Organelle genomics has become its own field of study. Much information can be gleaned from the study of cell organelles. The differences in the genomes of organelles, such as the mitochondrion and the chloroplast are amenable to phylogenetic and cladistic studies. These differences include the genome sequence, GC%, genome length and gene order. The conserved nature of the organelle genomes and the gene inventory of both mitochondrial and chloroplast genomes also make this easier to accomplish. This paper includes a review of existing organelle genome software. These include gene annotation and genome visualization tools as well as organelle gene databases for both mitochondrion and plastid. A new R tool, available on github, called “Organelle DNA Lineages”, or ODL, was written to compare and classify organelle genomes based on their genome sequence and gene order. The software was run on the mitochondrial genomes of a set of 51 cephalopod species, delineating ten separate monophyletic groups, including argonauts, nautiluses, octopuses, cuttlefish, and six squid groups. This new tool can help enrich and expand the field of organelle genomics.
KeywordsOrganelleGenomeMitochondrionPlastidOrganelle DNA LineageChloroplast
Boore, J.L., Collins, T.M., Stanton, D., Daehler, L.L. and Brown, W.M. (1995) Deducing the Pattern of Arthropod Phylogeny from Mitochondrial DNA Rearrangements. Nature, 376, 163-165. https://doi.org/10.1038/376163a0
Boore, J.L., Lavrov, D.V. and Brown, W.M. (1998) Gene Translocation Links Insects and Crustaceans. Nature, 392, 667-668. https://doi.org/10.1038/33577
Aguileta, G., de Vienne, D.M., Ross, O.N., Hood, M.E., Giraud, T., Petit, E. and Gabaldón, T. (2014) High Variability of Mitochondrial Gene Order among Fungi. Genome Biology and Evolution, 6, 451-465. https://doi.org/10.1093/gbe/evu028
Ravi, V., Khurana, J.P., Tyagi, A.K. and Khurana, P. (2008) An Update on Chloroplast Genomes. Plant Systematics and Evolution, 271, 101-122. https://doi.org/10.1007/s00606-007-0608-0
Friedman, J.R. and Nunnari, J. (2014) Mitochondrial Form and Function. Nature, 505, 335-343. https://doi.org/10.1038/nature12985
Suomalainen, A. and Battersby, B.J. (2018) Mitochondrial Diseases: The Contribution of Organelle Stress Responses to Pathology. Nature reviews: Molecular Cell Biology, 19, 77-92. https://doi.org/10.1038/nrm.2017.66
Yan, C., Duanmu, X., Zeng, L., Liu, B. and Song, Z. (2019) Mitochondrial DNA: Distribution, Mutations, and Elimination. Cells, 8, 379. https://doi.org/10.3390/cells8040379
Supinski, G.S., Schroder, E.A. and Callahan, L.A. (2020) Mitochondria and Critical Illness. Chest, 157, 310-322.
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., Schreier, P.H., Smith, A.J., Staden, R. and Young, I.G. (1981) Sequence and Organization of the Human Mitochondrial Genome. Nature, 290, 457-465. https://doi.org/10.1038/290457a0
Goodman, S.R. (2007) Medical Cell Biology. Third Edition, Academic Press, Cambridge.
Hirakawa, Y. and Watanabe, A. (2019) Organellar DNA Polymerases in Complex Plastid-Bearing Algae. Biomolecules, 9, 140. https://doi.org/10.3390/biom9040140
Moriyama, T., Terasawa, K. and Sato, N. (2011) Conservation of POPs, the Plant Organellar DNA Polymerases, in Eukaryotes. Protist, 162, 177-187. https://doi.org/10.1016/j.protis.2010.06.001
Jiao, Y., Jia, H.M., Li, X.W., Chai, M.L., Jia, H.J., Chen, Z., Wang, G.Y., Chai, C.Y., van de Weg, E. and Gao, Z.S. (2012) Development of Simple Sequence Repeat (SSR) Markers from a Genome Survey of Chinese Bayberry (Myrica rubra). BMC Genomics, 13, 201. https://doi.org/10.1186/1471-2164-13-201
Li, X., Gao, H., Wang, Y., Song, J., Henry, R., Wu, H., Hu, Z., Yao, H., Luo, H., Luo, K., Pan, H. and Chen, S. (2013). Complete Chloroplast Genome Sequence of Magnolia grandiflora and Comparative Analysis with Related Species. Science China. Life Sciences, 56, 189-198.
Zheng, X.-M., Wang, J.R., Feng, L., Liu, S., Pang, H.B., Qi, L., Li, J., Sun, Y., Qiao, W.H., Zhang, L.F., Cheng, Y.L. and Yang, Q.W. (2017) Inferring the Evolutionary Mechanism of the Chloroplast Genome Size by Comparing Whole-Chloroplast Genome Sequences in Seed Plants. Scientific Reports, 7, Article No. 1555.
Wakasugi, T., Tsudzuki, T. and Sugiura, M. (2001) The Genomics of Land Plant Chloroplasts: Gene Content and Alteration of Genomic Information by RNA Editing. Photosynthesis Research, 70, 107-118. https://doi.org/10.1023/A:1013892009589
Wolfe, K.H., Li, W.H. and Sharp, P.M. (1987) Rates of Nucleotide Substitution Vary Greatly among Plant Mitochondrial, Chloroplast, and Nuclear DNAs. Proceedings of the National Academy of Sciences of the United States of America, 84, 9054-9058. https://doi.org/10.1073/pnas.84.24.9054
Wise, R.R. (2006) The Diversity of Plastid Form and Function. Advances in Photosynthesis and Respiration Book 23. Springer, Berlin, 3-26.
Bernt, M., Merkle, D., Ramsch, K., Fritzsch, G., Perseke, M., Bernhard, D., Schlegel, M., Stadler, P.F. and Middendorf, M. (2007) CREx: Inferring Genomic Rearrangements Based on Common Intervals. Bioinformatics (Oxford, England), 23, 2957-2958. https://doi.org/10.1093/bioinformatics/btm468
Jameson, D., Gibson, A.P., Hudelot, C. and Higgs, P.G. (2003) OGRe: A Relational Database for Comparative Analysis of Mitochondrial Genomes. Nucleic Acids Research, 31, 202-206. https://doi.org/10.1093/nar/gkg077
Feijao, P.C., Neiva, L.S., de Azeredo-Espin, A.M. and Lessinger, A.C. (2006) AMiGA: The Arthropodan Mitochondrial Genomes Accessible Database. Bioinformatics, 22, 902-903. https://doi.org/10.1093/bioinformatics/btl021
Lupi, R., de Meo, P.D., Picardi, E., D’Antonio, M., Paoletti, D., Castrignanò, T., Pesole, G. and Gissi, C. (2010) MitoZoa: A Curated Mitochondrial Genome Database of Metazoans for Comparative Genomics Studies. Mitochondrion, 10, 192-199. https://doi.org/10.1016/j.mito.2010.01.004
Pütz, J., Dupuis, B., Sissler, M. and Florentz, C. (2007) Mamit-tRNA, a Database of Mammalian Mitochondrial tRNA Primary and Secondary Structures, RNA (New York, N.Y.), 13, 1184-1190.
de Vasconcelos, A.T., Guimaraes, A.C., Castelletti, C.H., Caruso, C.S., Ribeiro, C., Yokaichiya, F., Armoa, G.R., Pereira, G., da Silva, I.T., Schrago, C.G., Fernandes, A.L., da Silveira, A.R., Carneiro, A.G., Carvalho, B.M., Viana, C.J., Gramkow, D., Lima, F.J., Corrêa, L.G., Mudado, M., Nehab-Hess, P., et al. (2005) MamMiBase: A Mitochondrial Genome Database for Mammalian Phylogenetic Studies. Bioinformatics (Oxford, England), 21, 2566-2567. https://doi.org/10.1093/bioinformatics/bti326
Bernt, M., Braband, A., Middendorf, M., Misof, B., Rota-Stabelli, O. and Stadler, P.F. (2013) Bioinformatics Methods for the Comparative Analysis of Metazoan Mitochondrial Genome Sequences. Molecular Phylogenetics and Evolution, 69, 320-327. https://doi.org/10.1016/j.ympev.2012.09.019
Hartmann, T., Bernt, M. and Middendorf, M. (2018) EqualTDRL: Illustrating Equivalent Tandem Duplication Random Loss Rearrangements. BMC Bioinformatics, 19, 192. https://doi.org/10.1186/s12859-018-2170-x
Iwasaki, W., Fukunaga, T., Isagozawa, R., Yamada, K., Maeda, Y., Satoh, T.P., Sado, T., Mabuchi, K., Takeshima, H., Miya, M. and Nishida, M. (2013) MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline. Molecular Biology and Evolution, 30, 2531-2540. https://doi.org/10.1093/molbev/mst141
Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. and Stadler, P.F. (2013) MITOS: Improved De Novo Metazoan Mitochondrial Genome Annotation. Molecular Phylogenetics and Evolution, 69, 313-319. https://doi.org/10.1016/j.ympev.2012.08.023
Donath, A., Jühling, F., Al-Arab, M., Bernhart, S.H., Reinhardt, F., Stadler, P.F., Middendorf, M. and Bernt, M. (2019) Improved Annotation of Protein-Coding Genes Boundaries in Metazoan Mitochondrial Genomes. Nucleic Acids Research, 47, 10543-10552. https://doi.org/10.1093/nar/gkz833
Guyeux, C., Charr, J.C., Tran, H., Furtado, A., Henry, R.J., Crouzillat, D., Guyot, R. and Hamon, P. (2019) Evaluation of Chloroplast Genome Annotation Tools and Application to Analysis of the Evolution of Coffee Species. PLoS ONE, 14, e0216347.
Wyman, S.K., Jansen, R.K. and Boore, J.L. (2004) Automatic Annotation of Organellar Genomes with DOGMA. Bioinformatics (Oxford, England), 20, 3252-3255. https://doi.org/10.1093/bioinformatics/bth352
Singh, B.P., Kumar, A., Kaur, H., Singh, H. and Nagpal, A.K. (2020) CpGDB: A Comprehensive Database of Chloroplast Genomes. Bioinformation, 16, 171-175. https://doi.org/10.6026/97320630016171
Liu C., Shi L., Zhu Y., Chen H., Zhang J., Lin X. and Guan, X. (2012) CpGAVAS, an Integrated Web Server for the Annotation, Visualization, Analysis, and GenBank Submission of Completely Sequenced Chloroplast Genome Sequences. BMC Genomics, 13, 715. https://doi.org/10.1186/1471-2164-13-715
Shi, L., Chen, H., Jiang, M., Wang, L., Wu, X., Huang, L. and Liu, C. (2019) CPGAVAS2, an Integrated Plastome Sequence Annotator and Analyzer. Nucleic Acids Research, 47, W65-W73. https://doi.org/10.1093/nar/gkz345
Cheng, J., Zeng, X., Ren, G. and Liu, Z. (2013) CGAP: A New Comprehensive Platform for the Comparative Analysis of Chloroplast Genomes. BMC Bioinformatics, 14, 95. https://doi.org/10.1186/1471-2105-14-95
Tillich, M., Lehwark, P., Pellizzer, T., Ulbricht-Jones, E.S., Fischer, A., Bock, R. and Greiner, S. (2017) GeSeq—Versatile and Accurate Annotation of Organelle Genomes. Nucleic Acids Research, 45, W6-W11.
Sablok, G., Mudunuri, S.B., Patnana, S., Popova, M., Fares, M.A. and Porta, N.L. (2013) ChloroMitoSSRDB: Open Source Repository of Perfect and Imperfect Repeats in Organelle Genomes for Evolutionary Genomics. DNA Research, 20, 127-133. https://doi.org/10.1093/dnares/dss038
Bernt, M. and Middendorf, M. (2011) A Method for Computing an Inventory of Metazoan Mitochondrial Gene Order Rearrangements. BMC Bioinformatics, 12, S6.
Boore, J.L. (2006) The Complete Sequence of the Mitochondrial Genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics, 7, 182. https://doi.org/10.1186/1471-2164-7-182
Robison, B.H., Reisenbichler, K.R., Hunt, J.C. and Haddock, S.H. (2003) Light Production by the Arm Tips of the Deep-Sea Cephalopod Vampyroteuthis infernalis. The Biological Bulletin, 205, 102-109. https://doi.org/10.2307/1543231
Takumiya, M., Kobayashi, M., Tsuneki, K. and Furuya, H. (2005) Phylogenetic Relationships among Major Species of Japanese Coleoid Cephalopods (Mollusca: Cephalopoda) Using Three Mitochondrial DNA Sequences. Zoological Science, 22, 147-155. https://doi.org/10.2108/zsj.22.147
Yokobori, S., Lindsay, D.J., Yoshida, M., Tsuchiya, K., Yamagishi, A., Maruyama, T. and Oshima, T. (2007) Mitochondrial Genome Structure and Evolution in the Living Fossil Vampire Squid, Vampyroteuthis infernalis, and Extant Cephalopods. Molecular Phylogenetics and Evolution, 44, 898-910. https://doi.org/10.1016/j.ympev.2007.05.009
Xu, L., Wang, X. and Du, F. (2020) The Complete Mitochondrial Genome of Loliginid Squid (Uroteuthis chinensis) from Minnan-Taiwan Bank Fishing Ground. Mitochondrial DNA. Part B, Resources, 5, 428-429. https://doi.org/10.1080/23802359.2019.1703599
Uribe, J.E. and Zardoya, R. (2017) Revisiting the Phylogeny of Cephalopoda Using Complete Mitochondrial Genomes. Journal of Molluscan Studies, 83, 133-144. https://doi.org/10.1093/mollus/eyw052
Kawashima, Y., Nishihara, H., Akasaki, T., Nikaido, M., Tsuchiya, K., Segawa, S. and Okada, N. (2013) The Complete Mitochondrial Genomes of Deep-Sea Squid (Bathyteuthis abyssicola), Bob-Tail Squid (Semirossia patagonica) and Four Giant Cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharaonis), and Their Application to the Phylogenetic Analysis of Decapodiformes. Molecular Phylogenetics and Evolution, 69, 980-993.