Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae).
Paul Sunnucks,Dinah F. Hales +1 more
TLDR
It is concluded that a proportion of the inferred change in the nonmitochondrial sequences occurred before transposition, and that Sitobion aphids (and other species exhibiting mtDNA transposition) may be important for studying the molecular evolution of mtDNA and pseudogenes.Abstract:
Polymerase chain reaction (PCR) products corresponding to 803 bp of the cytochrome oxidase subunits I and II region of mitochondrial DNA (mtDNA COI-II) were deduced to consist of multiple haplotypes in three Sitobion species. We investigated the molecular basis of these observations. PCR products were cloned, and six clones from one individual per species were sequenced. In each individual, one sequence was found commonly, but also two or three divergent sequences were seen. The divergent sequences were shown to be nonmitochondrial by sequencing from purified mtDNA and Southern blotting experiments. All seven nonmitochondrial clones sequenced to completion were unique. Nonmitochondrial sequences have a high proportion of unique sites, and very few characters are shared between nonmitochondrial clones to the exclusion of mtDNA. From these data, we infer that fragments of mtDNA have been transposed separately (probably into aphid chromosomes), at a frequency only known to be equalled in humans. The transposition phenomenon appears to occur infrequently or not at all in closely related genera and other aphids investigated. Patterns of nucleotide substitution in mtDNA inferred over a parsimony tree are very different from those in transposed sequences. Compared with mtDNA, nonmitochondrial sequences have less codon position bias, more even exchanges between A, G, C and T, and a higher proportion of nonsynonymous replacements. Although these data are consistent with the transposed sequences being under less constraint than mtDNA, changes in the nonmitochondrial sequences are not random: there remains significant position bias, and probable excesses of synonymous replacements and of conservative inferred amino acid replacements. We conclude that a proportion of the inferred change in the nonmitochondrial sequences occurred before transposition. We believe that Sitobion aphids (and other species exhibiting mtDNA transposition) may be important for studying the molecular evolution of mtDNA and pseudogenes. However, our data highlight the need to establish the true evolutionary relationships between sequences in comparative investigations.read more
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Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA
Daniel J. Funk,Kevin E. Omland +1 more
TL;DR: This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized.
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
Stephen Richards,Richard A. Gibbs,Nicole M. Gerardo,Nancy A. Moran,Atsushi Nakabachi,David L. Stern,Denis Tagu,Alex C.C. Wilson,Donna M. Muzny,Christie Kovar,Andy Cree,Joseph Chacko,Mimi N. Chandrabose,Marvin Diep Dao,Huyen Dinh,Ramatu Ayiesha Gabisi,Sandra Hines,Jennifer Hume,Shalini N. Jhangian,Vandita Joshi,Lora Lewis,Yih Shin Liu,John Lopez,Margaret Morgan,Ngoc Nguyen,Geoffrey Okwuonu,San Juana Ruiz,Jireh Santibanez,Rita A. Wright,Gerald R. Fowler,Matthew Hitchens,Ryan J. Lozado,Charles Moen,David Steffen,James T. Warren,Jingkun Zhang,Lynne V. Nazareth,Dean Chavez,Clay Davis,Sandra L. Lee,Bella Mayurkumar Patel,Ling Ling Pu,Stephanie Bell,Angela Jolivet Johnson,Selina Vattathil,Rex Lee Williams,Shuji Shigenobu,Shuji Shigenobu,Phat M. Dang,Mizue Morioka,Takema Fukatsu,Toshiaki Kudo,Shin-ya Miyagishima,Huaiyang Jiang,Kim C. Worley,Fabrice Legeai,Jean-Pierre Gauthier,Olivier Collin,Lan Zhang,Hsiu Chuan Chen,Olga Ermolaeva,Wratko Hlavina,Yuri Kapustin,Boris Kiryutin,Paul Kitts,Donna Maglott,Terence Murphy,Kim D. Pruitt,Victor Sapojnikov,Alexandre Souvorov,Françoise Thibaud-Nissen,Francisco Câmara,Roderic Guigó,Mario Stanke,Victor V. Solovyev,Peter Kosarev,Don Gilbert,Toni Gabaldón,Jaime Huerta-Cepas,Marina Marcet-Houben,Miguel Pignatelli,Andrés Moya,Claude Rispe,Morgane Ollivier,Hadi Quesneville,Emmanuelle Permal,Carlos Llorens,Ricardo Futami,Dale Hedges,Hugh M. Robertson,Tyler Alioto,Marco Mariotti,Naruo Nikoh,John P. McCutcheon,Gaelen R. Burke,Alexandra Kamins,Amparo Latorre,Peter D. Ashton,Federica Calevro,Hubert Charles,Stefano Colella,Angela E. Douglas,Georg Jander,Derek H. Jones,Gérard Febvay,Lars G. Kamphuis,Philip F. Kushlan,Sandy J. Macdonald,John S Ramsey,Julia Schwartz,Stuart Seah,Gavin H. Thomas,Augusto F. Vellozo,Augusto F. Vellozo,Bodil N. Cass,Patrick H. Degnan,Bonnie L. Hurwitz,Teresa E. Leonardo,Ryuichi Koga,Boran Altincicek,Caroline Anselme,Hagop S. Atamian,Seth M. Barribeau,Martin De Vos,Elizabeth J. Duncan,Jay D. Evans,Murad Ghanim,Abdelaziz Heddi,Isgouhi Kaloshian,Carole Vincent-Monégat,Ben J. Parker,Vicente Pérez-Brocal,Vicente Pérez-Brocal,Yvan Rahbé,Chelsea J. Spragg,Javier Tamames,Daniel Tamarit,Cecilia Tamborindeguy,Andreas Vilcinskas,Ryan D. Bickel,Jennifer A. Brisson,Thomas Butts,Chun-che Chang,Olivier Christiaens,Gregory K. Davis,Elizabeth Duncan,David E. K. Ferrier,Masatoshi Iga,Ralf Janssen,Hsiao-ling Lu,Alistair P. McGregor,Toru Miura,Guy Smagghe,James M Smith,Maurijn van der Zee,Rodrigo A. Velarde,Megan J. Wilson,Peter K. Dearden,Owain R. Edwards,Owain R. Edwards,Karl H.J. Gordon,Roland Hilgarth,Stanley Dean Rider,Dayalan G. Srinivasan,Tom Walsh,Asano Ishikawa,Stéphanie Jaubert-Possamai,Brian Fenton,Wenting Huang,Guillaume Rizk,Dominique Lavenier,Jacques Nicolas,Carole M. Smadja,Jing-Jiang Zhou,Filipe G. Vieira,Xiao Li He,Renhu Liu,Julio Rozas,Linda M. Field,Peter M. Campbell,James C. Carolan,Carol I. J. Fitzroy,Karen T. Reardon,Gerald R. Reeck,Gerald R. Reeck,Karam B. Singh,T. L. Wilkinson,Jurgen Huybrechts,Mohatmed Abdel-latief,Alain Robichon,Jan A. Veenstra,Frank Hauser,Giuseppe Cazzamali,Martina Schneider,Michael Williamson,Elisabeth Stafflinger,Karina K. Hansen,Cornelis J. P. Grimmelikhuijzen,Daniel R. G. Price,Marina C. Caillaud,Eric Van Fleet,Qinghu Ren,John A. Gatehouse,Véronique Brault,Baptiste Monsion,Jason Diaz,Laura Hunnicutt,Ho Jong Ju,Ximo Pechuan,José Aguilar,Teresa Cortes,Benjamín Ortiz-Rivas,David Martínez-Torres,Aviv Dombrovsky,Richard Dale,T.G. Emyr Davies,Martin S. Williamson,Andrew K. Jones,David B. Sattelle,Sally M. Williamson,Adrian J. Wolstenholme,Ludovic Cottret,David G. Heckel,Wayne B. Hunter +223 more
TL;DR: The genome of the pea aphid shows remarkable levels of gene duplication and equally remarkable gene absences that shed light on aspects of aphid biology, most especially its symbiosis with Buchnera.
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