Genome Project Solutions
Some of our scientists' publications on mitochondrial genomes:
Medina, M., S. Lal, Y. Valles, T. Takaoka, B. Dayrat, J. L. Boore and T. Goslinger, 2011 Crawling through time: Transition of snails to slugs dating back to the Paleozoic based on mitochondrial phylogenomics. Marine Genomics 4: 51-59. Rota-Stabelli, O., E. Kayal, D. Gleeson, J. Daub, J. L. Boore, M. Telford, D. Pisani, M. Blaxter and D. Lavrov, 2010 Ecdysozoan mitogenomics: Evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biology and Evolution 2: 425-440. Nardi, F., A. Carapelli, J. L. Boore, G. Roderick, R. Dallai and F. Frati, 2010 Domestication of olive fly through a multi-regional host shift to cultivated olives: Comparative dating using complete mitochondrial genomes. Molecular Phylogenetics and Evolution 57: 678-686. Rawlings, T. A., M. J. MacInnis, R. Bieler, J. L. Boore and T. M. Collins, 2010 Sessile snails, dynamic genomes: Gene rearrangements within the mitochondrial genome of a family of caenogastropod molluscs. BMC Genomics 11: 440. Stone, C. L., M. L. Posada Buitrago, J. L. Boore and R. D. Frederick, 2010 Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae. Mycologia 102: 887-897. Torricelli, G., A. Carapelli, P. Convey, F. Nardi, J. L. Boore and F. Frati, 2009 High divergence across the whole mitochondrial genome in the “pan-Antarctic” springtail Friesea grisea: Evidence for cryptic species? Gene 449: 30-40. Masta, S. E., S. J. Longhorn and J. L. Boore, 2009 Arachnid relationships based on mitochondrial genomes: Asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Molecular Phylogenetics and Evolution 50: 117-128. Masta, S. E, and J. L. Boore, 2008 Parallel evolution of truncated transfer RNA structure in arachnid mitochondrial genomes. Molecular Biology and Evolution 25: 949-959. Vallès, Y., K. Halanych and J. L. Boore, 2008 Group II introns break new boundaries: Presence in an animal genome. PLoS One 3(1): e1488. Fujita, M. K., J. L. Boore and C. Moritz, 2007 Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotial binoei; Squamata, Gekkonidae). Molecular Biology and Evolution 24: 2775-2786. Martin, F. N., D. Bensasson, B. M. Tyler and J. L. Boore, 2007 Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. Current Genetics 51: 285-296. Krampis, K., B. Tyler and J. L. Boore, 2006 Extensive variation in nuclear mitochondrial DNA content between the genomes of Phytophthora sojae and Phytophthora ramorum. Molecular Plant-Microbial Interactions 19: 1329-36. Vallès, Y., and J. L. Boore, 2006 Lophotrochozoan mitochondrial genomes. Integrative and Comparative Biology 46: 544-557. Podsiadlowski, L., A. Carapelli, F. Nardi, R. Dallai, M. Koch, J. L. Boore and F. Frati, 2006 The mitochondrial genomes of Campodea fragilis and C. lubbocki (Hexapoda: Diplura): high genetic divergence in a morphologically uniform taxon. Gene 381: 49-61. Carapelli, A., L. Vannini, F. Nardi, J. L. Boore, L. Beani, R. Dallai and F. Frati, 2006 The mitochondrial genome of the entomophagous endoparasitoid Xenos vesparum (Insecta: Strepsiptera). Gene 376: 248-259. Boore, J. L., 2006 The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics 7: 182. Simison, W. B., D. R. Lindberg and J. L. Boore, 2006 Rolling circle amplification of metazoan mitochondrial genomes. Molecular Phylogenetics and Evolution 39: 562-567. Medina, M., A. G. Collins, T. L. Takaoka, J. Kuehl and J. L. Boore, 2006 Naked stony corals: Skeleton loss in Scleractinia. Proceedings of the National Academy of Sciences 103: 9096-9100. Parham, J. F., J. R. Macey, T. J. Papenfuss, C. R. Feldmam, O. Türkozan, R. Polymeni and J. L. Boore, 2006 The phylogeny of Mediterranean tortoises and their close relatives based on complete mitochondrial genome sequences from museum specimens. Molecular Phylogenetics and Evolution 38: 50-64. Parham, J. F., C. R. Feldman and J. L. Boore, 2006 The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): Description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA. BMC Evolutionary Biology 6: 11. Mueller, R. L., and J. L. Boore, 2005 Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Molecular Biology and Evolution 22: 2104-2112. Place, A. R., X. Feng, C. R. Steve, H. M. Fourcade and J. L. Boore, 2005 Genetic markers in Blue Crabs (Callinectes sapidus) II: Complete mitochondrial genome sequence and characterization of genetic variation. Journal of Experimental Marine Biology and Ecology 319: 15–27. Macey, J. R., J. J. Fong, J. V. Kuehl, S. Shafiei, N. B. Ananjeva, T. J. Papenfuss and J. L. Boore, 2005 The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii. Molecular Phylogenetics and Evolution 36: 188-193. Boore, J. L., J. R. Macey and M. Medina, 2005 Sequencing and comparing whole mitochondrial genomes of animals. In Molecular Evolution: Producing the Biochemical Data, Part B (E. A. Zimmer and E. Roalson, eds.). Volume 395 of the Methods in Enzymology series, Elsevier, Burlington, Massachusetts, pp. 311-348. Carapelli, A., F. Nardi, R. Dallai, J. L. Boore, P. Lio and F. Frati, 2005 Relationships between hexapods and crustaceans based on mitochondrial genomics. In Crustacean and Arthropod Relationships. (Stefan Koenemann and Ronald A. Jenner, eds.). pp. 295-306. Boore, J. L., M. Medina and L. A. Rosenberg, 2004 Complete sequences of two highly rearranged molluscan mitochondrial genomes, those of the scaphopod Graptacme eborea and of the bivalve Mytilus edulis. Molecular Biology and Evolution 21: 1492–1503. Helfenbein, K. G., H. M. Fourcade, R. G. Vanjani and J. L. Boore, 2004 The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister-group to protostomes. Proceedings of the National Academy of Sciences USA 101: 10639-10643. Ruiz-Trillo, I., M. Riutort, H. M. Fourcade, J. Baguñà and J. L. Boore, 2004 Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes. Molecular Phylogenetics and Evolution 33: 321-332. Macey, J. R., T. J. Papenfuss, J. V. Kuehl, H. M. Fourcade and J. L. Boore, 2004 Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genome sequences. Molecular Phylogenetics and Evolution 33: 22-31. Mueller, R. L., J. R. Macey, M. Jaekel, D. B. Wake and J. L. Boore, 2004 Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders: Novel insights from complete mitochondrial genome sequences. Proceedings of the National Academy of Sciences USA 101: 13820-13825. Boore, J. L., 2004 Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura. BMC Genomics 5: 67. Lavrov, D., W. M. Brown and J. L. Boore, 2004 Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proceedings of the Royal Society of London B 271: 537-544. Helfenbein, K. G., and J. L. Boore, 2004 The mitochondrial genome of Phoronis architecta—Comparisons demonstrate that phoronids are lophotrochozoan protostomes. Molecular Biology and Evolution 21: 153-157. Masta, S. E., and J. L. Boore, 2004 The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Molecular Biology and Evolution 21: 893-902. Nardi, F., G. Spinsanti, J. L. Boore, A. Carapelli, R. Dallai and F. Frati, 2003 Hexapod origins, monophyletic or paraphyletic? Science 299: 1887-1889. Passamonti, M., J. L. Boore and V. Scali, 2003 Molecular evolution and recombination in gender-associated mitochondrial DNAs of the Manila clam Tapes philippinarum. Genetics 164: 603–611. Boore, J. L., and J. Staton, 2002 The mitochondrial genome of the sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca. Molecular Biology and Evolution 19: 127-137. Lavrov, D. V., J. L. Boore and W. M. Brown, 2002 Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and non-random loss. Molecular Biology and Evolution 19: 163-169.
Nickisch-Rosenegk, M. von, W. M. Brown and J. L. Boore, 2001 Sequence and structure of the mitochondrial genome of the tapeworm Hymenolepis diminuta: Gene arrangement indicates that platyhelminths are derived eutrochozoans. Molecular Biology and Evolution 18: 721-730.
Boore, J. L., 2001 Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii. Molecular Biology and Evolution 18: 1413-1416. Helfenbein, K. G., W. M. Brown and J. L. Boore, 2001 The complete mitochondrial genome of a lophophorate, the brachiopod Terebratalia transversa. Molecular Biology and Evolution 18: 1734-1744. Wollscheid-Lengeling, E., J. L. Boore, W. M. Brown, and H. Wägele, 2001 The phylogeny of Nudibranchia (Opisthobranchia, Gastropoda, Mollusca) reconstructed by three molecular markers. Organisms, Diversity and Evolution 1: 241-256. Boore, J. L., 2000 The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In Comparative Genomics (D. Sankoff and J. Nadeau, eds.). Computational Biology Series vol 1, Kluwer Academic Publishers, Dordrecht, Netherlands, pp. 133-147. Lavrov, D., J. L. Boore and W. M. Brown, 2000 The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. Molecular Biology and Evolution 17: 813-824. Lavrov, D., W. M. Brown, and J. L. Boore, 2000 A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proceedings of the National Academy of Sciences USA 97: 13738-13742. Boore, J. L., L. L. Daehler and W. M. Brown, 1999 Complete sequence, gene arrangement and genetic code of mitochondrial DNA of the cephalochordate Branchiostoma floridae (“Amphioxus”). Molecular Biology and Evolution 16: 410-418. Boore, J. L., 1999 Animal mitochondrial genomes. Nucleic Acids Research 27: 1767-1780. Boore, J. L. and S. I Fuerstenberg, 1999 Entomoeba histolytica—A derived mitochondriate eukaryote? Trends in Microbiology 7: 426-428. Boore, J. L., 1997 Transmission of mitochondrial DNA—Playing favorites? Bioessays 19: 751-753. Boore, J. L. and W. M. Brown, 1995 The complete DNA sequence of the mitochondrial genome of the annelid worm Lumbricus terrestris. Genetics 141: 305-319. Yost, H. J., C. R. Phillips, J. L. Boore, J. Bertman, B. Whalen and M. V. Danilchik, 1995 Relocation of mitochondrial RNA to the prospective dorsal midline during Xenopus embryogenesis. Developmental Biology 170: 83-90. Boore, J. L. and W. M. Brown, 1994 The complete DNA sequence of the mitochondrial genome of the Black Chiton Katharina tunicata. Genetics 138: 423-443. Hoffmann, R. J., J. L. Boore and W. M. Brown, 1992 A novel mitochondrial genome organization for the Blue Mussel, Mytilus edulis. Genetics 131: 397-412.
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