Visualization of digital expression profiles on the nuclear genome of the mating-type minus strain by Kyoto Chlamydomonas Genome Database (KCGD): Expression from the mating-type locus and CO2-limiting stress responses
Hideya Fukuzawa1, Takeaki Kubo1, Mari Yanase1, Katsuyuki T. Yamato1, Yutaka Suzuki2, Sumio Sugano2, Takehiko Itoh3, Takeaki Taniguchi5, and Asao Fujiyama5
1) Grad. Sch. of Biostudies, Kyoto Univ., Japan
2) Int. and Interdisci. Studies, Univ. of Tokyo, Japan
3) Grad. Sch. of Biosci. Biotech., TIT, Japan
4) Mitsubishi Res. Inst., Japan
5) Nat. Inst. of Genetics, Japan
To understand the biological responses to the environmental changes, it is important to access the genomic and transcriptomic data. To establish genomic information of the mating-type minus strain, genomic libraries were constructed using DNA samples from C-9 wild type cells using BAC/Fosmid vectors. The nucleotide sequence of the genomic region of 292,719-bp covering the R-domain and its proximate regions on the chromosome 6 of the strain C-9 mt (-) was determined and compared with that of the corresponding region of the mt (+) strain. End sequences of the full-length cDNA and BAC/Fosmid clones were mapped on the genome sequence of the mating-type plus strain CC-503 (JGI ver. 4.0). Mapping analysis of the end-sequences of BAC/Fosmid clones revealed that twenty-two scaffolds, which were previously not integrated into the chromosomes, were integrated into the 17 chromosomes. By considering the sequence of the R-domain and mapping information, the genome sequence of mating-type minus strain C-9, was generated. To analyze cellular responses to nutrient-limiting stress, including CO2-limiting stress, end sequences of mRNAs from the cells that suffered to various stress conditions, were analyzed by Illumina GAIIx. The genomic and transcriptome resources were integrated into an expression database, Kyoto Chlamydomonas Genome Database (KCGD; Expression of the newly identified genes on the mating-type locus and CO2-limiting stress responses will be discussed based on the expression profiles.
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