Identification of 315 genes essential for early zebrafish development - PubMed (original) (raw)

Identification of 315 genes essential for early zebrafish development

Adam Amsterdam et al. Proc Natl Acad Sci U S A. 2004.

Abstract

We completed a large insertional mutagenesis screen in zebrafish to identify genes essential for embryonic and early larval development. We isolated 525 mutants, representing lesions in approximately 390 different genes, and we cloned the majority of these. Here we describe 315 mutants and the corresponding genes. Our data suggest that there are roughly 1,400 embryonic-essential genes in the fish. Thus, we have mutations in approximately 25% of these genes and have cloned approximately 22% of them. Re-screens of our collection to identify mutants with specific developmental defects suggest that approximately 50 genes are essential for the development of some individual organs or cell types. Seventy-two percent of the embryonic-essential fish genes have homologues in yeast, 93% have homologues in invertebrates (fly or worm), and 99% have homologues in human. Yeast and worm orthologues of genes that are essential for early zebrafish development have a strong tendency to be essential for viability in yeast and for embryonic development in the worm. Thus, the trait of being a genetically essential gene is conserved in evolution. This mutant collection should be a valuable resource for diverse studies of cell and developmental biology.

Copyright 2004 The National Academy of Sciencs of the USA

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Figures

Fig. 1.

Fig. 1.

Genes essential for zebrafish embryonic development identified by insertional mutagenesis. Genes are listed by mutant number and sorted by evolutionary conservation and gene function. Phenotypic descriptions are available in Table 3, and images are available at

http://web.mit.edu/ccr/pnas\_zebrafish\_mutant\_images/index.html

.

Fig. 2.

Fig. 2.

Types of genes whose mutation in zebrafish leads to an embryonic visible phenotype. The genes are assigned to the same categories as in Fig. 1 although some categories have been combined.

Fig. 3.

Fig. 3.

Evolutionary conservation of essential zebrafish genes. Horizonal lines on the Left represent 315 different genes. The genes are listed in the same order as in Fig. 1. In the first four colored columns, the presence of a colored box indicates the presence of one or more homologous genes (

blastp

E value of <10–5) in yeast (either S. cerevisiae or S. pombe), C. elegans, D. melanogaster, or H. sapiens. Green boxes indicate genes without homologues in yeast but with homologues in other SCEs such as Giardia, Plasmodium, Trypanosoma, and/or Chlamydomonas. Thus, yellow boxes represent genes conserved through yeast, green are those found in SCEs other than yeast, red are those found in invertebrates but not SCEs, and blue are vertebrate-specific. The last two genes (with no colored boxes) seem to be fish-specific. The black boxes in the last three columns indicate genes whose mutation leads to one of three phenotypes: cystic kidney, chondrogenesis defects, or reduction or lack of melanocyte pigmentation.

Fig. 4.

Fig. 4.

Essentialness of genes is evolutionarily conserved. Shown is an analysis of S. cerevisiae (Left) and C. elegans (Right) genes that are homologous to the essential fish genes. In each case, the leftmost columns represent 315 essential fish genes, the red columns show how many of these have homologues in yeast (214) or worm (272), and the blue columns show which have a 1:1 orthologue or “ancestor” gene in yeast (176) or worm (235). The dark green columns represent the number of these yeast or worm orthologues that are essential in their respective species, 135 of the 176 yeast genes, and 155 of the 235 worm genes. The pea green columns show the number that would be predicted to be essential at random, 33 of the 176 yeast genes, and 15 of the 235 worm genes. Thus, the difference between the dark green and pea green columns is the enrichment. In the case of the worm, the pale green extensions to the two green columns represent projections of how many of the orthologues would be found to be essential if 100% of the worm genes had been successfully knocked down by RNAi; this estimate prorates both for the reported failure rate of RNAi and the number of genes for which no RNAi data have been reported. This calculation estimates that 216 of the 235 worm genes are likely to be essential whereas only 22 would be expected to be at random. Note that the percentage of worm orthologues that are essential that is stated in the text does not include the genes for which no RNAi data have been reported.

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