AJMB  Vol.11 No.4 , October 2021
Prediction of Monophyletic Groups Based on Gene Order and Sequence Similarity in Organelle DNA
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Abstract: 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.
Cite this paper: Cserhati, M. (2021) Prediction of Monophyletic Groups Based on Gene Order and Sequence Similarity in Organelle DNA. American Journal of Molecular Biology, 11, 83-99. doi: 10.4236/ajmb.2021.114008.

[1]   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.

[2]   Boore, J.L., Lavrov, D.V. and Brown, W.M. (1998) Gene Translocation Links Insects and Crustaceans. Nature, 392, 667-668.

[3]   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.

[4]   Ravi, V., Khurana, J.P., Tyagi, A.K. and Khurana, P. (2008) An Update on Chloroplast Genomes. Plant Systematics and Evolution, 271, 101-122.

[5]   Friedman, J.R. and Nunnari, J. (2014) Mitochondrial Form and Function. Nature, 505, 335-343.

[6]   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.

[7]   Yan, C., Duanmu, X., Zeng, L., Liu, B. and Song, Z. (2019) Mitochondrial DNA: Distribution, Mutations, and Elimination. Cells, 8, 379.

[8]   Supinski, G.S., Schroder, E.A. and Callahan, L.A. (2020) Mitochondria and Critical Illness. Chest, 157, 310-322.

[9]   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.

[10]   Goodman, S.R. (2007) Medical Cell Biology. Third Edition, Academic Press, Cambridge.

[11]   Hirakawa, Y. and Watanabe, A. (2019) Organellar DNA Polymerases in Complex Plastid-Bearing Algae. Biomolecules, 9, 140.

[12]   Moriyama, T., Terasawa, K. and Sato, N. (2011) Conservation of POPs, the Plant Organellar DNA Polymerases, in Eukaryotes. Protist, 162, 177-187.

[13]   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.

[14]   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.

[15]   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.

[16]   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.

[17]   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.

[18]   Wise, R.R. (2006) The Diversity of Plastid Form and Function. Advances in Photosynthesis and Respiration Book 23. Springer, Berlin, 3-26.

[19]   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.

[20]   Conant, G.C. and Wolfe, K.H. (2008) GenomeVx: Simple Web-Based Creation of Editable Circular Chromosome Maps. Bioinformatics (Oxford, England), 24, 861-862.

[21]   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.

[22]   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.

[23]   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.

[24]   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.

[25]   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.

[26]   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.

[27]   Hartmann, T., Bernt, M. and Middendorf, M. (2018) EqualTDRL: Illustrating Equivalent Tandem Duplication Random Loss Rearrangements. BMC Bioinformatics, 19, 192.

[28]   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.

[29]   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.

[30]   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.

[31]   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.

[32]   Wyman, S.K., Jansen, R.K. and Boore, J.L. (2004) Automatic Annotation of Organellar Genomes with DOGMA. Bioinformatics (Oxford, England), 20, 3252-3255.

[33]   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.

[34]   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.

[35]   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.

[36]   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.

[37]   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.

[38]   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.

[39]   Bernt, M. and Middendorf, M. (2011) A Method for Computing an Inventory of Metazoan Mitochondrial Gene Order Rearrangements. BMC Bioinformatics, 12, S6.

[40]   Boore, J.L. (2006) The Complete Sequence of the Mitochondrial Genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics, 7, 182.

[41]   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.

[42]   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.

[43]   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.

[44]   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.

[45]   Uribe, J.E. and Zardoya, R. (2017) Revisiting the Phylogeny of Cephalopoda Using Complete Mitochondrial Genomes. Journal of Molluscan Studies, 83, 133-144.

[46]   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.