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What if I told you that, more than two billion years ago, some tiny living thing started to live inside another living thing … and never left? And now, the descendants of both of those things are in you?

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References:
Chemical and membrane similarities between prokaryotes and organelles:
Margolin W. 2005. FTSZ and the division of prokaryotic cells and organelles. Nature Reviews Molecular Cell Biology 6(11): 862-871.
doi:10.1038/nrm1745
Wise RR, Hoober JK. 2007. Structure and function of plastids. Springer, Berlin. (Chapter 5)
ISBN 9781402065705
Zeth K, Thein M. 2010. Porins in prokaryotes and eukaryotes: common themes and variations. Biochemical Journal 431(1): 13-22.
DOI: 10.1042/BJ20100371
Fischer K, Weber A, Brink S, Arbinger B, Schünemann D, Borchert S, Heldt HW, Popp B, Link TA, Eckeskorn C, Flügge U-I. 1994. Molecular cloning and functional characterization of two new members of the porin family. The Journal of Biological Chemistry 269(41): 25754-25760.
http://www.jbc.org/content/269/41/25754.long
Fairman JW, Noinaj N, Buchanan SK. 2011. The structural biology of β-barrel membrane proteins: a summary of recent reports. Current Opinion in Structural Biology 21(4): 523-531.
https://doi.org/10.1016/j.sbi.2011.05.005
Mileykovskaya E, Dowhan W. 2009. Cardiolipin membrane domains in prokaryotes and eukaryotes. Biochimica et Biophysica Acta (BBA) – Biomembranes 1788(10): 2084-2091.
https://doi.org/10.1016/j.bbamem.2009.04.003
Organelle genomes, organelle dependence on the host cells:
Timmis JN, Ayliffe MA, Huang CY, Martin W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature Reviews Genetics 5: 123-135.
doi:10.1038/nrg1271
Andersson SGE, Zomorodipour A, Andersson JO, Sicheritz-Pontén T, Alsmark UCM, Podowski RM, Näslund AK, Eriksson A-S, Winkler HH, Kurland CG. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396: 133-140.
doi:10.1038/24094
Stoebe B, Kowallik KV. 1999. Gene-cluster analysis in chloroplast genomics. Trends in Genetics 15, 344–347.
http://dx.doi.org/10.1016/S0168-9525(99)01815-6
Douglas A, Raven JA. 2003. Genomes at the interface between bacteria and organelles. Philosophical Transactions B 358(1429): 5-18.
doi: 10.1098/rstb.2002.1188
Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeue de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Pühler A, Martin WF. 2013. Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biology and Evolution 5(1): 31-44.
https://doi.org/10.1093/gbe/evs117
History of the idea:
Sagan, L. 1967. On the origin of mitosing cells. Journal of Theoretical Biology 14(3): 225-274.
https://doi.org/10.1016/0022-5193(67)90079-3
Oldest fossil appearances:
Bengtson S, Sallstedt T,Belivanova V, Whitehouse M. 2017. Three-dimensional preservation of cellular and subcellular structures suggest 1.6 billion-year-old crown-group red algae. PLOS Biology 15(3): e2000735.
https://doi.org/10.1371/journal.pbio.2000735
Bengtson S, Rasmussen B, Ivarsson M, Muhling J, Broman C, Marone F, Stampononi M, Bekker A. 2017. Fungus-like mycelial fossils in 2.4-billion-year-old vesicular basalt. Nature Ecology & Evolution 1, Article number: 0141 (2017)
doi:10.1038/s41559-017-0141