ArticleDevelopment genes and evolution2015
Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader.
Article in Development genes and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 34 citations in OpenAlex.
- Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles.Molecular biology and evolution · 2025Article
- Tracing Homopolymers in Oikopleura dioica's Mitogenome.Genome biology and evolution · 2024Article
- Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.Genome biology and evolution · 2024Article
- Extreme genome scrambling in marine planktonicGenome research · 2024Article
- Maternal patterns of inheritance alter transcript expression in eggs.BMC genomics · 2023Article
- Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing.BMC genomics · 2021Article
- Modular Evolution and Population Variability ofFrontiers in cell and developmental biology · 2021Article
- Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata.Genome biology and evolution · 2020Article
- A chordate species lackingProceedings of the National Academy of Sciences of the United States of America · 2020Article
- ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.Nucleic acids research · 2018Article
- Modified whole-mount in situ hybridisation and immunohistochemistry protocols without removal of the vitelline membrane in the appendicularian Oikopleura dioica.Development genes and evolution · 2017Article
- Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa.Journal of plankton researchReview
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA sequencing analysis was carried out to characterize egg and larval transcriptomes in the appendicularian, Oikopleura dioica, a planktonic chordate, which is characterized by rapid development and short life cycle of 5 days, using a Japanese population of the organism. De novo transcriptome assembly matched with 16,423 proteins corresponding to 95.4% of the protein-encoding genes deposited in the OikoBase, the genome database of the Norwegian population. Nucleotide and amino acid sequence identities between the Japanese and Norwegian O. dioica were estimated to be around 91.0 and 94.8%, respectively. We discovered 175 novel protein-encoding genes: 144 unigenes were common to both the Japanese and Norwegian populations, whereas 31 unigenes were not found in the OikoBase genome reference. Among the total 12,311 unigenes, approximately 63% were detected in egg-stage RNAs, whereas 99% were detected in larval stage RNAs; 3772 genes were up-regulated, and 1336 genes were down-regulated more than four-fold in the larvae. Gene ontology analyses characterized gene activities in these two developmental stages. We found a messenger RNA (mRNA) 5' trans-spliced leader, which was observed in 40.8% of the total unique transcripts. It showed preferential linkage to adenine at the 5' ends of the downstream exons. Trans-splicing was observed more frequently in egg mRNAs compared with larva-specific mRNAs.
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