{"doi":"10.1371/journal.pone.0254308","title":"Comparative analysis of transcriptomic profiles among ascidians, zebrafish, and mice: Insights from tissue-specific gene expression","abstract":"<jats:p>\n                    Tissue/organ-specific genes (TSGs) are important not only for understanding organ development and function, but also for investigating the evolutionary lineages of organs in animals. Here, we investigate the TSGs of 9 adult tissues of an ascidian,\n                    <jats:italic>Ciona intestinalis</jats:italic>\n                    Type A (\n                    <jats:italic>Ciona robusta</jats:italic>\n                    ), which lies in the important position of being the sister group of vertebrates. RNA-seq and qRT-PCR identified the\n                    <jats:italic>Ciona</jats:italic>\n                    TSGs in each tissue, and BLAST searches identified their homologs in zebrafish and mice. Tissue distributions of the vertebrate homologs were analyzed and clustered using public RNA-seq data for 12 zebrafish and 30 mouse tissues. Among the vertebrate homologs of the\n                    <jats:italic>Ciona</jats:italic>\n                    TSGs in the neural complex, 48% and 63% showed high expression in the zebrafish and mouse brain, respectively, suggesting that the central nervous system is evolutionarily conserved in chordates. In contrast, vertebrate homologs of\n                    <jats:italic>Ciona</jats:italic>\n                    TSGs in the ovary, pharynx, and intestine were not consistently highly expressed in the corresponding tissues of vertebrates, suggesting that these organs have evolved in\n                    <jats:italic>Ciona</jats:italic>\n                    -specific lineages. Intriguingly, more TSG homologs of the\n                    <jats:italic>Ciona</jats:italic>\n                    stomach were highly expressed in the vertebrate liver (17–29%) and intestine (22–33%) than in the mouse stomach (5%). Expression profiles for these genes suggest that the biological roles of the\n                    <jats:italic>Ciona</jats:italic>\n                    stomach are distinct from those of their vertebrate counterparts. Collectively,\n                    <jats:italic>Ciona</jats:italic>\n                    tissues were categorized into 3 groups: i) high similarity to the corresponding vertebrate tissues (neural complex and heart), ii) low similarity to the corresponding vertebrate tissues (ovary, pharynx, and intestine), and iii) low similarity to the corresponding vertebrate tissues, but high similarity to other vertebrate tissues (stomach, endostyle, and siphons). The present study provides transcriptomic catalogs of adult ascidian tissues and significant insights into the evolutionary lineages of the brain, heart, and digestive tract of chordates.\n                  </jats:p>","journal":"PLOS ONE","year":2021,"id":666067,"datarank":0.4335557636844247,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"self_citation_contribution":0.4335557636844247,"citation_network_contribution":0.0,"self_endowment_contribution":0.4335557636844247,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":17,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1739357,"name":"Tomohiro Osugi","orcid":"0000-0001-6987-9576","position":1,"is_corresponding":false},{"id":1487814,"name":"Akira Shiraishi","orcid":"0000-0003-3456-3074","position":2,"is_corresponding":false},{"id":1739360,"name":"Azumi Wada","orcid":null,"position":3,"is_corresponding":false},{"id":1487815,"name":"Honoo Satake","orcid":"0000-0003-1165-3624","position":4,"is_corresponding":false},{"id":1739356,"name":"Shin Matsubara","orcid":"0000-0002-7794-534X","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Comparative analysis of transcriptomic profiles among ascidians, zebrafish, and mice: Insights from tissue-specific gene expression","abstract":"<jats:p>\n                    Tissue/organ-specific genes (TSGs) are important not only for understanding organ development and function, but also for investigating the evolutionary lineages of organs in animals. Here, we investigate the TSGs of 9 adult tissues of an ascidian,\n                    <jats:italic>Ciona intestinalis</jats:italic>\n                    Type A (\n                    <jats:italic>Ciona robusta</jats:italic>\n                    ), which lies in the important position of being the sister group of vertebrates. RNA-seq and qRT-PCR identified the\n                    <jats:italic>Ciona</jats:italic>\n                    TSGs in each tissue, and BLAST searches identified their homologs in zebrafish and mice. Tissue distributions of the vertebrate homologs were analyzed and clustered using public RNA-seq data for 12 zebrafish and 30 mouse tissues. Among the vertebrate homologs of the\n                    <jats:italic>Ciona</jats:italic>\n                    TSGs in the neural complex, 48% and 63% showed high expression in the zebrafish and mouse brain, respectively, suggesting that the central nervous system is evolutionarily conserved in chordates. In contrast, vertebrate homologs of\n                    <jats:italic>Ciona</jats:italic>\n                    TSGs in the ovary, pharynx, and intestine were not consistently highly expressed in the corresponding tissues of vertebrates, suggesting that these organs have evolved in\n                    <jats:italic>Ciona</jats:italic>\n                    -specific lineages. Intriguingly, more TSG homologs of the\n                    <jats:italic>Ciona</jats:italic>\n                    stomach were highly expressed in the vertebrate liver (17–29%) and intestine (22–33%) than in the mouse stomach (5%). Expression profiles for these genes suggest that the biological roles of the\n                    <jats:italic>Ciona</jats:italic>\n                    stomach are distinct from those of their vertebrate counterparts. Collectively,\n                    <jats:italic>Ciona</jats:italic>\n                    tissues were categorized into 3 groups: i) high similarity to the corresponding vertebrate tissues (neural complex and heart), ii) low similarity to the corresponding vertebrate tissues (ovary, pharynx, and intestine), and iii) low similarity to the corresponding vertebrate tissues, but high similarity to other vertebrate tissues (stomach, endostyle, and siphons). The present study provides transcriptomic catalogs of adult ascidian tissues and significant insights into the evolutionary lineages of the brain, heart, and digestive tract of chordates.\n                  </jats:p>","is_dataset_classified":null,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"34559810","pmcid":"PMC8462739","openalex_id":"https://openalex.org/W3201228591","authors":[],"funders":[{"funder_name":"Japan Society for the Promotion of Science","grant_id":"JP19K16182","title":null}],"total_grants":1,"fwci":0.7692,"citation_percentile":0.6897502,"influential_citations":0,"citation_trend":[{"year":2023,"count":6},{"year":2024,"count":2},{"year":2025,"count":4},{"year":2026,"count":5}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0254308&type=printable","host_type":"journal"},{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0254308&type=printable","host_type":"publisher"},{"url":"https://dx.plos.org/10.1371/journal.pone.0254308","host_type":"publisher"},{"url":"https://doi.org/10.1371/journal.pone.0254308","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/34559810","host_type":"repository"},{"url":"http://europepmc.org/pmc/articles/PMC8462739","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8462739","host_type":"repository"},{"url":"https://doaj.org/article/597f272c40b14264ac7e69dbe66d1b3b","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC8462739","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC8462739?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Marine Ecology and Invasive Species","Developmental Biology and Gene Regulation","Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities","Animals","Biological Evolution","Ciona intestinalis","Female","Gene Expression Regulation","Gene Regulatory Networks","Mice","Organ Specificity","Transcriptome","Zebrafish"],"mesh_terms":["Animals","Ciona intestinalis","Biological Evolution","Female","Gene Expression Regulation","Organ Specificity","Zebrafish","Mice","Gene Regulatory Networks","Transcriptome"],"keywords":["Ciona intestinalis","Ciona","Biology","Vertebrate","Zebrafish","Gene","Transcriptome","Genetics","Lineage (genetic)","Cell biology","Gene expression"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"},{"name":"go"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-13T13:10:07.775109Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}