1. Mukherjee S, Ray M, Ray S. Phagocytic efficiency and cytotoxic responses of Indian freshwater sponge (Eunapius carteri) cells isolated by density gradient centrifugation and flow cytometry: a morphofunctional analysis. Zoology (Jena). 2015;118(1):8-18.
2. Kawamoto H, Ikawa T, Masuda K, Wada H, Katsura Y. A map for lineage restriction of progenitors during hematopoiesis: the essence of the myeloid-based model. Immunol Rev. 2010;238(1):23-36.
3. Cooper MD, Alder MN. The evolution of adaptive immune systems. Cell. 2006;124(4): 815-822.
4. Boehm T. Evolution of vertebrate immunity. Curr Biol. 2012;22(17):R722-732.
5. Rosental B, Kowarsky M, Seita J, et al. Complex mammalian-like haematopoietic system found in a colonial chordate. Nature. 2018;564(7736):425-429.
6. Katsura Y, Kawamoto H. Stepwise lineage restriction of progenitors in lympho- myelopoiesis. Int Rev Immunol. 2001;20(1):1-20.
7. Kawamoto H, Ohmura K, Katsura Y. Direct evidence for the commitment of hematopoietic stem cells to T, B and myeloid lineages in murine fetal liver. Int Immunol. 1997;9(7):1011-1019.
8. Lu M, Kawamoto H, Katsube Y, Ikawa T, Katsura Y. The common myelolymphoid progenitor: a key intermediate stage in hemopoiesis generating T and B cells. J Immunol. 2002;169(7):3519-3525.
9. Masuda K, Kakugawa K, Nakayama T, Minato N, Katsura Y, Kawamoto H. T cell lineage determination precedes the initiation of TCR gene rearrangement. J Immunol. 2007;179(6):3699-3706.
10. Wada H, Masuda K, Satoh R, et al. Adult T-cell progenitors retain myeloid potential. Nature. 2008;452(7188):768-772.
11. Kawamoto H. A close developmental relationship between the lymphoid and myeloid lineages. Trends Immunol. 2006; 27(4):169-175.
12. Li J, Barreda DR, Zhang YA, et al. B lymphocytes from early vertebrates have potent phagocytic and microbicidal abilities. Nat Immunol. 2006; 7(10):1116-1124.
13. Nagasawa T, Nakayasu C, Rieger AM, Barreda DR, Somamoto T, Nakao M. Phagocytosis by thrombocytes is a conserved innate immune mechanism in lower vertebrates. Front Immunol. 2014;5:445.
14. Stokes EE, Firkin BG. Studies of the peripheral blood of the Port Jackson shark (Heterodontus portusjacksoni) with particular reference to the thrombocyte. Br J Haematol. 1971;20(4):427-435.
15. Sebe-Pedros A, Irimia M, Del Campo J, et al. Regulated aggregative multicellularity in a close unicellular relative of metazoa. Elife. 2013;2:e01287.
16. Consortium F, the RP, Clst, et al. A promoter- level mammalian expression atlas. Nature. 2014;507(7493):462-470.
17. Choi J, Baldwin TM, Wong M, et al. Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans. Nucleic Acids Res. 2019;47(D1): D780-D785.
18. Imai KS, Hino K, Yagi K, Satoh N, Satou Y. Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks. Development. 2004;131(16):4047-4058.
19. Satou Y, Kawashima T, Shoguchi E, Nakayama A, Satoh N. An integrated database of the ascidian, Ciona intestinalis: towards functional genomics. Zoolog Sci. 2005;22(8):837-843.
20. Suga H, Chen Z, de Mendoza A, et al. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat Commun. 2013;4:2325.
21. Sogabe S, Hatleberg WL, Kocot KM, et al. Pluripotency and the origin of animal multicellularity. Nature. 2019;570(7762): 519-522.
22. de Mendoza A, Suga H, Permanyer J, Irimia M, Ruiz-Trillo I. Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. Elife. 2015;4:e08904.
23. Fairclough SR, Chen Z, Kramer E, et al. Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta. Genome Biol. 2013;14(2):R15.
24. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20(1):238.
25. Ohmura K, Kawamoto H, Fujimoto S, Ozaki S, Nakao K, Katsura Y. Emergence of T, B, and myeloid lineage-committed as well as multipotent hemopoietic progenitors in the aorta-gonad-mesonephros region of day 10 fetuses of the mouse. J Immunol. 1999; 163(9):4788-4795.
26. Masuda K, Kubagawa H, Ikawa T, et al. Prethymic T-cell development defined by the expression of paired immunoglobulin- like receptors. EMBO J. 2005;24(23): 4052-4060.
27. Turner EC. Possible poriferan body fossils in early Neoproterozoic microbial reefs. Nature. 2021;596(7870):87-91.
28. Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D, Peterson KJ. The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science. 2011;334(6059):1091-1097.
29. Shalchian-Tabrizi K, Minge MA, Espelund M, et al. Multigene phylogeny of choanozoa and the origin of animals. PLoS One. 2008;3(5): e2098.
30. Torruella G, Derelle R, Paps J, et al. Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol Biol Evol. 2012;29(2):531-544.
31. Torruella G, de Mendoza A, Grau-Bove X, et al. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Curr Biol. 2015;25(18): 2404-2410.
32. Hartenstein V. Blood cells and blood cell development in the animal kingdom. Annu Rev Cell Dev Biol. 2006;22:677-712.
33. Soji T, Murata Y, Ohira A, Nishizono H, Tanaka M, Herbert DC. Evidence that hepatocytes can phagocytize exogenous substances. Anat Rec. 1992;233(4):543-546.
34. Villena JA, Cousin B, Penicaud L, Casteilla L. Adipose tissues display differential phagocytic and microbicidal activities depending on their localization. Int J Obes Relat Metab Disord. 2001;25(9):1275-1280.
35. Romana-Souza B, Chen L, Leonardo TR, Chen Z, DiPietro LA. Dermal fibroblast phagocytosis of apoptotic cells: a novel pathway for wound resolution. FASEB J. 2021;35(4):e21443.
36. Molkentin JD, Kalvakolanu DV, Markham BE. Transcription factor GATA-4 regulates cardiac muscle-specific expression of the alpha- myosin heavy-chain gene. Mol Cell Biol. 1994;14(7):4947-4957.
37. Milatovich A, Qiu RG, Grosschedl R, Francke U. Gene for a tissue-specific transcriptional activator (EBF or Olf-1), expressed in early B lymphocytes, adipocytes, and olfactory neurons, is located on human chromosome 5, band q34, and proximal mouse chromosome 11. Mamm Genome. 1994;5(4):211-215.
38. Liu X, Rowan SC, Liang J, et al. Categorization of lung mesenchymal cells in development and fibrosis. iScience. 2021; 24(6):102551.
39. Nerlov C, Graf T. PU.1 induces myeloid lineage commitment in multipotent hematopoietic progenitors. Genes Dev. 1998;12(15):2403-2412.
40. Tsujimura H, Tamura T, Gongora C, et al. ICSBP/IRF-8 retrovirus transduction rescues dendritic cell development in vitro. Blood. 2003;101(3):961-969.
41. Shayman JA, Tesmer JJG. Lysosomal phospholipase A2. Biochim Biophys Acta Mol Cell Biol Lipids. 2019;1864(6):932-940.
42. Mota AC, Dominguez M, Weigert A, Snodgrass RG, Namgaladze D, Brune B. Lysosome-dependent LXR and PPARdelta activation upon efferocytosis in human macrophages. Front Immunol. 2021;12: 637778.
43. Xie H, Ye M, Feng R, Graf T. Stepwise reprogramming of B cells into macrophages. Cell. 2004;117(5):663-676.
44. Laiosa CV, Stadtfeld M, Xie H, de Andres- Aguayo L, Graf T. Reprogramming of committed T cell progenitors to macrophages and dendritic cells by C/EBP alpha and PU.1 transcription factors. Immunity. 2006;25(5):731-744.
45. Collombet S, van Oevelen C, Sardina Ortega JL, et al. Logical modeling of lymphoid and myeloid cell specification and transdifferentiation. Proc Natl Acad Sci U S A. 2017;114(23):5792-5799.
46. Cirovic B, Schonheit J, Kowenz-Leutz E, et al. C/EBP-induced transdifferentiation reveals granulocyte-macrophage precursor-like plasticity of B cells. Stem Cell Rep. 2017;8(2): 346-359.
47. Suh HC, Gooya J, Renn K, Friedman AD, Johnson PF, Keller JR. C/EBPalpha determines hematopoietic cell fate in multipotential progenitor cells by inhibiting erythroid differentiation and inducing myeloid differentiation. Blood. 2006;107(11): 4308-4316.
48. Zhang DE, Zhang P, Wang ND, Hetherington CJ, Darlington GJ, Tenen DG. Absence of granulocyte colony-stimulating factor signaling and neutrophil development in CCAAT enhancer binding protein alpha- deficient mice. Proc Natl Acad Sci U S A. 1997;94(2):569-574.
49. Zhang P, Iwasaki-Arai J, Iwasaki H, et al. Enhancement of hematopoietic stem cell repopulating capacity and self-renewal in the absence of the transcription factor C/EBP alpha. Immunity. 2004;21(6):853-863.
50. Giladi A, Paul F, Herzog Y, et al. Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis. Nat Cell Biol. 2018;20(7):836-846.
51. Piunti A, Shilatifard A. Epigenetic balance of gene expression by Polycomb and COMPASS families. Science. 2016;352(6290): aad9780.
52. Wang H, Wang L, Erdjument-Bromage H, et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature. 2004;431(7010): 873-878.
53. Ikawa T, Masuda K, Endo TA, et al. Conversion of T cells to B cells by inactivation of polycomb-mediated epigenetic suppression of the B-lineage program. Genes Dev. 2016;30(22):2475-2485.
54. Sebe-Pedros A, Degnan BM, Ruiz-Trillo I. The origin of Metazoa: a unicellular perspective. Nat Rev Genet. 2017;18(8):498-512.
55. Cavalier-Smith T, Chao EE. Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution. J Mol Evol. 2003;56(5):540-563.
56. Steenkamp ET, Wright J, Baldauf SL. The protistan origins of animals and fungi. Mol Biol Evol. 2006;23(1):93-106.
57. Ros-Rocher N, Perez-Posada A, Leger MM, Ruiz-Trillo I. The origin of animals: an ancestral reconstruction of the unicellular-to- multicellular transition. Open Biol. 2021; 11(2):200359.
58. Stibbs HH, Owczarzak A, Bayne CJ, DeWan P. Schistosome sporocyst-killing Amoebae isolated from Biomphalaria glabrata. J Invertebr Pathol. 1979;33(2):159-170.
59. Owczarzak A, Stibbs HH, Bayne CJ. The destruction of Schistosoma mansoni mother sporocysts in vitro by amoebae isolated from Biomphalaria glabrata: an ultrastructural study. J Invertebr Pathol. 1980;35(1):26-33.
60. Sebe-Pedros A, de Mendoza A, Lang BF, Degnan BM, Ruiz-Trillo I. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol Biol Evol. 2011;28(3):1241-1254.
61. Sebe-Pedros A, Ballare C, Parra-Acero H, et al. The dynamic regulatory genome of Capsaspora and the origin of animal multicellularity. Cell. 2016;165(5):1224-1237.
62. Kindred JE. Phagocytosis and clotting in the perivisceral fluid of Arbacia. Biol Bull. 1921; 41(3):144-152.
63. Yamamoto R, Morita Y, Ooehara J, et al. Clonal analysis unveils self-renewing lineage- restricted progenitors generated directly from hematopoietic stem cells. Cell. 2013; 154(5):1112-1126.
64. Parrinello D, Parisi M, Parrinello N, Cammarata M. Ciona robusta hemocyte populational dynamics and PO-dependent cytotoxic activity. Dev Comp Immunol. 2020; 103:103519.
65. Hagerstrand H, Danieluk M, Bobrowska- Hagerstrand M, et al. The lamprey (Lampetra fluviatilis) erythrocyte; morphology, ultrastructure, major plasma membrane proteins and phospholipids, and cytoskeletal organization. Mol Membr Biol. 1999;16(2): 195-204.
66. Pancer Z, Amemiya CT, Ehrhardt GR, Ceitlin J, Gartland GL, Cooper MD. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature. 2004;430(6996):174-180.
67. Bajoghli B, Guo P, Aghaallaei N, et al. A thymus candidate in lampreys. Nature. 2011;470(7332):90-94.
68. Ohno S. Evolution by Gene Duplication. Springer; 1970.
69. Furlong RF, Holland PW. Were vertebrates octoploid? Philos Trans R Soc Lond B Biol Sci. 2002;357(1420):531-544.
70. Scott LM, Civin CI, Rorth P, Friedman AD. A novel temporal expression pattern of three C/EBP family members in differentiating myelomonocytic cells. Blood. 1992;80(7): 1725-1735.
71. Yamanaka R, Barlow C, Lekstrom-Himes J, et al. Impaired granulopoiesis, myelodysplasia, and early lethality in CCAAT/ enhancer binding protein epsilon-deficient mice. Proc Natl Acad Sci U S A. 1997;94(24): 13187-13192.
72. Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol. 2002; 52(Pt 2):297-354.
73. Yutin N, Wolf MY, Wolf YI, Koonin EV. The origins of phagocytosis and eukaryogenesis. Biol Direct. 2009;4:9.
74. Cabal-Hierro L, van Galen P, Prado MA, et al. Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nat Commun. 2020;11(1):1406.
75. Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell. 2012;149(2):467-482.
76. Lane AA, Chapuy B, Lin CY, et al. Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation. Nat Genet. 2014;46(6):618-623.
77. Yue F, Cheng Y, Breschi A, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014;515(7527):355-364.
78. Roman-Trufero M, Mendez-Gomez HR, Perez C, et al. Maintenance of undifferentiated state and self-renewal of embryonic neural stem cells by Polycomb protein Ring1B. Stem Cells. 2009;27(7):1559-1570.
79. Kawamoto S, Niwa H, Tashiro F, et al. A novel reporter mouse strain that expresses enhanced green fluorescent protein upon Cre-mediated recombination. FEBS Lett. 2000;470(3):263-268.
80. Sebe-Pedros A, Chomsky E, Pang K, et al. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat Ecol Evol. 2018;2(7):1176-1188.
81. Putnam NH, Srivastava M, Hellsten U, et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science. 2007;317(5834):86-94.
82. Srivastava M, Begovic E, Chapman J, et al. The Trichoplax genome and the nature of placozoans. Nature. 2008;454(7207):955-960.
83. Srivastava M, Simakov O, Chapman J, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 2010;466(7307):720-726.
84. King N, Westbrook MJ, Young SL, et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 2008;451(7180):783-788.
85. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22(21):2688- 2690.
86. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol. 2021;38(7):3022-3027.
87. Hosokawa H, Ungerback J, Wang X, et al. Transcription Factor PU.1 Represses and Activates Gene Expression in Early T Cells by Redirecting Partner Transcription Factor Binding. Immunity. 2018;48(6):1119-1134 e1117.
88. Hamada M, Goricki S, Byerly MS, Satoh N, Jeffery WR. Evolution of the chordate regeneration blastema: Differential gene expression and conserved role of notch signaling during siphon regeneration in the ascidian Ciona. Dev Biol. 2015;405(2):304- 315.
89. Ikawa T, Kawamoto H, Goldrath AW, Murre C. E proteins and Notch signaling cooperate to promote T cell lineage specification and commitment. J Exp Med. 2006;203(5):1329-1342.
90. Ikawa T, Kawamoto H, Wright LY, Murre C. Long-term cultured E2A-deficient hematopoietic progenitor cells are pluripotent. Immunity. 2004;20(3):349-360.
91. Kanda Y. Investigation of the freely available easy-to-use software 'EZR' for medical statistics. Bone Marrow Transplant. 2013;48(3):452-458.
92. Bedre R. reneshbedre/bioinfokit: Bioinformatics data analysis and visualization toolkit. Zenodo.; 2020.
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