The complete mitochondrial genome of Macrobrachium nipponense

Gene

Volumn 487, Issue 2, 2011, Pages 160-165

  Ma, Keyi ^a   Feng, Jianbin ^a   Lin, Jingyun ^a   Li, Jiale ^a  

^a SHANGHAI OCEAN UNIVERSITY   (China)

Author keywords

Long PCR; MtDNA; Phylogeny; Sequence analysis

Indexed keywords

ADENOSINE TRIPHOSPHATASE F0 SUBUNIT 6; ADENOSINE TRIPHOSPHATASE F0 SUBUNIT 8; AMINO ACID; CYTOCHROME C OXIDASE SUBUNIT 2; CYTOCHROME C OXIDASE SUBUNIT 3; LEUCINE; PROTEIN; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE SUBUNIT 1; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE SUBUNIT 3; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE SUBUNIT 4; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE SUBUNIT 4L; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE SUBUNIT 5; RIBOSOME RNA; RNA 12S; RNA 16S; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; CODON; CRUSTACEA; FEMALE; GENE IDENTIFICATION; GENE SEQUENCE; MACROBRACHIUM LANCHESTERI; MACROBRACHIUM NIPPONENSE; MACROBRACHIUM ROSENBERGII; MITOCHONDRIAL GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA STRUCTURE; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; CODON; DNA, MITOCHONDRIAL; FEMALE; GENES, RRNA; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; PALAEMONIDAE; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA;

MACROBRACHIUM LANCHESTERI; MACROBRACHIUM NIPPONENSE; MACROBRACHIUM ROSENBERGII; METAZOA;

EID: 80052873782     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2011.07.017     Document Type: Article

References (41)

1. Anderson S., et al. Sequence and organization of the human mitochondrial genome. Nature 1981, 290:457-465.
2. Avise J.C. Molecular Markers, Natural History and Evolution 1994, Chapman and Hall, New York, NY.
3. Avise J.C. Phylogeography: The History and Formation of Species 2000, Harvard University Press, Cambridge, Mass.
4. Beard C.B., Hamm D.M., Collins F.H. The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects. Insect Mol. Biol. 1993, 2:103-124.
5. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27:1767-1780.
6. Boore J.L., Brown W.M. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicate. Genetics 1994, 138:423-443.
7. Boore J.L., Brown W.M. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Mol. Biol. Evol. 2000, 17:87-106.
8. Curole A.P., Kocher T.D. Mitogenomics: digging deeper with complete mitochondrial genomes. Trends Ecol. Evol. 1999, 14:394-398.
9. Dimijian G.G. Evolving together: the biology of symbiosis, part 2. Proc. (Bayl UnivMed Cent) 2000, 13:381-390.
10. Feng J.B., Li J.L., Cheng X. Research progress on germplasm resources exploitation and protection of Macrobrachium nipponense. J. Shanghai Fish. Univ. 2008, 15:371-376.
11. Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome coxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 1994, 3:294-299.
12. Grande C., Templado J., Zardoya R. Evolution of gastropod mitochondrial genome arrangements. BMC Evol. Biol. 2008, 8:61.
13. Guindon S., Gascuel O. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
14. Harrison R.G. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol. Evol. 1989, 4:6-11.
15. Hedges S.B., Chen H., Kumar S., Wang D.Y., Thompson A.S., Watanabe H. A genomic timescale for the origin of eukaryotes. BMC Evol. Biol. 2001, 1:4.
16. Hoffmann R.J., Boore J.L., Brown W.M. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 1992, 131:397-412.
17. Jung S.O., et al. The complete mitochondrial genome of the intertidal copepod Tigriopus sp. (Copepoda, Harpacticidae) from Korea and phylogenetic considerations. Exp. Mar. Biol. Ecol. 2006, 333:251-262.
18. Ki J.S., Dahms H.U., Hwang J.S., Lee J.S. The complete mitochondrial genome of the hydrothermal vent crab Xenograpsus testudinatus (Decapoda, Brachyura). Comp. Biochem. Physiol. 2009, 4:290-299.
19. Ki J.S., Park H.G., Lee J.S. The complete mitochondrial genome of the cyclopoid copepod Paracyclopina nana: a novel gene order and atypical gene numbers with high gene divergence. Gene 2009, 435:13-22.
20. Ki J.S., Lee Y.M., Jung S.O., Horiguchi T., Cho H.S., Lee J.S. Mitochondrial genome of Thais clavigera (Mollusca: Gastropoda): affirmation of the conserved, ancestral gene pattern within the mollusks. Mol. Phylogenet. Evol. 2010, 54:1016-1020.
21. Kumazawa Y., Ota H., Nishida M., Ozawa T. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 1998, 150:313-329.
22. Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
23. Machida R.J., Miya M.U., Nishida M., Nishida S. Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Mar. Biotechnol. 2002, 4:406-417.
24. Martin J.W., Davis G.E. An updated classification of the recent Crustacea. Science Ser. Nat. Hist. Mus. 2001, 39. (LA Co.).
25. Miller A.D., Murphy N.P., Burridge C.P., Austin C.M. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar. Biotechnol. 2005, 7:339-349.
26. Mueller R.L. Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Syst. Biol. 2006, 55:289-300.
27. Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290:470-474.
28. Peng R., Zeng B., Meng X., Yue B., Zhang Z., Zou F. The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca). Gene 2007, 397:76-83.
29. Romero H., Zavala A., Musto H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res. 2000, 28:2084-2090.
30. Russo C.A., Takezaki N., Nei M. Efficiencies of different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 1996, 13:525-536.
31. Saito S., Tamura K., Aotsuka T. Replication origin of mitochondrial DNA in insects. Genetics 2005, 171:1695-1705.
32. Serb J.M., Lydeard C. Complete mtDNA Sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca). Mol. Biol. Evol. 2003, 20:1854-1866.
33. Tamura K., Aptsuka T. Rapid isolation method of animal mitochondrial DNA by the alkaline lysis procedure. Biochem. Genet. 1988, 26:815-819.
34. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
35. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
36. Ui W.H., Chan J.P., Tai S.Y., Won K. One-step PCR amplification of complete arthropod mitochondrial genomes. Mol. Phylogenet. Evol. 2001, 19:345-352.
37. Wolstenholme D.R. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 1992, 141:173-216.
38. Yamauchi M.M., Miya M., Nishida M. Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene 2002, 295:89-96.
39. Yu H.P., Miyake S. Five species of the genus Macrobrachium (Crustacea, Decapoda, Palaemonidae) from Taiwan. Ohmu 1972, 3:45-55.
40. Zardoya R., Meyer A. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 1996, 13:933-942.
41. Zheng R.L., Li J.L., Niu D.H. The complete DNA sequence of the mitochondrial genome of Sinonovacula constricta (Bivalvia: Solecurtidae). Acta. Oceanol. Sin. 2010, 29:88-92.