ANISEED 2015: a digital framework for the comparative developmental biology of ascidians

Abstract

Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.

Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona

“…They are available as a UCSC Genome Browser track for the Ci2 genome assembly (http://genome.ucsc.edu/)[FOR PEER REVIEW ONLY: http://genome-test.soe.ucsc.edu], with links to CRISPOR for off-target prediction and automated OSO-PCR primer design. This track is freely available for download to use on other browsers, like those of specific interest to the tunicate community such as ANISEED (Brozovic et al 2015) or GHOST (Satou et al 2005). …”

Bilaterian Giant Ankyrins Have a Common Evolutionary Origin and Play a Conserved Role in Patterning the Axon Initial Segment

“…Interestingly, we found a 14 Kb gap separating exons 38 and 39 which contained an unbroken 13.4 Kb ORF. A small EST cluster (clones cien56932, cijv010l23, cijv033b07, cidg851d03, cilv031p13 and 031ZG09) mapping within this ORF is expressed in the nervous system (Fig 2B, [51]), indicating that the ORF could encode a long exon for a giant ankyrin isoform. We therefore used PCR on cDNA from whole larvae to verify that this long ORF contains exonic sequence contiguous with the UPA domain on the 5’ end and the DD on the 3’ end; The intron/exon junctions we verified by PCR suggest a 13,344 bp exon lies within the long ORF.…”

The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness in the brain of a chordate sibling

“…Not only does its development result from a fixed pattern of cell lineage and result in a mere ~ 2600 cells in the larva of Ciona intestinalis (Satoh, 1999), but the genome, first in Ciona intestinalis (Dehal et al., 2002) and now in nine other species (Brozovic et al, 2016), has been sequenced. Even though the events of early neural development and the nervous system’s subsequent metamorphosis have been identified, together with many of their underlying causal gene networks (Satoh, 2003; Sasakura et al, 2012), the detailed cellular organization of their product, the CNS of the swimming larva, still remains almost entirely unresolved.…”