Woods Hole Oceanographic Inistitute (WHOI) Biology Dept. Seminar Speaker on Tuesday, May 16th.  Noon, Redfield Auditorium.
(sponsored by Superfund Basic Research Program at Boston University)


Chris T. Amemiya
Benaroya Research Institute at Virginia Mason University
http://www.vmresearch.org/investigators/amemiya_chris/index.shtml


OLD “FOUR LEGS” OR JUST AND OLD FISH? THE STORY OF THE LIVING COELACANTH AS REVEALED THROUGH COMPARATIVE GENOMICS.

 

The living coelacanth, Latimeria, is considered an evolutionary relict that has generated a great deal of intrigue since its discovery in 1938, with interests in its anatomy, physiology, ecology, interrelationships and even politics (Smith, 1956).  Due to its endangered status, the best practical approach to its study is from the "inside out," i.e., through comparative genomics.  To this end we have constructed high-representation bacterial artificial chromosome (BAC) libraries from the Indonesian coelacanth, Latimeria menadoensis, thus allowing indefinite preservation and surveying of its genome.  And while genomics per se does not provide information as to morphology and function, the information gleaned from the comparative genomics approach can be applied and assayed in other model systems for inferring function.  By using this approach we are addressing evolutionary and developmental (evo-devo) questions concerning the coelacanth. Sequencing of targeted loci such as the HOX, immunoglobulin and protocadherin clusters reveals trends in coelacanth genome evolution, particularly with regard to gene organization and evolutionary rates in both coding and noncoding regions.  The data lend support for using the coelacanth genome sequence as a "model genome" in order to better understand the logic of the genomes of higher vertebrates.

 

Smith, J. L. B.  1956. Old Fourlegs: The Story of the Coelacanth.  260 pp, Longman Green, London.



Danke, J., Miyake, T., Powers, T., Schein, J., Shin, H., Bosdet, I., Erdmann, M., Caldwell, R., and Amemiya, C. T. (2004). Genome resource for the Indonesian coelacanth, Latimeria menadoensis. J Exp Zoolog A Comp Exp Biol 301, 228-234. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14981781)


Noonan, J. P., Grimwood, J., Danke, J., Schmutz, J., Dickson, M., Amemiya, C. T., and Myers, R. M. (2004). Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res 14, 2397-2405. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15545497)


Shashikant, C., Bolanowski, S. A., Danke, J., and Amemiya, C. T. (2004). Hoxc8 early enhancer of the Indonesian coelacanth, Latimeria menadoensis. J Exp Zoolog B Mol Dev Evol 302, 557-563. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15470754)


other papers of interest:

Miyake, T., and Amemiya, C. T. (2004). BAC libraries and comparative genomics of aquatic chordate species. Comp Biochem Physiol C Toxicol Pharmacol 138, 233-244. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15533781)


Crow, K. D., Stadler, P. F., Lynch, V. J., Amemiya, C., and Wagner, G. P. (2006). The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol 23, 121-136. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16162861)