PUBLICATION

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Authors
Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H.
ID
ZDB-PUB-170202-7
Date
2016
Source
Nature Genetics   48(4): 427-37 (Journal)
Registered Authors
Amemiya, Chris, Amores, Angel, Bobe, Julien, Braasch, Ingo, Cañestro-García, Cristian, Gehrke, Andrew R., Litman, Gary W., Martin, Kyle, Meyer, Axel, Nakamura, Tetsuya, Ota, Tatsuya, Postlethwait, John H., Saha, Nil Ratan, Shubin, Neil, Smith, Jeramiah, Sun, Yi, Taylor, John, Venkatesh, Byrappa, Wang, Han, Wcisel, Dustin, Yoder, Jeffrey A.
Keywords
Embryogenesis, Gene expression, Gene regulation, Genomics, Sequencing
MeSH Terms
  • Animals
  • Evolution, Molecular
  • Female
  • Fishes/genetics*
  • Fishes/metabolism
  • Genome
  • Humans
  • Karyotype
  • Models, Genetic
  • Organ Specificity
  • Sequence Analysis, DNA
  • Transcriptome
PubMed
26950095 Full text @ Nat. Genet.
Abstract

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Genes / Markers
Figures
Figure Gallery
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes