Regulatory genes in the ancestral chordate genomes.
Changes or innovations in gene regulatory networks for the developmental program in the ancestral chordate genome appear to be a major component in the evolutionary process in which tadpole-type larvae, a unique characteristic of chordates, arose. These alterations may include new genetic interactions as well as the acquisition of new regulatory genes. Previous analyses of the Ciona genome revealed that many genes may have emerged after the divergence of the tunicate and vertebrate lineages. In this paper, we examined this possibility by examining a second non-vertebrate chordate genome. We conclude from this analysis that the ancient chordate included almost the same repertory of regulatory genes, but less redundancy than extant vertebrates, and that approximately 10% of vertebrate regulatory genes were innovated after the emergence of vertebrates. Thus, refined regulatory networks arose during vertebrate evolution mainly as preexisting regulatory genes multiplied rather than by generating new regulatory genes. The inferred regulatory gene sets of the ancestral chordate would be an important foundation for understanding how tadpole-type larvae, a unique characteristic of chordates, evolved.
Satou
Yutaka
Y
Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan. yutaka@ascidian.zool.kyoto-u.ac.jp.
Wada
Shuichi
S
Sasakura
Yasunori
Y
Satoh
Nori
N
D000818:Animals; D002816:Chordata, Nonvertebrate / Q000235:genetics*; D002938:Ciona intestinalis / Q000235:genetics*; D019143:Evolution, Molecular; D053263:Gene Regulatory Networks; D016678:Genome; D006801:Humans; D010802:Phylogeny
J Mol Biol. 2000 Sep 8;302(1):205-17
10964570
Science. 2006 Nov 10;314(5801):941-52
17095691
Dev Genes Evol. 2003 Jun;213(5-6):222-34
12736825
Nature. 2008 Jun 19;453(7198):1064-71
18563158
Dev Genes Evol. 2003 Jun;213(5-6):264-72
12739142
Nat Rev Mol Cell Biol. 2002 Jul;3(7):475-86
12094214
Mol Biol Evol. 2001 May;18(5):691-9
11319253
Dev Genes Evol. 2003 Jun;213(5-6):245-53
12743819
Bioinformatics. 2003 Aug 12;19(12):1572-4
12912839
Science. 2002 Dec 13;298(5601):2157-67
12481130
Dev Genes Evol. 2003 Jun;213(5-6):254-63
12739141
Dev Genes Evol. 2003 Jun;213(5-6):213-21
12736824
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
Development. 2003 Sep;130(18):4461-72
12900461
Nature. 2006 Feb 23;439(7079):965-8
16495997
Dev Cell. 2004 Mar;6(3):397-410
15030762
Syst Biol. 2003 Oct;52(5):696-704
14530136
Dev Genes Evol. 2003 Jun;213(5-6):235-44
12743820