorn M., Engelen S., Flegontova O., Guidi L., Horák A., Jaillon O., Lima Mendez G., Lukeš J., Malviya S., Morard R., Mulot M., Scalco E., Siano R., Vincent F., Zingone A., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Acinas S.G., Bork P., Bowler C., Gaill F., Gorsky G., Grimsley N., Hingcamp P., Iudicone D., Not F., Ogata H., Pesant S., Raes J., Sieracki M., Speich S., Stemmann L., Sunagawa S., Weissenbach J., Wincker P. & Karsenti E. (2015) Eukaryotic plankton diversity in the sunlit global ocean. Science (in press)
