ArticleGenome biology2008
Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed.
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- An Improved Chromosome-Level Genome Assembly and Comprehensive Annotation of the Model Ascidian Ciona savignyi.Scientific data · 2026Article
- A gene regulatory network for specification and morphogenesis of a Mauthner Cell homolog in non-vertebrate chordates.Developmental biology · 2025Article
- CRISPR/Cas9 Protocols for Disrupting Gene Function in the Non-vertebrate Chordate Ciona.Integrative and comparative biology · 2024Review
- Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network.Integrative and comparative biology · 2024Review
- A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates.Development (Cambridge, England) · 2024Article
- Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina.NAR genomics and bioinformatics · 2024Article
- Evolutionary origin of the chordate nervous system revealed by amphioxus developmental trajectories.Nature ecology & evolution · 2024Article
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- A change inbioRxiv : the preprint server for biology · 2024Article
- Extrinsic apoptosis participates to tail regression during the metamorphosis of the chordate Ciona.Scientific reports · 2024Article
- Gene expression in notochord and nuclei pulposi: a study of gene families across the chordate phylum.BMC ecology and evolution · 2023Article
- A lamprey neural cell type atlas illuminates the origins of the vertebrate brain.Nature ecology & evolution · 2023Article
- A digital twin reproducing gene regulatory network dynamics of early Ciona embryos indicates robust buffers in the network.PLoS genetics · 2023Article
- Single-Cell RNA Sequencing of the Testis ofCells · 2022Article
- d-Serine controls epidermal vesicle release via NMDA receptor, allowing tissue migration during the metamorphosis of the chordateScience advances · 2022Article
- Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
44 more citing papers are in PubMed but not listed here.
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20 authors.
Funding
Abstract
backgroundThe draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene prediction programs and in part to the fragmented nature of the assembly.
resultsWe have prepared a less-fragmented assembly on the basis of scaffold-joining guided by paired-end EST and bacterial artificial chromosome (BAC) sequences, and BAC chromosomal in situ hybridization data. The new assembly (115.2 Mb) is similar in length to the initial assembly (116.7 Mb) but contains 1,272 (approximately 50%) fewer scaffolds. The largest scaffold in the new assembly incorporates 95 initial-assembly scaffolds. In conjunction with the new assembly, we have prepared a greatly improved global gene model set strictly correlated with the extensive currently available EST data. The total gene number (15,254) is similar to that of the initial set (15,582), but the new set includes 3,330 models at genomic sites where none were present in the initial set, and 1,779 models that represent fusions of multiple previously incomplete models. In approximately half, 5'-ends were precisely mapped using 5'-full-length ESTs, an important refinement even in otherwise unchanged models.
conclusionUsing these new resources, we identify a population of non-canonical (non-GT-AG) introns and also find that approximately 20% of Ciona genes reside in operons and that operons contain a high proportion of single-exon genes. Thus, the present dataset provides an opportunity to analyze the Ciona genome much more precisely than ever.
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