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Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development

Kazuhiro W. Makabe1,*, Takeshi Kawashima1, Shuichi Kawashima2, Takuya Minokawa3, Asako Adachi1, Hiroshi Kawamura4, Hisayoshi Ishikawa4, Riho Yasuda1, Hiroki Yamamoto3, Keisuke Kondoh3, Sachiko Arioka3, Yasunori Sasakura1, Ako Kobayashi1, Kasumi Yagi1, Keisuke Shojima1, Yuki Kondoh4, Sumina Kido4, Mayu Tsujinami4, Nahoko Nishimura1, Miyuki Takahashi1, Tetsuji Nakamura1, Minoru Kanehisa2, Michio Ogasawara1, Takahito Nishikata4,5 and Hiroki Nishida3

1 Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
2 Institute of Chemical Research, Kyoto University, Uji 611-0011, Japan
3 Department of Biological Sciences, Tokyo Institute of Technology, Yokohama 226-8501, Japan
4 Department of Biology, Faculty of Science, Konan University, Kobe 658-8501, Japan
5 High Technology Research Center, Konan University, Kobe 658-8501, Japan



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  		Fig. 1. Sequence prevalence distributions for the fertilized egg ESTs of known and putative mRNA classes. The black bars represent mRNAs with high similarity to the GenBank data. The hatched bars represent sequences with no similarity to any known sequences. The white bars represent sequences with homology to the ESTs or cosmids from other organisms.

 


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  		Fig. 2. Summary of EST sequences. A total of 4240 cDNA clones (B) and 2221 clusters (A) were divided into four general categories, defined by sequence similarity searches.

 


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  		Fig. 3. Examples of clones showing maternal localization at the eight-cell stage. (A) 006C18. A clone categorized as mitochondria-like. (B) 006C14. The signals are seen only in the animal blastomeres. (C) 011F11. The signals are detected in the a4.2, b4.2 and A4.1 blastomere pairs, but not in the B4.1 blastomere pair. (D) 009D13, which encodes HrPEM. The signals are localized in the postplasm. (E) 003E02. The signals are detected only in the a4.2 blastomere pair. (F) 011B23. The signals are seen in the a4.2 and A4.1 anterior blastomere pairs. Lateral views. Anterior is towards the left. The animal pole is upwards.

 


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  		Fig. 4. Frequency of zygotic gene expression in different tissues. The 1206 unique genes that are expressed in the indicated tissues of the tailbud embryos are represented. Note that a single gene can be expressed in multiple tissues.

 


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  		Fig. 5. Examples of the genes zygotically expressed in a single tissue in the tailbud embryos. (A) 011L13, which is expressed in the tail epidermis. (B) 006D03, which is expressed in the presumptive adhesive organ. (C) 008G19, which is expressed in a subset of the neural cells in the central nervous system. (D) 002E22, which is expressed in the larval tail muscle. (E) 008L23, which is expressed in the mesenchyme cells. (F) 008L18, which is expressed in the trunk lateral cells. (G) 005D16, which is expressed in the notochord. (H) 003D22, which is expressed in the endoderm/endodermal strand. Anterior is towards the left.

 


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  		Fig. 6. Examples of whole-mount in situ hybridization. (A) 001D02 in the 110-cell embryo. Vegetal view. Anterior is upwards. (B) 003O15 in the early tailbud embryo. The signals are seen in multiple regions in a complex manner in terms of cell lineage or germ layers. Anterior is towards the left. (C) 004D21 in the 110-cell embryo. The expression is detected in every blastomere except the endodermal cells. (D) 011F04. (E) 008B07. (F) 006L20. The maternal RNA of each clone is localized in the postplasm while the zygotic expression is seen in the epidermis and adhesive organ (D), the nervous system, adhesive organ and endodermal strand in (E) and in the trunk lateral cells (F), respectively.

 


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  		Fig. 7. Examples of the genes zygotically expressed in B7.6 cells. (A) 006K09 (belonging to the same cluster as 003D22 shown in Fig. 5H) expression in the eight-cell embryo. (B) 003D19, which is expressed in B7.6 and the nervous system. Arrow indicates B7.6. (C) 003C20, which is expressed in B7.6 and the mesenchyme. (D) 003H03, which is expressed in B7.6, the epidermis and the endoderm.

 




© The Company of Biologists Ltd 2001