Advanced

Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution

Chiu, CH; Dewar, K; Wagner, GP; Takahashi, K; Ruddle, F; Ledje, Christina LU ; Bartsch, P; Scemama, JL; Stellwag, E and Fried, C, et al. (2004) In Genome Research 14(1). p.11-17
Abstract
The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish possess duplicated Hox clusters that have undergone considerable sequence evolution. Whether these changes are associated with the duplication(s) that produced extra Hox clusters is unresolved because comparison with basal lineages is unavailable. We sequenced and analyzed the HoxA cluster of the bichir (Polypterus senegalus), a phylogenetically basal actinopterygian. Independent lines of evidence indicate that bichir has one HoxA cluster that is mosaic in its patterns of noncoding sequence conservation and gene retention relative to the HoxA... (More)
The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish possess duplicated Hox clusters that have undergone considerable sequence evolution. Whether these changes are associated with the duplication(s) that produced extra Hox clusters is unresolved because comparison with basal lineages is unavailable. We sequenced and analyzed the HoxA cluster of the bichir (Polypterus senegalus), a phylogenetically basal actinopterygian. Independent lines of evidence indicate that bichir has one HoxA cluster that is mosaic in its patterns of noncoding sequence conservation and gene retention relative to the HoxA clusters of human and shark, and the HoxAalpha and HoxAbeta clusters of zebrafish, pufferfish, and striped bass. HoxA cluster noncoding sequences conserved between bichir and euteleosts indicate that novel cis-sequences were acquired in the stem actinopterygians and maintained after cluster duplication. Hence, in the earliest actinopterygians, evolution of the single HoxA cluster was already more dynamic than in human and shark. This tendency peaked among teleosts after HoxA cluster duplication. (Less)
Please use this url to cite or link to this publication:
author
, et al. (More)
(Less)
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Genome Research
volume
14
issue
1
pages
11 - 17
publisher
Cold Spring Harbor Laboratory Press
external identifiers
  • pmid:14707166
  • wos:000187889600002
  • scopus:9144273767
ISSN
1549-5469
DOI
10.1101/gr.1712904
language
English
LU publication?
yes
id
630cbb5a-d9c4-4ed1-be22-870191a81057 (old id 290096)
date added to LUP
2007-10-17 16:56:46
date last changed
2017-10-22 04:45:26
@article{630cbb5a-d9c4-4ed1-be22-870191a81057,
  abstract     = {The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish possess duplicated Hox clusters that have undergone considerable sequence evolution. Whether these changes are associated with the duplication(s) that produced extra Hox clusters is unresolved because comparison with basal lineages is unavailable. We sequenced and analyzed the HoxA cluster of the bichir (Polypterus senegalus), a phylogenetically basal actinopterygian. Independent lines of evidence indicate that bichir has one HoxA cluster that is mosaic in its patterns of noncoding sequence conservation and gene retention relative to the HoxA clusters of human and shark, and the HoxAalpha and HoxAbeta clusters of zebrafish, pufferfish, and striped bass. HoxA cluster noncoding sequences conserved between bichir and euteleosts indicate that novel cis-sequences were acquired in the stem actinopterygians and maintained after cluster duplication. Hence, in the earliest actinopterygians, evolution of the single HoxA cluster was already more dynamic than in human and shark. This tendency peaked among teleosts after HoxA cluster duplication.},
  author       = {Chiu, CH and Dewar, K and Wagner, GP and Takahashi, K and Ruddle, F and Ledje, Christina and Bartsch, P and Scemama, JL and Stellwag, E and Fried, C and Prohaska, SJ and Stadler, PF and Amemiya, CT},
  issn         = {1549-5469},
  language     = {eng},
  number       = {1},
  pages        = {11--17},
  publisher    = {Cold Spring Harbor Laboratory Press},
  series       = {Genome Research},
  title        = {Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution},
  url          = {http://dx.doi.org/10.1101/gr.1712904},
  volume       = {14},
  year         = {2004},
}