Mai, N., Chrzanowska-Lightowlers, Z.M. and Lightowlers, R.N. (2017) The process of mammalian mitochondrial protein synthesis. Cell Tissue Res., 367, 5-20.
Ott, M., Amunts, A. and Brown, A. (2016) Organization and regulation of mitochondrial protein synthesis. Annual Rev. Biochem., 85, 77-101.
Salinas, T., Remacle, C. and Maréchal-Drouard, L. (2013) Mitochondrial translation in green algae and higher plants. In: Duchêne, AM (ed). Translation in Mitochondria and Other Organelles. Springer, Heidelberg; NY; Dordrecht; London, pp. 181-206.
Binder, S. and Brennicke, A. (2003) Gene expression in plant mitochondria: Transcriptional and post-transcriptional control. Philos. Trans. R. Soc. Lond. B. Biol. Sci., 358, 181-188.
Hammani, K. and Giegé, P. (2014) RNA metabolism in plant mitochondria. Trends Plant Sci., 19, 380-389.
Merchant, S.S., Prochnik, S.E., Vallon, O., Harris, E.H., Karpowicz, S.J., Witman, G.B., Terry, A., Salamov, A., Fritz-Laylin, L.K., Maréchal-Drouard, L. et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science, 318, 245-250.
Remacle, C., Cardol, P., Coosemans, N., Gaisne, M. and Bonnefoy, N. (2006) High-efficiency biolistic transformation of Chlamydomonas mitochondria can be used to insert mutations in complex I genes. Proc. Natl. Acad. Sci. U.S.A., 103, 4771-4776.
Salinas, T., Larosa, V., Cardol, P., Maréchal-Drouard, L. and Remacle, C. (2013) Respiratory-deficient mutants of the unicellular green alga Chlamydomonas: A review. Biochimie, 100, 207-218.
Grant, D. and Chiang, K.S. (1980) Physical mapping and characterization of Chlamydomonas mitochondrial DNA molecules: Their unique ends, sequence homogeneity, and conservation. Plasmid, 4, 82-96.
Boer, P.H. and Gray, M.W. (1988) Scrambled ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA. Cell, 55, 399-411.
Duby, F., Cardol, P., Matagne, R.F. and Remacle, C. (2001) Structure of the telomeric ends of mt DNA, transcriptional analysis and complex I assembly in the dum24 mitochondrial mutant of Chlamydomonas reinhardtii. Mol. Gen. Genet., 266, 109-114.
Gray, M.W. and Boer, P.H. (1988) Organization and expression of algal (Chlamydomonas reinhardtii) mitochondrial DNA. Philos. Trans. R. Soc. Lond. B. Biol. Sci., 319, 135-147.
Boer, P.H. and Gray, M.W. (1988) Genes encoding a subunit of respiratory NADH dehydrogenase (ND1) and a reverse transcriptase-like protein (RTL) are linked to ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA. EMBO J., 7, 3501-3508.
Ma, D.P., Yang, Y.W., King, T.Y. and Hasnain, S.E. (1990) The mitochondrial apocytochrome b gene from Chlamydomonas reinhardtii. Plant Mol. Biol., 15, 357-359.
Harris, E. (2001) Chlamydomonas as a model organism. Annu. Rev. Plant Phys. Plant Mol. Biol., 52, 363-406.
Stein, J. (1973) Handbook of Phycological methods: Culture methods and growth measurements. Cambridge University Press, Cambridge; London; NY; New Rochelle; Melbourne; Sydney.
Salinas, T., Duby, F., Larosa, V., Coosemans, N., Bonnefoy, N., Motte, P., Maréchal-Drouard, L. and Remacle, C. (2012) Co-evolution of mitochondrial tRNA import and codon usage determines translational efficiency in the green alga Chlamydomonas. PLoS Genet., 8, e1002946.
Loppes, R. and Radoux, M. (2001) Identification of short promoter regions involved in the transcriptional expression of the nitrate reductase gene in Chlamydomonas reinhardtii. Plant Mol. Biol., 45, 215-227.
Doublet, V., Ubrig, E., Alioua, A., Bouchon, D., Marcade, I. and Maréchal-Drouard, L. (2015) Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustacean Armadillidium vulgare. RNA Biol., 12, 1159-1168.
Cavaiuolo, M., Kuras, R., Wollman, FA., Choquet, Y. and Vallon, O. (2017) Small RNA profiling in Chlamydomonas: Insights into chloroplast RNA metabolism. Nucleic Acids Res., doi:10.1093/nar/gkx668.
Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
Barnett, D.W., Garrison, E.K., Quinlan, A.R., Stromberg, M.P. and Marth, G.T. (2011) BamTools: A C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27, 1691-1692.
Makaroff, C.A., Apel, I.J. and Palmer, J.D. (1990) Characterization of radish mitochondrial atpA: Influence of nuclear background on transcription of atpA-associated sequences and relationship with male-sterility. Plant Mol. Biol., 15, 735-746.
Quinlan, A.R. (2014) BEDTools: The Swiss-Army Tool for genome feature analysis. Curr. Protoc. Bioinform., 47, 11-34.
Criscuolo, A. (2011) morePhyML: Improving the phylogenetic tree space exploration with PhyML 3. Mol. Phylogenet. Evol., 61, 944-948.
Emanuelsson, O., Brunak, S., von Heijne, G. and Nielsen, H. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc., 2, 953-971.
Tardif, M., Atteia, A., Specht, M., Cogne, G., Rolland, N., Brugiere, S., Hippler, M., Ferro, M., Bruley, C., Peltier, G. et al. (2012) PredAlgo: A new subcellular localization prediction tool dedicated to green algae. Mol. Biol. Evol., 29, 3625-3639.
Ruwe, H., Wang, G., Gusewski, S. and Schmitz-Linneweber, C. (2016) Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms. Nucleic Acids Res., 44, 7406-7417.
Boer, P.H. and Gray, M.W. (1986) The URF 5 gene of Chlamydomonas reinhardtii mitochondria: DNA sequence and mode of transcription. EMBO J., 5, 21-28.
Boer, P.H. and Gray, M.W. (1991) Short dispersed repeats localized in spacer regions of Chlamydomonas reinhardtii mitochondrial DNA. Curr. Genet., 19, 309-312.
Lange, H., Sement, F.M., Canaday, J. and Gagliardi, D. (2009) Polyadenylation-assisted RNA degradation processes in plants. Trends Plant Sci., 14, 497-504.
Smith, D.R. and Lee, R.W. (2011) Nucleotide diversity of the colorless green alga Polytomella parva (Chlorophyceae, Chlorophyta): High for the mitochondrial telomeres, surprisingly low everywhere else. J. Eukaryot. Microbiol., 58, 471-473.
Pröschold, T., Harris, E.H. and Coleman, A.W. (2005) Portrait of a species: Chlamydomonas reinhardtii. Genetics, 170, 1601-1610.
Ojala, D., Merkel, C., Gelfand, R. and Attardi, G. (1980) The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell, 22, 393-403.
Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F. et al. (1981) Sequence and organization of the human mitochondrial genome. Nature, 290, 457-465.
Bonnard, G., Gobert, A., Arrive, M., Pinker, F., Salinas-Giegé, T. and Giegé, P. (2016) Transfer RNA maturation in Chlamydomonas mitochondria, chloroplast and the nucleus by a single RNase P protein. Plant J., 87, 270-280.
Boehm, E., Zaganelli, S., Maundrell, K., Jourdain, A.A., Thore, S. and Martinou, J.C. (2017) FASTKD1 and FASTKD4 have opposite effects on expression of specific mitochondrial RNAs, depending upon their endonuclease-like RAP domain. Nucleic Acids Res., 45, 6135-6146.
Boulouis, A., Drapier, D., Razafimanantsoa, H., Wostrikoff, K., Tourasse, N.J., Pascal, K., Girard-Bascou, J., Vallon, O., Wollman, F.A. and Choquet, Y. (2015) Spontaneous dominant mutations in chlamydomonas highlight ongoing evolution by gene diversification. Plant Cell, 27, 984-1001.
Zimmer, S.L., Fei, Z. and Stern, D.B. (2008) Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features. Genetics, 179, 125-136.
Yehudai-Resheff, S., Zimmer, S.L., Komine, Y. and Stern, D.B. (2007) Integration of chloroplast nucleic acid metabolism into the phosphate deprivation response in Chlamydomonas reinhardtii. Plant Cell, 19, 1023-1038.
Chang, H., Lim, J., Ha, M. and Kim, V.N. (2014) TAIL-seq: Genome-wide determination of poly(A) tail length and 3 end modifications. Mol. Cell, 53, 1044-1052.
Hirayama, T., Matsuura, T., Ushiyama, S., Narusaka, M., Kurihara, Y., Yasuda, M., Ohtani, M., Seki, M., Demura, T., Nakashita, H. et al. (2013) A poly(A)-specific ribonuclease directly regulates the poly(A) status of mitochondrial mRNA in Arabidopsis. Nat. Commun., 4, 2247-2255.
Horton, T.L. and Landweber, L.F. (2000) Mitochondrial RNAs of myxomycetes terminate with non-encoded 3 poly(U) tails. Nucleic Acids Res., 28, 4750-4754.
Aphasizhev, R., Suematsu, T., Zhang, L. and Aphasizheva, I. (2016) Constructive edge of uridylation-induced RNA degradation. RNA Biol., 13, 1078-1083.
Zimmer, S.L., Schein, A., Zipor, G., Stern, D.B. and Schuster, G. (2009) Polyadenylation in Arabidopsis and Chlamydomonas organelles: The input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase. Plant J., 59, 88-99.
Nedelcu, A.M., Lee, R.W., Lemieux, C., Gray, M.W. and Burger, G. (2000) The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome. Genome Res., 10, 819-831.
Sikorski, P.J., Zuber, H., Philippe, L., Sement, F.M., Canaday, J., Kufel, J., Gagliardi, D. and Lange, H. (2015) Distinct 18S rRNA precursors are targets of the exosome complex, the exoribonuclease RRP6L2 and the terminal nucleotidyltransferase TRL in Arabidopsis thaliana. Plant J., 83, 991-1004.
Ibrahim, F., Rymarquis, L.A., Kim, E.J., Becker, J., Balassa, E., Green, P.J. and Cerutti, H. (2010) Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas. Proc. Natl Acad. Sci. U.S.A., 107, 3906-3911.
Yehudai-Resheff, S. and Schuster, G. (2000) Characterization of the E.coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependence. Nucleic Acids Res., 28, 1139-1144.