CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality

Abstract

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5.

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters

“…A promising application of KEGG OC is to perform an automatic KO/GO assignment and pathway reconstruction for newly sequenced genomes, which will be made possible by using the KAAS (KEGG Automatic Annotation Server) system (18). An example of this application is shown as a function of CIPRO, the Ciona intestinalis protein database (19), where homologs were identified by KAAS with KEGG OC to help manual annotation by curators. These data are provided as links in CIPRO for users to obtain further biological implication.…”

Microinjection and 4D Fluorescence Imaging in the Eggs and Embryos of the Ascidian Phallusia mammillata

“…An example of a 4D low-light level imaging experiment can be seen in Fig. 2b -this embryo was imaged from the 76-cell stage to the late tailbud stage II [ 9 ] without development being adversely affected.…”

“…Ciona intestinalis was the fi rst ascidian to have its genome sequenced [ 6 ] and has provided an exceptional wealth of information concerning gene expression patterns during development. Excellent Web-based resources exist housing genomic and transcriptomic data sets: [ 7 ] Aniseed ( http://aniseed-ibdm.univ-mrs.fr/ ), [ 8 ] GHOST ( http:// hoya.zool.kyoto-u.ac.jp/SearchGenomekh.html#CDNA ) as well as proteomic data CIPRO [ 9 ] ( http://cipro.ibio.jp/2.5/ ) and a 3D atlas of embryonic stages FABA [ 10 ] ( http://chordate.bpni.bio.keio. ac.jp/faba/1.3/top.html ).…”

Evolutionary crossroads in developmental biology: the tunicates

“…Images courtesy of the Four-Dimensional Ascidian Body Atlas (FABA) database (Hotta et al, 2007). PRIMER Development 138 (11) Finally, powerful computational methods and infrastructures have been developed for solitary ascidians, in particular C. intestinalis, which facilitate genomic data analysis and the integration of molecular and anatomical data into virtual representations of embryogenesis (Tassy et al, 2010;Endo et al, 2010).…”

“…The breeding of C. intestinalis and C. savignyi in the laboratory (Hendrickson et al, 2004;Joly et al, 2007) has also permitted the development of germ-line transgenesis by electroporation (Matsuoka et al, 2005), a technique that has been subsequently improved by the use of the Minos transposon, which opens the way to insertional mutagenesis and enhancer-trap assays . Finally, powerful computational methods and infrastructures have been developed for solitary ascidians, in particular C. intestinalis, which facilitate genomic data analysis and the integration of molecular and anatomical data into virtual representations of embryogenesis (Tassy et al, 2010;Endo et al, 2010).The colonial ascidians B. schlosseri and B. leachi can be readily cultured on glass slides in the laboratory (generation time 2-3 months) (Boyd et al, 1986). These animals, which produce few embryos, are particularly adapted to the study of blastogenesis and regeneration.…”