Transcriptomic analysis reveals functional compartmentalization of the digestive tract in

Andrews S, Krueger F, Segonds-Pichon A, Biggins L, Krueger C, Wingett S (2010) FastQC. A quality control tool for high throughput sequence data 370

Arendt D, Technau U, Wittbrodt J (2001) Evolution of the bilaterian larval foregut. Nature 409:81–85. https://doi.org/10.1038/35051075

Article  CAS  PubMed  Google Scholar 

Arp AJ, Menon JG, Julian D (1995) Multiple mechanisms provide tolerance to environmental sulfide in Urechis caupo. Am Zool. https://doi.org/10.1093/icb/35.2.132

Article  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boyle MJ, Seaver EC (2008) Developmental expression of foxA and gata genes during gut formation in the polychaete annelid, Capitella sp. I. Evol Dev 10:89–105. https://doi.org/10.1111/j.1525-142x.2007.00216.x

Article  CAS  PubMed  Google Scholar 

Chen H, Boutros PC (2011) VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12:35. https://doi.org/10.1186/1471-2105-12-35

Article  PubMed  PubMed Central  Google Scholar 

Chen J, Wang Y, Yang Z, Liu D, Jin Y, Li X, Deng Y, Wang B, Zhang Z, Ma Y (2023) Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data. BMC Genomics 24:248. https://doi.org/10.1186/s12864-023-09358-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng Y, Chen R, Chen J, Huang W, Chen J (2024) A chromosome-level genome assembly of the Echiura Urechis unicinctus. Sci Data 11:90. https://doi.org/10.1038/s41597-023-02885-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. https://doi.org/10.1093/bioinformatics/bts635

Article  CAS  PubMed  Google Scholar 

Gu Z (2022) Complex heatmap visualization. iMeta 1:e43. https://doi.org/10.1002/imt2.43

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y (2017) A single-cell survey of the small intestinal epithelium. Nature 551:333–339. https://doi.org/10.1038/nature24489

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336:1268–1273. https://doi.org/10.1126/science.1223490

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hou X, Wei M, Li Q, Zhang T, Zhou D, Kong D, Xie Y, Qin Z, Zhang Z (2019) Transcriptome analysis of larval segment formation and secondary loss in the echiuran worm Urechis unicinctus. Int J Mol Sci 20:1806. https://doi.org/10.3390/ijms20081806

Article  CAS  PubMed  PubMed Central  Google Scholar 

Julian D, Passman WE, Arp AJ (1996) Water lung and body wall contributions to respiration in an echiuran worm. Respir Physiol 106:187–198. https://doi.org/10.1016/s0034-5687(96)00073-4

Article  CAS  PubMed  Google Scholar 

Kim KT, Kim MA, Kim WJ, Jung MM, Kim DH, Sohn YC (2024) Transcriptome analysis of East Asian common octopus, Octopus sinensis, paralarvae. Genes Genomics 46:955–966. https://doi.org/10.1007/s13258-024-01537-3

Article  CAS  PubMed  Google Scholar 

Kim Y, Lee C-J, Ryu K-B, Aryal YP, Jo S, Seo D-C, Song J-H, Jeong B-G, Lee M-J, An S-H (2026) Integrated morphological and transcriptomic analysis of sucker development in Octopus minor. Anim Cells Syst 30:307–319. https://doi.org/10.1080/19768354.2026.2638580

Article  CAS  Google Scholar 

Li N, Song S, Tang Y (1995) The life history of the Urechis unicinctus (Von. Draschi). Shandong Yu Ye 12:24–27

CAS  Google Scholar 

Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930. https://doi.org/10.1093/bioinformatics/btt656

Article  CAS  PubMed  Google Scholar 

McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A 110:3229–3236. https://doi.org/10.1073/pnas.1218525110

Article  PubMed  PubMed Central  Google Scholar 

Mo H, Liu K, An X, Chen Y, Yu J, Yu H, Yao M, Song W, Li Y, Wang L (2025) Molecular cloning, expression analysis, and functional characterization of Intelectin-1 from Chinese giant salamanders (Andrias davidianus). Genes Genomics 47:843–853. https://doi.org/10.1080/08997659.2017.1349007

Article  CAS  PubMed  Google Scholar 

Moor AE, Harnik Y, Ben-Moshe S, Massasa EE, Rozenberg M, Eilam R, Halpern KB, Itzkovitz S (2018) Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. Cell 175:1156–1167. https://doi.org/10.1016/j.cell.2018.08.063

Article  CAS  PubMed  Google Scholar 

Ryu K-B, Jo G-H, Gil Y-C, Jeon D, Choi N-R, Jung S-H, Jo S, An HS, Lee H-Y, Eyun S-i (2023) Eye development and developmental expression of crystallin genes in the long arm octopus, Octopus minor. Front Mar Sci 10:1136602. https://doi.org/10.3389/fmars.2023.1136602

Article  Google Scholar 

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578. https://doi.org/10.1038/nprot.2012.016

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng Q, Wang Y, Chen J, Li Y, Zhao F, Liu D, Wei M, Kong D, Chen Z, Zhang Z (2022) Effects of salinity on the growth, physiological characteristics, and intestinal microbiota of the Echiura worm (Urechis unicinctus). Front Mar Sci 9:912023. https://doi.org/10.3389/fmars.2022.912023

Article  Google Scholar 

Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, Benner C, Chanda SK (2019) Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 10:1523. https://doi.org/10.1038/s41467-019-09234-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Žídek R, Machoň O, Kozmik Z (2018) Wnt/β-catenin signalling is necessary for gut differentiation in a marine annelid, Platynereis dumerilii. EvoDevo 9:14. https://doi.org/10.1186/s13227-018-0100-7

Article  PubMed  PubMed Central  Google Scholar 

Zorn AM, Wells JM (2009) Vertebrate endoderm development and organ formation. Annu Rev Cell Dev Biol 25:221–251. https://doi.org/10.1146/annurev.cellbio.042308.113344

Article  CAS  PubMed  PubMed Central  Google Scholar 

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