The mitochondrial genome of Euphausia superba (Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers

Molecular Biology Reports

Volumn 37, Issue 2, 2010, Pages 771-784

  Shen, Xin ^a,b   Wang, Haiqing ^b   Ren, Jianfeng ^b   Tian, Mei ^a   Wang, Minxiao ^b  

^a HUAIHAI INSTITUTE OF TECHNOLOGY   (China)

^b INSTITUTE OF OCEANOLOGY   (China)

Author keywords

Euphausiacea; Gene rearrangement; Malacostraca; Mitochondrial genome; Phylogenomics

Indexed keywords

RIBOSOME RNA; TRANSFER RNA; MITOCHONDRIAL DNA;

ARTICLE; CODON USAGE; CONTROLLED STUDY; EUPHAUSIA SUPERBA; EUPHAUSIACEA; GENE FUNCTION; GENE REARRANGEMENT; GENE SEQUENCE; GENE TRANSLOCATION; GENETIC MARKER; GENETIC ORGANIZATION; GENETIC VARIABILITY; MITOCHONDRIAL GENOME; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENETIC TREE; PLANT GENOME; RNA TRANSPORT; TAXONOMY; ANIMAL; ANTARCTICA; CONFORMATION; CRUSTACEA; GENETICS; PHYLOGENY; RNA GENE;

BRACHYURA; CARIDEA; CRUSTACEA; EUPHAUSIA SUPERBA; EUPHAUSIACEA; EUPHAUSIIDAE; MALACOSTRACA; PANCRUSTACEA; PENAEIDAE; STOMATOPODA;

ANIMALS; ANTARCTIC REGIONS; BASE SEQUENCE; CRUSTACEA; DNA, MITOCHONDRIAL; EUPHAUSIACEA; GENES, RRNA; GENETIC MARKERS; GENETIC VARIATION; GENOME, MITOCHONDRIAL; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, TRANSFER;

EID: 77950911920     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-009-9602-7     Document Type: Article

References (45)

1. Boore JL, Collins TM, Stanton D et al (1995) Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 376(6536):163-165. doi:10.1038/376163a0
2. Boore JL, Lavrov DV, Brown WM (1998) Gene translocation links insects and crustaceans. Nature 392(6677):667-668. doi: 10.1038/33577 (Pubitemid 28207777)
3. Boore JL, Macey JR, Medina M (2005) Sequencing and comparing whole mitochondrial genomes of animals. Methods Enzymol 395:311-348. doi:10.1016/S0076-6879(05)95019-2 (Pubitemid 40754376)
4. Dellaporta SL, Xu A, Sagasser S et al (2006) Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci USA 103(23):8751-8756. doi:10.1073/pnas.0602076103 (Pubitemid 43878091)
5. Shen X, Ren JF, Cui ZX et al (2007) The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations. Gene 403(1-2):98-109. doi:10.1016/j.gene. 2007.06.021 (Pubitemid 47488699)
6. Jongwutiwes S, Putaporntip C, Iwasaki T et al (2005) Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax. Mol Biol Evol 22(8):1733-1739. doi: 10.1093/molbev/msi168 (Pubitemid 41373584)
7. Boore JL, Brown WM (1998) Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev 8(6):668-674. doi:10.1016/S0959-437X(98)80035-X (Pubitemid 28558529)
8. Brierley AS (2008) Antarctic ecosystem: are deep krill ecological outliers or portents of a paradigm shift? Curr Biol 18(6):R252-R254. doi:10.1016/j.cub.2008.01.022 (Pubitemid 351389780)
9. Brierley AS, Fernandes PG, Brandon MA et al (2002) Antarctic krill under sea ice: elevated abundance in a narrow band just south of ice edge. Science 295(5561):1890-1892. doi:10.1126/ science.1068574
10. Clarke A, Tyler PA (2008) Adult antarctic krill feeding at abyssal depths. Curr Biol 18(4):282-285. doi:10.1016/j.cub.2008.01.059 (Pubitemid 351258347)
11. Machida RJ, Miya MU, Yamauchi MM et al (2004) Organization of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca). Mar Biotechnol 6(3):238-250. doi:10.1007/s10126-003-0016-6 (Pubitemid 40653948)
12. Cheng S, Chang SY, Gravitt P et al (1994) Long PCR. Nature 369(6482):684-685. doi:10.1038/369684a0 (Pubitemid 24199477)
13. EwingB,GreenP (1998)Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8(3):186-194 (Pubitemid 28177230)
14. Ewing B, Hillier L, Wendl MC et al (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8(3):175-185 (Pubitemid 28177229)
15. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8(3):195-202
16. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17): 3252-3255. doi:10.1093/ bioinformatics/bth352 (Pubitemid 39619219)
17. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955-964. doi:10.1093/nar/25.5.955 (Pubitemid 27298263)
18. Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52(5-6):267-274. doi:10.1007/s00294-007-0161-y (Pubitemid 350090630)
19. Rozas J, Sanchez-DelBarrio JC, Messeguer X et al (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19(18):2496-2497. doi:10.1093/bioinformatics/ btg359
20. Hickerson MJ, Cunningham CW (2000) Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura). Mol Biol Evol 17(4):639-644
21. Wilson K, Cahill V, Ballment E et al (2000) The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods? Mol Biol Evol 17(6):863-874
22. Yamauchi M, Miya M, NishidaM(2002) Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene 295(1):89-96. doi:10.1016/S0378- 1119(02)00824-7
23. Yamauchi MM, Miya MU, Machida RJ et al (2004) PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus). Mar Biotechnol 6(5):419-429. doi:10.1007/ s10126-003-0036-2
24. Yamauchi MM, Miya MU, Nishida M (2003) Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura). Gene 311:129-135. doi:10.1016/S0378-1119(03)00582-1 (Pubitemid 36830809)
25. Miller AD, Murphy NP, Burridge CP et al (2005) Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar Biotechnol 7(4):339-349. doi:10.1007/s101 26-004-4077-8
26. Miller AD, Nguyen TT, Burridge CP et al (2004) Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed. Gene 331:65-72. doi:10.1016/j.gene. 2004.01.022
27. Place AR, Feng X, Steven CR et al (2005) Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation. J Exp Mar Biol Ecol 319(1-2):15-27. doi:10.1016/j.jembe.2004.03.024 (Pubitemid 40707671)
28. Segawa RD, Aotsuka T (2005) The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication. Gene 355:28-39. doi:10.1016/j.gene.2005.05.020 (Pubitemid 41133329)
29. Sun H, Zhou K, Song D (2005) Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements. Gene 349:207-217. doi: 10.1016/j.gene.2004.12.036
30. Kilpert F, Podsiadlowski L (2006) The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics 7:241. doi:10.1186/1471-2164-7-241 (Pubitemid 44509393)
31. Miller AD, AustinCM(2006) The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol Phylogenet Evol 38(3):565-574. doi:10.1016/j.ympev.2005.10. 001
32. Ivey JL, Santos SR (2007) The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae). Gene 394(1-2):35-44. doi:10.1016/j.gene.2007.01.009 (Pubitemid 46601763)
33. Cook CE (2005) The complete mitochondrial genome of the stomatopod crustacean Squilla mantis. BMC Genomics 6:105. doi:10.1186/1471-2164-6-105 (Pubitemid 41372434)
34. Yang JS, Nagasawa H, Fujiwara Y et al (2008) The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): a novel arrangement and incomplete tRNA suite. BMC Genomics 9:257. doi:10.1186/1471-2164-9-257 (Pubitemid 351943969)
35. Martin JW, DavisGE(2001) An updated classification of the recent crustacea. Natural History Museum of Los Angeles County, Los Angeles
36. Thompson JD, Gibson TJ, Plewniak F et al (1997) The CLUSTAL- X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876-4882. doi:10.1093/nar/25.24.4876 (Pubitemid 28022245)
37. Tamura K, Dudley J, Nei M et al (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596-1599. doi:10.1093/molbev/msm092 (Pubitemid 47236692)
38. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5):696-704. doi:10.1080/10635150390235520 (Pubitemid 37365050)
39. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12): 1572-1574. doi:10.1093/bioinformatics/btg180 (Pubitemid 37038874)
40. Posada D (2006) ModelTest server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res 34(Web server issue):W700-W703
41. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21(9):2104-2105. doi:10.1093/bioinformatics/bti263 (Pubitemid 40668057)
42. Abascal F, Posada D, Zardoya R (2007) MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol 24(1):1-5. doi:10.1093/molbev/msl136 (Pubitemid 46026273)
43. Ojala D, Montoya J, Attardi G (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature 290(5806): 470-474. doi:10.1038/290470a0 (Pubitemid 11159076)
44. Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature 435(7038):17. doi:10.1038/435017b
45. Seifert KA, Samson RA, Dewaard JR et al (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci USA 104(10):3901-3906. doi: 10.1073/pnas.0611691104 (Pubitemid 47181551)