The complete mitogenome and phylogenetic analysis of Bombyx mandarina strain Qingzhou

Molecular Biology Reports

Volumn 37, Issue 6, 2010, Pages 2599-2608

  Hu, Xiao Long ^a   Cao, Guang Li ^a   Xue, Ren Yu ^a   Zheng, Xiao Jian ^a   Zhang, Xing ^a   Duan, Hai Rong ^a   Gong, Cheng Liang ^a  

^a SOOCHOW UNIVERSITY   (China)

Author keywords

Bombyx mandarina; Bombyx mori; Mitochondrial DNA; Molecular phylogeny; Nuclear mitochondrial pseudogenes

Indexed keywords

ADENINE; CYTOSINE; GUANINE; MITOCHONDRIAL DNA; MITOCHONDRIAL PROTEIN; MITOCHONDRIAL RNA; NUCLEAR PROTEIN; THYMINE; TRANSFER RNA; RIBOSOME RNA; SILK;

ANIMAL CELL; ARTICLE; CHINA; CONTROLLED STUDY; GENE SEQUENCE; LEPIDOPTERA; MOTH; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PSEUDOGENE; RNA STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SILKWORM; STOP CODON; STRAIN DIFFERENCE; ANIMAL; AT RICH SEQUENCE; BIOSYNTHESIS; BOMBYX; CELL NUCLEUS; GENE; GENETICS; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MOLECULAR GENETICS; OPEN READING FRAME; TIME;

ANIMALS; AT RICH SEQUENCE; BASE SEQUENCE; BOMBYX; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, INSECT; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; PSEUDOGENES; RNA, RIBOSOMAL; RNA, TRANSFER; SILK; TIME FACTORS;

ANTHERAEA PERNYI; BOMBYX MANDARINA; BOMBYX MORI; TRIFOLIUM;

EID: 77955664915     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-009-9781-2     Document Type: Article

References (60)

1. KP Arunkumar M Muralidhar J Nagaraju 2006 Molecular phylogeny of silk moths reveals the origin of domesticated silk moth, Bombyx mori from Chinese Bombyx mandarina and paternal inheritance of Antheraea proylei mitochondrial DNA Mol Phylogen Evol 40 419 427 10.1016/j.ympev.2006.02.023 1:CAS:528: DC%2BD28XntFWqsLw%3D (Pubitemid 44056283)
2. Y Banno T Nakamura E Nagashima H Fujii H Doira 2004 M chromosome of the wild silkworm, Bombyx mandarina (n = 27), corresponds to two chromosomes in the domesticated silkworm, Bombyx mori (n = 28) Genome 47 96 101 10.1139/g03-112 1:CAS:528:DC%2BD2cXivFGqsb8%3D 15060606 (Pubitemid 38504135)
3. CB Beard D Mills FH Collins 1993 The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects Insect Mol Biol 2 103 124 10.1111/j.1365-2583.1993.tb00131.x 1:CAS:528:DyaK2cXitV2rsL8%3D 9087549
4. D Bensasson DX Zhang DL Hartl GM Hewitt 2001 Mitochondrial pseudogenes: evolution's misplaced witnesses Trends Ecol Evol 16 314 321 10.1016/S0169- 5347(01)02151-6 11369110 (Pubitemid 32706648)
5. MJ Bibb RA Van Etten CT Wright MW Walberg DA Clayton 1981 Sequence and gene organization of mouse mitochondrial DNA Cell 26 167 180 10.1016/0092-8674(81)90300-7 1:CAS:528:DyaL38XkslOltA%3D%3D 7332926
6. JL Boore 1999 Animal mitochondrial genomes Nucleic Acids Res 27 1767 1780 10.1093/nar/27.8.1767 1:CAS:528:DyaK1MXivVersbo%3D 10101183 (Pubitemid 29209617)
7. TM Boyce ME Zwick CF Aquadro 1989 Mitochondrial DNA in the bark weevils: size, structure and heteroplasmy Genetics 123 825 836 1:CAS:528: DyaK3cXkvFylsQ%3D%3D 2612897
8. A Brehm DJ Harris M Hernandez V Cabrera J Larruga F Pinto AM Gonzalez 2001 Structure and evolution of the mitochondrial DNA complete control region in the Drosophila subobscura subgroup Insect Mol Biol 10 573 578 10.1046/j.0962-1075.2001.00295.x 1:CAS:528:DC%2BD38Xps1Gn 11903626 (Pubitemid 34010040)
9. SL Cameron MF Whiting 2008 The complete mitochondrial genome of the tobacco hornworm, Manduca sexta (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths Gene 408 112 123 10.1016/j.gene.2007.10.023 1:CAS:528:DC%2BD1cXhvFygsQ%3D%3D 18065166
10. SY Cha HJ Yoon EM Lee MH Yoon JS Hwang BR Jin YS Han I Kim 2007 The complete nucleotide sequence and gene organization of the mitochondrial genome of the bumblebee, Bombus ignitus (Hymenoptera: Apidae) Gene 392 206 220 10.1016/j.gene.2006.12.031 1:CAS:528:DC%2BD2sXjs1Cgsbg%3D 17321076 (Pubitemid 46482852)
11. DO Clary DR Wolstenholme 1985 The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code J Mol Evol 22 252 271 10.1007/BF02099755 1:CAS:528:DyaL28Xht1eqtb4%3D 3001325 (Pubitemid 16178191)
12. DO Clary DR Wolstenholme 1987 Drosophila mitochondrial DNA: conserved sequences in the A + T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNA J Mol Evol 25 116 125 10.1007/BF02101753 1:CAS:528:DyaL2sXmtFakt78%3D 3116271
13. BS Coates DV Sumerford RL Hellmich LC Lewis 2005 Partial mitochondrial genome sequences of Ostrinia nubilalis and Ostrinia furnicalis Int J Biol Sci 1 13 18 1:CAS:528:DC%2BD2MXjs1eltLs%3D 15951845
14. RH Crozier YC Crozier 1993 The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization Genetics 133 97 117 1:CAS:528:DyaK3sXisVyrtrc%3D 8417993
15. EM Dotson CB Beard 2001 Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiata Insect Mol Biol 10 205 215 10.1046/j.1365-2583.2001.00258.x 1:CAS:528:DC%2BD3MXlt1ahtbc%3D 11437912 (Pubitemid 32602225)
16. YX Fu WH Li 1997 Estimating the age of the common ancestor of a sample of DNA sequences Mol Biol Evol 14 195 199 1:CAS:528:DyaK2sXhtVKhurc%3D 9029798
17. T Gamo Y Ohtsuka 1980 Phylogenetic studies on the racial differentiation of the silkworm, Bombyx mori, on the basis of polymorphic genes in haemolymph proteins Bull Sericul Exp Sta 28 15 50
18. MW Gray 1989 Origin and evolution of mitochondrial DNA Annu Rev Cell Biol 5 25 50 10.1146/annurev.cb.05.110189.000325 1:CAS:528:DyaK3cXhslOqug%3D%3D 2688706
19. M Hajibabaei DH Janzen JM Burns W Hallwachs PDN Hebert 2006 DNA barcodes distinguish species of tropical Lepidoptera Proc Natl Acad Sci USA 103 968 971 10.1073/pnas.0510466103 16418261 (Pubitemid 43212205)
20. Hemudu Relics Archaeological Team 1980 Main discoveries of the second excavation of Hemudu sites in Zhejiang Cult Relics 5 1
21. K Inohira T Hara ET Matsuura 1997 Nucleotide sequence divergence in the A + T-rich region of mitochondrial DNA in Drosophila simulans and Drosophila mauritiana Mol Biol Evol 14 814 822 1:CAS:528:DyaK2sXltVeju7s%3D 9254919
22. Jiang YL (1982) The origin and differentiation of domesticated silkworms. Jiangsu Scientific and Technical Press, Nanjing
23. AC Junqueira AC Lessinger TT Torres FR da Silva AL Vettore P Arruda AM Azeredo-Espin 2004 The mitochondrial genome of the blowfly Chrysomya chloropyga (Diptera: Calliphoridae) Gene 339 7 15 10.1016/j.gene.2004.06.031 1:CAS:528:DC%2BD2cXnsVKjtb8%3D 15363841 (Pubitemid 39201123)
24. E Kawaguchi 1934 Chromosome behaviour in tetraploid female of the silkworm J Sericult Sci Jpn 5 73 79 (in Japanese)
25. I Kim CJ Phillips JA Monjeau EC Birney K Noack DE Pumo 1998 Habitat islands, genetic diversity, and gene flow in a Patagonian rodent Mol Ecol 7 667 678 10.1046/j.1365-294x.1998.00369.x 1:STN:280:DyaK1czgsVyhuw%3D%3D 9640647 (Pubitemid 28288511)
26. I Kim JS Bae HD Sohn PD Kang KS Ryu BH Sohn, et al. 2000 Genetic homogeneity in the domestic silkworm, Bombyx mori, and phylogenetic relationship between B. mori and the wild silkworm, B. mandarina using mitochondrial COI gene sequences Int J Indust Entomol 1 9 17 1:STN:280:DC%2BD38zktFKrug%3D%3D
27. I Kim EM Lee KY Seol EY Yun YB Lee JS Hwang BR Jin 2006 The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae) Insect Mol Biol 15 217 225 10.1111/j.1365-2583.2006.00630.x 1:CAS:528: DC%2BD28XksVWlsL4%3D 16640732
28. S Kumar K Tamura M Nei 2004 MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment Brief Bioinform 2 150 163 10.1093/bib/5.2.150
29. DV Lavrov WM Brown JL Boore 2000 A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus Proc Natl Acad Sci USA 97 13738 13742 10.1073/pnas.250402997 1:CAS:528:DC%2BD3cXoslynsrk%3D 11095730
30. ES Lee KS Shin MS Kim H Park S Cho CB Kim 2006 The mitochondrial genome of the smaller tea tortrix Adoxophyes honmai (Lepidoptera: Tortricidae) Gene 373 52 57 10.1016/j.gene.2006.01.003 1:CAS:528:DC%2BD28Xktlaqu7s%3D 16488090
31. A Li Q Zhao S Tang Z Zhang S Pan G Shen 2005 Molecular phylogeny of the domesticated silkworm, Bombyx mori, based on the sequences of mitochondrial cytochrome b genes J Genet 84 137 142 10.1007/BF02715839 1:CAS:528: DC%2BD2MXhtFSkt77E 16131713
32. Y Liu Y Li M Pan F Dai X Zhu C Lu Z Xiang 2008 The complete mitochondrial genome of the Chinese oak silkmoth, Antheraea pernyi (Lepidoptera: Saturniidae) Acta Biochim Biophys Sin 40 693 703 1:CAS:528:DC%2BD1cXhtFegtbnP 18685785
33. C Lu HS Yu ZH Xiang 2002 Molecular systematic studies on Chinese Mandarina silkworm (Bombyx mandarina M.) and domestic silkworm (Bombyx mori L.) Sci Agri Sinica 35 94 101 1:CAS:528:DC%2BD38XhsFKgu7g%3D (in Chinese)
34. H Maekawa N Takada K Mikitani T Ogura N Miyajima H Fujiwara M Kobayashi O Ninaki 1988 Nucleolus organizers in the wild silkworm Bombyx mandarina and the domesticated silkworm B. mori Chromosoma (Historical Archive) 96 263 269 10.1007/BF00286912 1:CAS:528:DyaL1cXktVWktLk%3D
35. M Minato 1966 The last viaduct of Japan Islands Earth Sci 85 86 2 11 (in Japanese with English summary)
36. A Monforte E Barrio A Latorre 1993 Characterization of the length polymorphism in the A + T-rich region of the Drosophila obscura group species J Mol Evol 36 214 223 10.1007/BF00160476 1:CAS:528:DyaK3sXhvVCqtrw%3D 8483159
37. C Moritz TE Dowling WM Brown 1987 Evolution of animal mitochondrial DNA: relevance for population biology and systematics Annu Rev Ecol Syst 18 269 292 10.1146/annurev.es.18.110187.001413
38. A Murakami HT Imai 1974 Cytological evidence for holocentric chromosomes of the silkworms, Bombyx mori and B. mandarina (Bombycidae, Lepidoptera) Chromosoma 47 167 178 10.1007/BF00331804 1:STN:280:DyaE2M7jtVCnsA%3D%3D 4141955
39. E Negrisolo A Minelli G Valle 2004 Extensive gene order rearrangement in the mitochondrial genome of the centipede Scutigera coleoptrata J Mol Evol 58 413 423 10.1007/s00239-003-2563-x 1:CAS:528:DC%2BD2cXjslOrtrw%3D 15114420 (Pubitemid 38501415)
40. D Ojala J Montoya G Attardi 1981 tRNA punctuation model of RNA processing in human mitochondria Nature 290 470 474 10.1038/290470a0 1:CAS:528: DyaL3MXksFKmtLo%3D 7219536 (Pubitemid 11159076)
41. MH Pan QY Yu YL Xia FY Dai YQ Liu C Lu Z Zhang ZH Xiang 2008 Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bombyx mandarina (Lepidoptera: Bombycidae) Life Sci 51 693 701 10.1007/s11427-008-0097-6 1:CAS:528:DC%2BD1cXhtFOisrrK
42. NT Perna TD Kocher 1995 Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes J Mol Evol 41 353 358 10.1007/BF01215182 1:CAS:528:DyaK2MXnslWnt7g%3D 7563121
43. DM Rand RG Harrison 1989 Molecular population genetics of mtDNA size variation in crickets Genetics 121 551 569 1:CAS:528:DyaL1MXhvVOjur4%3D 2565855
44. P Salvato M Simonato A Battisti E Negrisolo 2008 The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae) Genomics 9 1 15
45. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning, a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Woodbury, NY
46. D Sankoff G Leduc N Antoine B Paquin BF Lang R Cedergren 1992 Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome Proc Natl Acad Sci USA 89 6575 6579 10.1073/pnas.89.14.6575 1:CAS:528: DyaK38XltVKku7o%3D 1631158
47. AS Schultheis LA Weigt AC Hendricks 2002 Arrangement and structural conservation of the mitochondrial control region of two species of Plecoptera: utility of tandem repeat-containing regions in studies of population genetics and evolutionary history Insect Mol Biol 11 605 610 10.1046/j.1365-2583.2002. 00371.x 1:STN:280:DC%2BD38nmtFyjsA%3D%3D 12421418 (Pubitemid 35436627)
48. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876 4882 10.1093/nar/25.24.4876 1:CAS:528:DyaK1cXntFyntQ%3D%3D 9396791 (Pubitemid 28022245)
49. DR Wolstenholme 1992 Animal mitochondrial DNA: structure and evolution Int Rev Cyt 141 173 216 10.1016/S0074-7696(08)62066-5 1:CAS:528: DyaK3sXkt1Wgs78%3D
50. DR Wolstenholme DO Clary 1985 Sequence evolution of Drosophila mitochondrial DNA Genetics 109 725 744 1:CAS:528:DyaL2MXhvFyrsL8%3D 3921427
51. T Yagi T Katoh A Chichvarkhin T Shinkawa K Omoto 2001 Molecular phylogeny of butterflies Parnassius glacialis and P. stubbendorfii at various localities in East Asia Genes Genet Syst 76 229 234 10.1266/ggs.76.229 1:CAS:528: DC%2BD3MXosF2rsr4%3D 11732631 (Pubitemid 32958775)
52. Y Yamauchi C HoeVer A Yamamoto H Takeda R Ishihara H Maekawa R Sato S Su-Il M Sumida MA Wells K Tsuchida 2000 cDNA and deduced amino acid sequences of apolipophorin-IIIs from Bombyx mori and Bombyx mandarina Arch Insect Biochem Physiol 43 16 21 10.1002/(SICI)1520-6327(200001)43:1<16::AID-ARCH3>3.0. CO;2-W 1:CAS:528:DC%2BD3cXkt1SltQ%3D%3D 10613959
53. N Yoshitake 1967 Phylogenetic aspects on the origin of Japanese race of the silkworm, Bombyx mori J Sericult Sci Jpn 37 83 87
54. N Yoshitake 1968 Phylogenetic aspects on the origin of Japanese race of the silkworm, Bombyx mori L J Sericult Sci Jpn 37 83 87
55. N Yoshitake M Akiyama 1965 Distribution of the blood esterase types in various strains of the silkworm, Bombyx mori J Sericult Sci Jpn 34 99 103
56. K Yukuhiro H Sezutsu M Itoh K Shimizu Y Banno 2002 Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the wild mulberry silkmoth, Bombyx mandarina, and its close relative, the domesticated silkmoth, Bombyx mori Mol Biol Evol 19 1385 1389 1:CAS:528:DC%2BD38XmtF2rs70%3D 12140251
57. EV Zakharov MS Caterino FA Sperling 2004 Molecular phylogeny, historical biogeography, and divergence time estimates for swallowtail butterflies of the genus Papilio (Lepidoptera: Papilionidae) Syst Biol 53 193 215 10.1080/10635150490423403 15205049 (Pubitemid 38611180)
58. DX Zhang GM Hewitt 1996 Nuclear integrations: challenges for mitochondrial DNA markers Trends Ecol Evol 11 247 251 10.1016/0169-5347(96) 10031-8 (Pubitemid 126381581)
59. DX Zhang GM Hewitt 1997 Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies Biochem Syst Evol 25 99 120 10.1016/S0305-1978(96)00042-7 (Pubitemid 27193428)
60. D Zhang JM Szymura GM Hewitt 1995 Evolution and structural conservation of the control region of insect mitochondrial DNA J Mol Evol 40 382 391 10.1007/BF00164024 1:CAS:528:DyaK2MXltVeksbg%3D 7769615