Akaike H., (1973). “Information theory and an extension of the maximum likelihood principle,” in Proceedings of the Second International Symposium on Inference Theory, eds Petrov B. N., Csàki F., (Budapest: Akadémiai Kiadó), 267–281.
Amorim A., Fernandes T., Taveira N., (2019). Mitochondrial DNA in human identification: a review. PeerJ. 7:e7314. 10.7717/peerj.7314 31428537
Artuso L., Romano A., Verri T., Domenichini A., Argenton F., Santorelli F. M., et al. (2012). Mitochondrial DNA metabolism in early development of zebrafish (Danio rerio). Biochim. Biophys. Acta 1817 1002–1011. 10.1016/j.bbabio.2012.03.019 22465854
Bertrand J. Y., Kim A. D., Violette E. P., Stachura D. L., Cisson J. L., Traver D., (2007). Definitive hematopoiesis initiates through a committed erythromyeloid progenitor in the zebrafish embryo. Development 134 4147–4156. 10.1242/dev.012385 17959717
Bill B. R., Petzold A. M., Clark K. J., Schimmenti L. A., Ekker S. C., (2009). A primer for morpholino use in zebrafish. Zebrafish 6 69–77. 10.1089/zeb.2008.0555 19374550
Boczonadi V., Muller J. S., Pyle A., Munkley J., Dor T., Quartararo J., et al. (2014). EXOSC8 mutations alter mRNA metabolism and cause hypomyelination with spinal muscular atrophy and cerebellar hypoplasia. Nat. Commun. 5:4287. 10.1038/ncomms5287 24989451
Brockerhoff S. E., Rieke F., Matthews H. R., Taylor M. R., Kennedy B., Ankoudinova I., et al. (2003). Light stimulates a transducin-independent increase of cytoplasmic Ca2+ and suppression of current in cones from the zebrafish mutant nof. J. Neurosci. 23 470–480. 10.1523/jneurosci.23-02-00470.2003 12533607
Cheng K. C., (2004). A life-span atlas for the zebrafish. Zebrafish 1:69. 10.1089/zeb.2004.1.69 18248218
Ebert K. M., Liem H., Hecht N. B., (1988). Mitochondrial DNA in the mouse preimplantation embryo. J. Reprod. Fertil. 82 145–149. 10.1530/jrf.0.0820145 3339575
Ekstrand M. I., Falkenberg M., Rantanen A., Park C. B., Gaspari M., Hultenby K., et al. (2004). Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13 935–944. 10.1093/hmg/ddh109 15016765
Fakruddin M., Wei F. Y., Suzuki T., Asano K., Kaieda T., Omori A., et al. (2018). Defective mitochondrial tRNA taurine modification activates global proteostress and leads to mitochondrial disease. Cell Rep. 22 482–496. 10.1016/j.celrep.2017.12.051 29320742
Glickman N. S., Yelon D., (2002). Cardiac development in zebrafish: coordination of form and function. Semin. Cell. Dev. Biol. 13 507–513. 10.1016/s1084952102001040 12468254
Haack T. B., Kopajtich R., Freisinger P., Wieland T., Rorbach J., Nicholls T. J., et al. (2013). ELAC2 mutations cause a mitochondrial RNA processing defect associated with hypertrophic cardiomyopathy. Am. J. Hum. Genet. 93 211–223. 10.1016/j.ajhg.2013.06.006 23849775
Hance N., Ekstrand M. I., Trifunovic A., (2005). Mitochondrial DNA polymerase gamma is essential for mammalian embryogenesis. Hum. Mol. Genet. 14 1775–1783. 10.1093/hmg/ddi184 15888483
Howe K., Clark M. D., Torroja C. F., Torrance J., Berthelot C., Muffato M., et al. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature 496 498–503. 10.1038/nature12111 23594743
Ihaka R. G. R., (1996). R: A language for data analysis and graphics. J. Comput. Graph. Stat. 5 299–314.
Kimmel C. B., Ballard W. W., Kimmel S. R., Ullmann B., Schilling T. F., (1995). Stages of embryonic development of the zebrafish. Dev. Dyn. 203 253–310. 10.1002/aja.1002030302 8589427
Larbuisson A., Dalcq J., Martial J. A., Muller M., (2013). Fgf receptors Fgfr1a and Fgfr2 control the function of pharyngeal endoderm in late cranial cartilage development. Differentiation 86 192–206. 10.1016/j.diff.2013.07.006 24176552
Larsson N. G., Wang J., Wilhelmsson H., Oldfors A., Rustin P., Lewandoski M., et al. (1998). Mitochondrial transcription factor A is necessary for mtDNA maintenance and embryogenesis in mice. Nat. Genet. 18 231–236. 10.1038/ng0398-231 9500544
Lindsey J., (1999). Models for Repeated Measurements, 2nd Edn. Oxford: Oxford University Press.
McGough I. J., Vincent J. P., (2016). Exosomes in developmental signalling. Development 143 2482–2493. 10.1242/dev.126516 27436038
Metodiev M. D., Thompson K., Alston C. L., Morris A. A., He L., Assouline Z., et al. (2016). Recessive mutations in TRMT10C cause defects in mitochondrial RNA processing and multiple respiratory chain deficiencies. Am. J. Hum. Genet. 99:246. 10.1016/j.ajhg.2016.06.013 27392079
Mi H., Huang X., Muruganujan A., Tang H., Mills C., Kang D., et al. (2017). PANTHER version 11: expanded annotation data from gene ontology and reactome pathways, and data analysis tool enhancements. Nucleic Acids Res. 45 D183–D189. 10.1093/nar/gkw1138 27899595
Murayama E., Kissa K., Zapata A., Mordelet E., Briolat V., Lin H. F., et al. (2006). Tracing hematopoietic precursor migration to successive hematopoietic organs during zebrafish development. Immunity 25 963–975. 10.1016/j.immuni.2006.10.015 17157041
Otten A. B., Smeets H. J., (2015). Evolutionary defined role of the mitochondrial DNA in fertility, disease and ageing. Hum. Reprod. Update 21 671–689. 10.1093/humupd/dmv024 25976758
Otten A. B. C., Kamps R., Lindsey P., Gerards M., Pendeville-Samain M., Muller M., et al. (2019). Tfam knockdown results in reduction of mtDNA copy number, OXPHOS deficiency and abnormalities in Zebrafish embryos. bioRxiv [preprint]. 10.1101/843318
Otten A. B., Theunissen T. E., Derhaag J. G., Lambrichs E. H., Boesten I. B., Winandy M., et al. (2016). Differences in strength and timing of the mtDNA bottleneck between zebrafish germline and non-germline cells. Cell Rep. 16 622–630. 10.1016/j.celrep.2016.06.023 27373161
Parisi M. A., Xu B., Clayton D. A., (1993). A human mitochondrial transcriptional activator can functionally replace a yeast mitochondrial HMG-box protein both in vivo and in vitro. Mol. Cell. Biol. 13 1951–1961. 10.1128/mcb.13.3.1951 8441424
Pauli A., Montague T. G., Lennox K. A., Behlke M. A., Schier A. F., (2015). Antisense oligonucleotide-mediated transcript knockdown in zebrafish. PLoS One 10:e0139504. 10.1371/journal.pone.0139504 26436892
Powell C. A., Nicholls T. J., Minczuk M., (2015). Nuclear-encoded factors involved in post-transcriptional processing and modification of mitochondrial tRNAs in human disease. Front. Genet. 6:79. 10.3389/fgene.2015.00079 25806043
Richardson R., Tracey-White D., Webster A., Moosajee M., (2017). The zebrafish eye-a paradigm for investigating human ocular genetics. Eye 31 68–86. 10.1038/eye.2016.198 27612182
Santos T. A., El Shourbagy S., St John J. C., (2006). Mitochondrial content reflects oocyte variability and fertilization outcome. Fertil. Steril. 85 584–591. 10.1016/j.fertnstert.2005.09.017 16500323
Semino C. E., Allende M. L., (2000). Chitin oligosaccharides as candidate patterning agents in zebrafish embryogenesis. Int. J. Dev. Biol. 44 183–193.
Shutt T. E., Bestwick M., Shadel G. S., (2011). The core human mitochondrial transcription initiation complex: it only takes two to tango. Transcription 2 55–59. 10.4161/trns.2.2.14296 21468229
Stackley K. D., Beeson C. C., Rahn J. J., Chan S. S., (2011). Bioenergetic profiling of zebrafish embryonic development. PLoS One 6:e25652. 10.1371/journal.pone.0025652 21980518
Thomas P. D., Campbell M. J., Kejariwal A., Mi H., Karlak B., Daverman R., et al. (2003). PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 13 2129–2141. 10.1101/gr.772403 12952881
Torrent M., Chalancon G., de Groot N. S., Wuster A., Madan Babu M., (2018). Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci. Signal. 11:eaat6409. 10.1126/scisignal.aat6409 30181241
Ventura-Clapier R., Garnier A., Veksler V., Joubert F., (2011). Bioenergetics of the failing heart. Biochim. Biophys. Acta. 1813 1360–1372. 10.1016/j.bbamcr.2010.09.006 20869993
Wagener F. A., Volk H. D., Willis D., Abraham N. G., Soares M. P., Adema G. J., et al. (2003). Different faces of the heme-heme oxygenase system in inflammation. Pharmacol. Rev. 55 551–571. 10.1124/pr.55.3.5 12869663
Wai T., Ao A., Zhang X., Cyr D., Dufort D., Shoubridge E. A., (2010). The role of mitochondrial DNA copy number in mammalian fertility. Biol. Reprod. 83 52–62. 10.1095/biolreprod.109.080887 20130269
Wan J., Yourshaw M., Mamsa H., Rudnik-Schoneborn S., Menezes M. P., Hong J. E., et al. (2012). Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration. Nat. Genet. 44 704–708. 10.1038/ng.2254 22544365
Yamamoto T., Iwata H., Goto H., Shiratuki S., Tanaka H., Monji Y., et al. (2010). Effect of maternal age on the developmental competence and progression of nuclear maturation in bovine oocytes. Mol. Reprod. Dev. 77 595–604. 10.1002/mrd.21188 20575084
Zhang J., Hamza I., (2018). Zebrafish as a model system to delineate the role of heme and iron metabolism during erythropoiesis. Mol. Genet. Metab. 128 204–212. 10.1016/j.ymgme.2018.12.007 30626549
Zhang X. Y., Rodaway A. R., (2007). SCL-GFP transgenic zebrafish: in vivo imaging of blood and endothelial development and identification of the initial site of definitive hematopoiesis. Dev. Biol. 307 179–194. 10.1016/j.ydbio.2007.04.002 17559829