Annotation and Identification of Symbiodinium Genes

A set of gene model predictions (Gene Model ver. 1) was generated mainly with AUGUSTUS [4 (link)], and a genome browser has been established using the Generic Genome Browser (JBrowser) [79 (link)]. Annotation and identification of Symbiodinium genes were performed using three methods or combinations of methods: reciprocal BLAST analyses, screening of gene models against the Pfam database [80 (link)] at an E-value cutoff of 0.001, and phylogenetic analyses. Gene annotations are available at the genome browser site (http://marinegenomics.oist.jp/gallery/). Scaffold 1 of both SymA and SymC manifested similarities to a bacterial genome, which was identified by genome sequencing of Symbiodinium minutum [4 (link)], but which was not included for gene annotation. Expansions of gene families were predicted by chi-square values from comparisons of gene numbers with Pfam domains.

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Shoguchi E., Beedessee G., Tada I., Hisata K., Kawashima T., Takeuchi T., Arakaki N., Fujie M., Koyanagi R., Roy M.C., Kawachi M., Hidaka M., Satoh N, & Shinzato C. (2018). Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. BMC Genomics, 19, 458.

Publication 2018

A gene At 001 Bacterial genome Gene Gene annotation Generic Genome

Corresponding Organization : The University of Tokyo

Other organizations : National Institute for Environmental Studies, University of the Ryukyus

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Protocol cited in 11 other protocols

Variable analysis

independent variables

Gene model predictions (Gene Model ver. 1) generated mainly with AUGUSTUS
Annotation and identification of Symbiodinium genes using three methods or combinations of methods: reciprocal BLAST analyses, screening of gene models against the Pfam database at an E-value cutoff of 0.001, and phylogenetic analyses

dependent variables

Expansions of gene families predicted by chi-square values from comparisons of gene numbers with Pfam domains

control variables

Scaffold 1 of both SymA and SymC, which were identified as similar to a bacterial genome and were not included for gene annotation

controls

Positive controls: Not explicitly mentioned.
Negative controls: Not explicitly mentioned.

Annotations

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