Protists and the Wild, Wild West of Gene Expression: New Frontiers, Lawlessness, and Misfits

Literature Cited

1. Aeschlimann SH, Jönsson F, Postberg J, Stover NA, Petera RL. 1.  et al. 2014. The draft assembly of the radically organized Stylonychia lemnae macronuclear genome. Genome Biol. Evol. 6:1707–23 [Google Scholar]
2. Andersson SGE, Kurland CG. 2.  1995. Genomic evolution drives the evolution of the translation system. Biochem. Cell Bio. 73:775–87 [Google Scholar]
3. Arnaiz O, Mathy N, Baudry C, Malinsky S, Aury JM. 3.  et al. 2012. The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PLOS Genet. 8:e1002984 [Google Scholar]
4. Barbrook AC, Dorrell RG, Burrows J, Plenderleith LJ, Nisbet RER. 4.  et al. 2012. Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae. Plant Mol. Biol. 79:347–57 [Google Scholar]
5. Barbrook AC, Howe CJ, Kurniawan DP, Tarr SJ. 5.  2010. Organization and expression of organellar genomes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365:785–97 [Google Scholar]
6. Boer P, Gray MW. 6.  1988. Scrambled ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA. Cell 55:399–411 [Google Scholar]
7. Boersema PJ, Kahraman A, Picotti P. 7.  2015. Proteomics beyond large-scale protein expression analysis. Curr. Opin. Biotechnol. 34:162–70 [Google Scholar]
8. Burki F. 8.  2014. The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harb. Perspect. Biol. 6:a016147 [Google Scholar]
9. Burki F, Corradi N, Sierra R, Pawlowski J, Meyer GR. 9.  et al. 2013. Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in rhizaria. Curr. Biol. 23:1541–47 [Google Scholar]
10. Carnes J, Trotter JR, Peltan A, Fleck M, Stuart K. 10.  2008. RNA editing in Trypanosoma brucei requires three different editosomes. Mol. Cell. Biol. 28:122–30 [Google Scholar]
11. Caron DA, Worden AZ, Countway PD, Demir E, Heidelberg KB. 11.  2009. Protists are microbes too: a perspective. ISME J. 3:4–12 [Google Scholar]
12. Carradec Q, Götz U, Arnaiz O, Pouch J, Simon M. 12.  et al. 2015. Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia. Nucleic Acids Res. 43:1818–33 [Google Scholar]
13. Cervantes MD, Hamilton EP, Xiong J, Lawson MJ, Yuan D. 13.  et al. 2013. Selecting one of several mating types through gene segment joining and deletion in Tetrahymena thermophila. PLOS Biol. 11e1001518
14. Chalker DL, Yao MC. 14.  2011. DNA elimination in ciliates: Transposon domestication and genome surveillance. Annu. Rev. Genet. 45:227–46 [Google Scholar]
15. Chen SH, Habib G, Yang CY, Gu ZW, Lee BR. 15.  et al. 1987. Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science 238:363–66 [Google Scholar]
16. Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM. 16.  et al. 2014. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell 158:1187–98 [Google Scholar]
17. Cocquyt E, Verbruggen H, Leliaert F, De Clerck O. 17.  2010. Evolution and cytological diversification of the green seaweeds (Ulvophyceae). Mol. Biol. Evol. 27:2052–61 [Google Scholar]
18. Corell RA, Feagin JE, Riley GR, Strickland T, Guderian JA. 18.  et al. 1993. Trypanosoma brucei minicircles encode multiple guide RNAs which can direct editing of extensively overlapping sequences. Nucleic Acids Res. 21:4313–20 [Google Scholar]
19. Covello P, Gray M. 19.  1993. On the evolution of RNA editing. Trends Genet. 9:265–68 [Google Scholar]
20. Coyne RS, Lhuillier-Akakpo M, Duharcourt S. 20.  2012. RNA-guided DNA rearrangements in ciliates: Is the best genome defence a good offence?. Biol. Cell 104:309–25 [Google Scholar]
21. Dang Y, Green BR. 21.  2009. Substitutional editing of Heterocapsa triquetra chloroplast transcripts and a folding model for its divergent chloroplast 16S rRNA. Gene 442:73–80 [Google Scholar]
22. del Campo J, Sieracki ME, Molestina R, Keeling P, Massana R. 22.  et al. 2014. The others: our biased perspective of eukaryotic genomes. Trends Ecol. Evol. 29:252–59 [Google Scholar]
23. Doolittle WF. 23.  2012. Evolutionary biology: a ratchet for protein complexity. Nature 481:270–71 [Google Scholar]
24. Dorrell RG, Howe CJ. 24.  2012. Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors. PNAS 109:18879–84 [Google Scholar]
25. Drager RG, Hallick RB. 25.  1993. A complex twintron is excised as four individual introns. Nucleic Acids Res. 21:2389–94 [Google Scholar]
26. Edqvist J, Burger G, Gray MW. 26.  2000. Expression of mitochondrial protein-coding genes in Tetrahymena pyriformis. J. Mol. Biol. 297:381–93 [Google Scholar]
27. Fan J, Schnare MN, Lee RW. 27.  2003. Characterization of fragmented mitochondrial ribosomal RNAs of the colorless green alga Polytomella parva. Nucleic Acids Res. 31:769–78 [Google Scholar]
28. Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF. 28.  2012. Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell 151:1243–55 [Google Scholar]
29. Farajollahi S, Maas S. 29.  2010. Molecular diversity through RNA editing: A balancing act. Trends Genet. 26:221–30 [Google Scholar]
30. Feagin JE, Abraham JM, Stuart K. 30.  1988. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei. Cell 53:413–422 [Google Scholar]
31. Feagin JE, Harrell MI, Lee JC, Coe KJ, Sands BH. 31.  et al. 2012. The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. PLOS ONE 7:e38320 [Google Scholar]
32. Flegontov P, Gray MW, Burger G, Lukeš J. 32.  2011. Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa?. Curr. Genet. 57:225–32 [Google Scholar]
33. Flipphi M, Fekete E, Ág N, Scazzocchio C, Karaffa L. 33.  2013. Spliceosome twin introns in fungal nuclear transcripts. Fungal Genet. Biol. 57:48–57 [Google Scholar]
34. Frantz C, Ebel C, Paulus F, Imbault P. 34.  2000. Characterization of trans-splicing in Euglenoids. Curr. Genet. 37:349–55 [Google Scholar]
35. Fučíková K, Lewis PO, González-Halphen D, Lewis LA. 35.  2014. Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of Sphaeropleales (Chlorophyta). Genome Biol. Evol. 6:2170–80 [Google Scholar]
36. Gao F, Roy SW, Katz LA. 36.  2015. Analyses of alternatively processed genes in ciliates provide insights into the origins of scrambled genomes and may provide a mechanism for speciation. mBio 6:e01998–14 [Google Scholar]
37. Gilbert W. 37.  1978. Why genes in pieces?. Nature 271:501 [Google Scholar]
38. Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ. 38.  et al. 2006. Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. PNAS 103:9566–71 [Google Scholar]
39. Glanz S, Kück U. 39.  2009. Trans-splicing of organelle introns—a detour to continuous RNAs. BioEssays 31:921–34 [Google Scholar]
40. Gommans WM, Mullen SP, Maas S. 40.  2009. RNA editing: a driving force for adaptive evolution?. BioEssays 31:1137–45 [Google Scholar]
41. Goodenough U, Heitman J. 41.  2014. Origins of eukaryotic sexual reproduction. Cold Spring Harb. Perspect. Biol. 6:a016154 [Google Scholar]
42. Gray MW, Lukeš J, Archibald JM, Keeling PJ, Doolittle WF. 42.  2010. Irremediable complexity?. Science 330:920–21 [Google Scholar]
43. Hallick RB, Hong L, Drager RG, Favreau MR, Monfort A. 43.  et al. 1993. Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res. 21:3537–44 [Google Scholar]
44. Heinonen TY, Schnare MN, Young PG, Gray MW. 44.  1987. Rearranged coding segments, separated by a transfer RNA gene, specify the two parts of a discontinuous large subunit ribosomal RNA in Tetrahymena pyriformis mitochondria. J. Biol. Chem. 262:2879–87 [Google Scholar]
45. Hjort K, Goldberg AV, Tsaousis AD, Hirt RP, Embley TM. 45.  2010. Diversity and reductive evolution of mitochondria among microbial eukaryotes. Philos. Trans. R. Soc. B 365:713–27 [Google Scholar]
46. Horowitz S, Gorovsky MA. 46.  1985. An unusual genetic code in nuclear genes of Tetrahymena. PNAS 82:2452–55 [Google Scholar]
47. Jackson CJ, Norman JE, Schnare MN, Gray MW, Keeling PJ. 47.  et al. 2007. Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria. BMC Biol. 5:41 [Google Scholar]
48. Jackson CJ, Waller RF. 48.  2013. A widespread and unusual RNA trans-splicing type in dinoflagellate mitochondria. PLOS ONE 8:e56777 [Google Scholar]
49. Janouškovec J, Sobotka R, Lai DH, Flegontov P, Koník P. 49.  et al. 2013. Split photosystem protein, linear-mapping topology and growth of structural complexity in the plastid genome of Chromera velia. Mol. Biol. Evol. 30:2447–62 [Google Scholar]
50. Janouškovec J, Tikhonenkov DV, Burki F, Howe AT, Kolísko M. 50.  et al. 2015. Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives. PNAS 112:10200–7 [Google Scholar]
51. Jedelský PL, Doležal P, Rada P, Pyrih J, Smíd O. 51.  et al. 2011. The minimal proteome in the reduced mitochondrion of the parasitic protist Giardia intestinalis. PLOS ONE 6:e17285 [Google Scholar]
52. Ji YE, Mericle BL, Rehkopf DH, Anderson JD, Feagin JE. 52.  1996. The Plasmodium falciparum 6 kb element is polycistronically transcribed. Mol. Biochem. Parasitol 81:211–23 [Google Scholar]
53. Jobson RW, Qiu YL. 53.  2008. Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift?. Biol. Dir. 3:43 [Google Scholar]
54. Kamikawa R, Inagaki Y, Tokoro M, Roger AJ, Hashimoto T. 54.  2011. Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing. Curr. Biol. 21:311–15 [Google Scholar]
55. Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE. 55.  et al. 2014. The marine microbial eukaryote transcriptome sequencing project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLOS Biol. 12:e1001889 [Google Scholar]
56. Keeling PJ, Doolittle WF. 56.  1996. A non-canonical genetic code in an early diverging eukaryotic lineage. EMBO J. 15:2285–90 [Google Scholar]
57. Keeling PJ, Leander BS. 57.  2003. Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix. J. Mol. Biol. 326:1337–49 [Google Scholar]
58. Keeling PJ, Leander BS, Lukeš J. 58.  2010. Reply to Speijer: Does complexity necessarily arise from selective advantage?. PNAS 107:E26 [Google Scholar]
59. Kelly S, Kramer S, Schwede A, Maini PK, Gull K. 59.  et al. 2012. Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes. Open Biol. 2:120033 [Google Scholar]
60. Knight RD, Freeland SJ, Landweber LF. 60.  2001. Rewiring the keyboard: Evolvability of the genetic code. Nat. Rev. Genet. 2:49–58 [Google Scholar]
61. Kolisko M, Boscaro V, Burki F, Lynn DH, Keeling PJ. 61.  2014. Single-cell transcriptomics for microbial eukaryotes. Curr. Biol. 24:R1081–82 [Google Scholar]
62. Kuo RC, Zhang H, Zhuang Y, Hannick L, Lin S. 62.  2013. Transcriptomic study reveals widespread spliced leader trans-splicing, short 5′-UTRs and potential complex carbon fixation mechanisms in the euglenoid alga Eutreptiella sp. PLOS ONE 8:e60826 [Google Scholar]
63. Lane CE, van den Heuvel K, Kozera C, Curtis BA, Parsons BJ. 63.  et al. 2007. Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. PNAS 104:19908–13 [Google Scholar]
64. Lang BF, Jakubkova M, Hegedusova E, Daoud R, Forget L. 64.  et al. 2014. Massive programmed translational jumping in mitochondria. PNAS 111:5926–31 [Google Scholar]
65. Lang-Unnasch N, Aiello DP. 65.  1999. Sequence evidence for an altered genetic code in the Neospora caninum plastid. Int. J. Parasitol. 29:1557–62 [Google Scholar]
66. Lasda EL, Blumenthal T. 66.  2011. Trans-splicing. Wiley Interdiscip. Rev. RNA 2:417–34 [Google Scholar]
67. Le P, Fisher PR, Barth C. 67.  2009. Transcription of the Dictyostelium discoideum mitochondrial genome occurs from a single initiation site. RNA 15:2321–30 [Google Scholar]
68. Libby E, Ratcliff WC. 68.  2014. Ratcheting the evolution of multicellularity. Science 346:426–27 [Google Scholar]
69. Lukeš J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW. 69.  2011. How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63:528–37 [Google Scholar]
70. Lukeš J, Guilbride DL, Votýpka J, Zíková A, Benne R. 70.  et al. 2002. Kinetoplast DNA network: evolution of an improbable structure. Eukaryot. Cell 4:495–502 [Google Scholar]
71. Lukeš J, Leander BS, Keeling PJ. 71.  2009. Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. PNAS 106:9963–70 [Google Scholar]
72. Lynch M. 72.  2007. The frailty of adaptive hypotheses for the origins of organismal complexity. PNAS 104:8597–604 [Google Scholar]
73. Lynch M. 73.  2007. The Origins of Genome Architecture Sunderland, MA: Sinauer
74. Lynch M, Conery JS. 74.  2003. The origins of genome complexity. Science 302:1401–4 [Google Scholar]
75. Marande W, Burger G. 75.  2007. Mitochondrial DNA as a genomic jigsaw puzzle. Science 318:415 [Google Scholar]
76. Marchetti A, Schruth DM, Durkin CA, Parker MS, Kodner RB. 76.  et al. 2012. Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. PNAS 109:E317–25 [Google Scholar]
77. Martínez-Calvillo S, Vizuet-de-Rueda JC, Florencio-Martínez LE, Manning-Cela RG, Figueroa-Angulo EE. 77.  2010. Gene expression in trypanosomatid parasites. J. Biomed. Biotechnol. 2010:525241 [Google Scholar]
78. Maruyama S, Sugahara J, Kanai A, Nozaki H. 78.  2010. Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes. Mol. Biol. Evol. 27:1070–76 [Google Scholar]
79. Masuda I, Matsuzaki M, Kita K. 79.  2010. Extensive frameshift at all AGG and CCC codons in the mitochondrial cytochrome c oxidase subunit 1 gene of Perkinsus marinus (Alveolata; Dinoflagellata). Nucleic Acids Res. 38:6186–94 [Google Scholar]
80. Matsumoto T, Ishikawa SA, Hashimoto T, Inagaki Y. 80.  2011. A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum. Mol. Phylogenet. Evol. 60:68–72 [Google Scholar]
81. Maynard Smith JM, Szathmary E. 81.  1995. The Major Transitions in Evolution Oxford, UK: Oxford Univ. Press
82. McFadden GI, Reith ME, Munholland J, Lang-Unnasch N. 82.  1996. Plastid in human parasites. Nature 381:482 [Google Scholar]
83. Metzker ML. 83.  2010. Sequencing technologies—the next generation. Nat. Rev. Genet. 11:31–46 [Google Scholar]
84. Moore CE, Archibald JM. 84.  2009. Nucleomorph genomes. Annu. Rev. Genet. 43:251–64 [Google Scholar]
85. Moreira S, Breton S, Burger G. 85.  2012. Unscrambling genetic information at the RNA level. Wiley Interdiscip. Rev. RNA 3:213–28 [Google Scholar]
86. Mungpakdee S, Shinzato C, Takeuchi T, Kawashima T, Koyanagi R. 86.  et al. 2014. Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome. Genome Biol. Evol. 6:1408–22 [Google Scholar]
87. Nowacki M, Shetty K, Landweber LF. 87.  2011. RNA-mediated epigenetic programming of genome rearrangements. Annu. Rev. Genomics Hum. Genet. 12:367–89 [Google Scholar]
88. Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG. 88.  et al. 2008. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 451:153–58 [Google Scholar]
89. Osawa S, Jukes TH. 89.  1989. Codon reassignment (codon capture) in evolution. J. Mol. Evol. 28:271–78 [Google Scholar]
90. Palmer JD. 90.  1997. Organelle genomes: going, going, gone. ! Science 275:790–91 [Google Scholar]
91. Pawlowski J. 91.  2013. The new micro-kingdoms of eukaryotes. BMC Biol. 11:40 [Google Scholar]
92. Prescott DM. 92.  1994. The DNA of ciliated protozoa. Microbiol. Rev. 58:233–67 [Google Scholar]
93. Rackham O, Shearwood AMJ, Mercer TR, Davies SM, Mattick JS. 93.  et al. 2011. Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA 17:2085–93 [Google Scholar]
94. Raz T, Kapranov P, Lipson D, Letovsky S, Milos PM. 94.  et al. 2011. Protocol dependence of sequencing-based gene expression measurements. PLOS ONE 6:e19287 [Google Scholar]
95. Rehkopf DH, Gillespie DE, Harrell MI, Feagin JE. 95.  2000. Transcriptional mapping and RNA processing of the Plasmodium falciparum mitochondrial mRNAs. Mol. Biochem. Parasitol. 105:91–103 [Google Scholar]
96. Richardson E, Dorrell RG, Howe CJ. 96.  2014. Genome-wide transcript profiling reveals the coevolution of plastid gene sequences and transcript processing pathways in the fucoxanthin dinoflagellate Karlodinium veneficum. Mol. Biol. Evol. 31:2376–86 [Google Scholar]
97. Rogozin IB, Carmel L, Csuros M, Koonin EV. 97.  2012. Origin and evolution of spliceosomal introns. Biol. Dir. 7:6150–57 [Google Scholar]
98. Roy SW, Hudson AJ, Joseph J, Yee J, Russell AG. 98.  2012. Numerous fragmented spliceosomal introns, AT-AC splicing, and an unusual dynein gene expression pathway in Giardia lamblia. Mol. Biol. Evol. 29:43–49 [Google Scholar]
99. Schmidt M, Geßner G, Luff M, Heiland I, Wagner V. 99.  et al. 2006. Proteomic analysis of the eyespot of Chlamydomonas reinhardtii provides novel insights into its components and tactic movements. Plant Cell 18:1908–30 [Google Scholar]
100. Schnare MN, Gray MW. 100.  1990. Sixteen discrete RNA components in the cytoplasmic ribosome of Euglena gracilis. J. Mol. Biol. 215:73–83 [Google Scholar]
101. Schoeberl UE, Mochizuki K. 101.  2011. Keeping the soma free of transposons: programmed DNA elimination in ciliates. J. Biol. Chem. 286:37045–52 [Google Scholar]
102. Simpson L, Shaw J. 102.  1989. RNA editing and the mitochondrial cryptogenes of kinetoplastid protozoa. Cell 57:355–66 [Google Scholar]
103. Slamovits CH, Keeling PJ. 103.  2009. Evolution of ultra-small spliceosomal introns in highly reduced nuclear genomes. Mol. Biol. Evol. 26:1699–705 [Google Scholar]
104. Slamovits CH, Saldarriaga JF, Larocque A, Keeling PJ. 104.  2007. The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes. J. Mol. Biol. 372:356–68 [Google Scholar]
105. Sloan DB. 105.  2015. Using plants to elucidate the mechanisms of cytonuclear co-evolution. N. Phytol. 205:1040–46 [Google Scholar]
106. Smith DR. 106.  2013. RNA-Seq data: a goldmine for organelle research. Brief. Funct. Genomics 12:454–56 [Google Scholar]
107. Smith DR. 107.  2015. Buying in to bioinformatics: an introduction to commercial sequence analysis software. Brief. Bioinform. 16:700–9 [Google Scholar]
108. Smith DR. 108.  2016. The past, present and future of mitochondrial genomics: Have we sequenced enough mtDNAs?. Brief. Funct. Genomics 15:47–54 [Google Scholar]
109. Smith DR, Asmail SR. 109.  2014. Next-generation sequencing data suggest that certain nonphotosynthetic green plants have lost their plastid genomes. N. Phytol. 204:7–11 [Google Scholar]
110. Smith DR, Keeling PJ. 110.  2015. Mitochondrial and plastid genome architecture: reoccurring themes but significant differences at the extremes. PNAS 11:10177–84 [Google Scholar]
111. Smith DR, Lee RW. 111.  2010. Low nucleotide diversity for the expanded organelle and nuclear genomes of Volvox carteri supports the mutational-hazard hypothesis. Mol. Biol. Evol. 27:2244–56 [Google Scholar]
112. Smith DR, Lee RW. 112.  2014. A plastid without a genome: Evidence from the nonphotosynthetic green alga Polytomella. Plant Phys. 164:1812–19 [Google Scholar]
113. Soma A, Onodera A, Sugahara J, Kanai A, Yachie N. 113.  et al. 2007. Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science 318:450–53 [Google Scholar]
114. Speijer D. 114.  2010. Constructive neutral evolution cannot explain current kinetoplastid panediting patterns. PNAS 107:E25 [Google Scholar]
115. Speijer D, Lukeš J, Eliáš M. 115.  2015. Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life. PNAS 112:8827–34 [Google Scholar]
116. Spencer DF, Gray MW. 116.  2011. Ribosomal RNA genes in Euglena gracilis mitochondrial DNA: fragmented genes in a seemingly fragmented genome. Mol. Genet. Genomics 285:19–31 [Google Scholar]
117. Stoltzfus A. 117.  1999. On the possibility of constructive neutral evolution. J. Mol. Evol. 49:169–81 [Google Scholar]
118. Sutton RE, Boothroyd JC. 118.  1986. Evidence for trans splicing in trypanosomes. Cell 47:527–35 [Google Scholar]
119. Swart EC, Bracht JR, Magrini V, Minx P, Chen X. 119.  et al. 2013. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLOS Biol 11:e1001473 [Google Scholar]
120. Swart EC, Nowacki M. 120.  2015. The eukaryotic way to defend and edit genomes by sRNA-targeted DNA deletion. Ann. N. Y. Acad. Sci.1341106–14
121. Tablizo FA, Lluisma AO. 121.  2014. The mitochondrial genome of the red alga Kappaphycus striatus (“Green Sacol” variety): complete nucleotide sequence, genome structure and organization, and comparative analysis. Mar. Genomics 18:155–61 [Google Scholar]
122. Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ. 122.  et al. 2014. Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics 15:374 [Google Scholar]
123. Umen JG. 123.  2013. Genetics: swinging ciliates' seven sexes. Curr. Biol. 23:R475–77 [Google Scholar]
124. Valach M, Moreira S, Kiethega GN, Burger G. 124.  2014. Trans-splicing and RNA editing of LSU rRNA in Diplonema mitochondria. Nucleic Acids Res. 42:2660–72 [Google Scholar]
125. Vlcek C, Marande W, Teijeiro S, Lukeš J, Burger G. 125.  2011. Systematically fragmented genes in a multipartite mitochondrial genome. Nucleic Acids Res. 39:979–88 [Google Scholar]
126. Waller RF, Jackson CJ. 126.  2009. Dinoflagellate mitochondrial genomes: Stretching the rules of molecular biology. BioEssays 31:237–45 [Google Scholar]
127. White TC, Rudenko G, Borst P. 127.  1986. Three small RNAs within the 10 kb trypanosome rRNA transcription unit are analogous to domain VII of other eukaryotic 28S rRNAs. Nucleic Acids Res. 14:9471–89 [Google Scholar]
128. Williams BA, Slamovits CH, Patron NJ, Fast NM, Keeling PJ. 128.  2005. A high frequency of overlapping gene expression in compacted eukaryotic genomes. PNAS 102:10936–41 [Google Scholar]
129. Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE. 129.  et al. 2015. Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science 347:1257594 [Google Scholar]
130. Záhonová K, Hadariová L, Vacula R, Yurchenko V, Eliáš M. 130.  et al. 2014. A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis. FEBS Lett. 588:783–88 [Google Scholar]
131. Zhang H, Campbell DA, Sturm NR, Dungan CF, Lin S. 131.  2011. Spliced leader RNAs, mitochondrial gene frameshifts and multi-protein phylogeny expand support for the genus Perkinsus as a unique group of alveolates. PLOS ONE 6:e19933 [Google Scholar]
132. Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR. 132.  et al. 2007. Spliced leader RNA trans-splicing in dinoflagellates. PNAS 104:4618–23 [Google Scholar]
133. Zhang Z, Green BR, Cavalier-Smith T. 133.  1999. Single gene circles in dinoflagellate chloroplast genomes. Nature 400:155–59 [Google Scholar]