Next generation sequencing and comparative analyses of Xenopus mitogenomes

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Lloyd, Rhiannon E ^a,c   Foster, Peter G ^b   Guille, Matthew ^a   Littlewood, D Timothy J ^b  

^a UNIVERSITY OF PORTSMOUTH   (United Kingdom)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^c INSTITUTE OF ZOOLOGY   (United Kingdom)

Author keywords

Comparative analyses; Mitochondrial DNA; Mitogenomics; Next generation sequencing; Phylogeny; Selection and molecular markers; Variation; Xenopus

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE (UBIQUINONE);

AMPLICON; ARTICLE; COX1 GENE; COX2 GENE; COX3 GENE; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE; GENE EXPRESSION; MITOCHONDRIAL GENOME; MITOCHONDRIAL RESPIRATION; NAD41 GENE; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PYROSEQUENCING; SEQUENCE ANALYSIS; XENOPUS; XENOPUS BOREALIS; XENOPUS LAEVIS; XENOPUS TROPICALIS; XENOPUS VICTORIANUS;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; EXPRESSED SEQUENCE TAGS; GENETIC MARKERS; GENETIC VARIATION; GENOME, MITOCHONDRIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MODELS, GENETIC; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; SELECTION, GENETIC; SPECIES SPECIFICITY; XENOPUS;

AMPHIBIA; ANURA; EUKARYOTA; XENOPUS BOREALIS; XENOPUS LAEVIS; XENOPUS TROPICALIS;

EID: 84866289893     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-496     Document Type: Article

References (48)

1. Wallace DC. Mitochondrial diseases in man and mouse. Science 1999, 283(5407):1482-1488. 10.1126/science.283.5407.1482, 10066162.
2. Avise JC. Molecular Marker, Natural History and Evolution 2004, 2nd.
3. Alacs EA, Georges A, FitzSimmons NN, Robertson J. DNA detective: a review of molecular approaches to wildlife forensics. Forensic Sci Med Pathol 2009, 6(3):180-194.
4. Jarman PG, Fentress SL, Katz DE. Mitochondrial DNA validation in a state laboratory. J Forensic Sci 2009, 54(1):95-102. 10.1111/j.1556-4029.2008.00924.x, 19067775.
5. Gibb GC, Kardailsky O, Kimball RT, Braun EL, Penny D. Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol Biol Evol 2007, 24(1):269-280.
6. Phillips MJ, Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol Phylogenet Evol 2003, 28(2):171-185. 10.1016/S1055-7903(03)00057-5, 12878457.
7. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, et al. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 2003, 26(1):121-138. 10.1016/S1055-7903(02)00332-9, 12470944.
8. Alam MS, Kurabayashi A, Hayashi Y, Sano N, Khan MR, Fujii T, Sumida M. Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus and Euphlyctis hexadactylus, from Bangladesh. Genes Genet Syst 2010, 85(3):219-232. 10.1266/ggs.85.219, 21041980.
9. Bi K, Bogart JP. Time and time again: unisexual salamanders (genus Ambystoma) are the oldest unisexual vertebrates. BMC Evol Biol 2010, 10:238. 10.1186/1471-2148-10-238, 3020632, 20682056.
10. San Mauro D, Gower DJ, Zardoya R, Wilkinson M. A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. Mol Biol Evol 2006, 23(1):227-234.
11. Zhang P, Chen YQ, Zhou H, Liu YF, Wang XL, Papenfuss TJ, Wake DB, Qu LH. Phylogeny, evolution, and biogeography of Asiatic Salamanders (Hynobiidae). Proc Natl Acad Sci U S A 2006, 103(19):7360-7365. 10.1073/pnas.0602325103, 1464346, 16648252.
12. The IUCN Red List of Threatened Species. Version 2011.2 2011, http://www.iucnredlist.org/(Downloaded 29 May 2012).
13. Kilpatrick AM, Briggs CJ, Daszak P. The ecology and impact of chytridiomycosis: an emerging disease of amphibians. Trends Ecol Evol 2010, 25(2):109-118. 10.1016/j.tree.2009.07.011, 19836101.
14. Maya-Soriano MJ, Holt WV, Lloyd RE. Biobanked Amphibian Samples Confirmed To Species Level Using 16S rRNA DNA Barcodes. Biopreservation Biobanking 2012, 10(1):22-28.
15. Pyron RA, Wiens JJ. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phylogenet Evol 2011, 61(2):543-583. 10.1016/j.ympev.2011.06.012, 21723399.
16. Meier R, Zhang G, Ali F. The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. Syst Biol 2008, 57(5):809-813. 10.1080/10635150802406343, 18853366.
17. Boore JL. The use of genome-level characters for phylogenetic reconstruction. Trends Ecol Evol 2006, 21(8):439-446. 10.1016/j.tree.2006.05.009, 16762445.
18. Zarowiecki MZ, Huyse T, Littlewood DT. Making the most of mitochondrial genomes-markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminthes: Digenea). Int J Parasitol 2007, 37(12):1401-1418. 10.1016/j.ijpara.2007.04.014, 17570370.
19. Sumida M, Kanamori Y, Kaneda H, Kato Y, Nishioka M, Hasegawa M, Yonekawa H. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. Genes Genet Syst 2001, 76(5):311-325. 10.1266/ggs.76.311, 11817647.
20. D'Errico I, Gadaleta G, Saccone C. Pseudogenes in metazoa: origin and features. Brief Funct Genomic Proteomic 2004, 3(2):157-167. 10.1093/bfgp/3.2.157, 15355597.
21. Wolff JN, Shearman DC, Brooks RC, Ballard JW. Selective enrichment and sequencing of whole mitochondrial genomes in the presence of nuclear encoded mitochondrial pseudogenes (numts). PLoS One 2012, 7(5):e37142. 10.1371/journal.pone.0037142, 3351421, 22606342.
22. Jex AR, Hall RS, Littlewood DT, Gasser RB. An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Res 2010, 38(2):522-533. 10.1093/nar/gkp883, 2811008, 19892826.
23. Timmermans MJ, Dodsworth S, Culverwell CL, Bocak L, Ahrens D, Littlewood DT, Pons J, Vogler AP. Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res 2010, 38(21):e197. 10.1093/nar/gkq807, 2995086, 20876691.
24. Harland RM, Grainger RM. Xenopus research: metamorphosed by genetics and genomics. Trends Genet 2011, 27(12):507-515. 10.1016/j.tig.2011.08.003, 21963197.
25. Roe BA, Ma DP, Wilson RK, Wong JF. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J Biol Chem 1985, 260(17):9759-9774.
26. Perna NT, Kocher TD. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 1995, 41(3):353-358. 10.1007/BF01215182, 7563121.
27. Castellana S, Vicario S, Saccone C. Evolutionary patterns of the mitochondrial genome in Metazoa: exploring the role of mutation and selection in mitochondrial protein coding genes. Genome Biol Evol 2011, 3:1067-1079.
28. Reyes A, Gissi C, Pesole G, Saccone C. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol Biol Evol 1998, 15(8):957-966. 10.1093/oxfordjournals.molbev.a026011, 9718723.
29. Sano N, Kurabayashi A, Fujii T, Yonekawa H, Sumida M. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the bell-ring frog, Buergeria buergeri (family Rhacophoridae). Genes Genet Syst 2004, 79(3):151-163. 10.1266/ggs.79.151, 15329496.
30. Ojala D, Merkel C, Gelfand R, Attardi G. The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 1980, 22(2 Pt 2):393-403.
31. Irisarri I, Vences M, San Mauro D, Glaw F, Zardoya R. Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae. BMC Evol Biol 2011, 11:114. 10.1186/1471-2148-11-114, 3111386, 21524293.
32. Evans BJ, Kelley DB, Tinsley RC, Melnick DJ, Cannatella DC. A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution. Mol Phylogenet Evol 2004, 33(1):197-213. 10.1016/j.ympev.2004.04.018, 15324848.
33. Frost DR. Amphibian Species of the World an Online Reference. Version 5.5. Electronic Database accessible at http://research.amnh.org/vz/herpetology/amphibia/. 2011(Downloaded 31 January, 2011).
34. Evans BJ, Kelley DB, Melnick DJ, Cannatella DC. Evolution of RAG-1 in polyploid clawed frogs. Mol Biol Evol 2005, 22(5):1193-1207. 10.1093/molbev/msi104, 15703243.
35. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19(18):2496-2497. 10.1093/bioinformatics/btg359, 14668244.
36. Vences M, Thomas M, Bonett RM, Vieites DR. Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philos Trans R Soc Lond B Biol Sci 2005, 360(1462):1859-1868. 10.1098/rstb.2005.1717, 1609216, 16221604.
37. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 1994, 3(5):294-299.
38. Xia Y, Gu HF, Peng R, Chen Q, Zheng YC, Murphy RW, Zeng XM. COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae). Mol Ecol Resour 2011, 12(1):48-56.
39. Rawlings TA, Collins TM, Bieler R. Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. Proc Natl Acad Sci U S A 2003, 100(26):15700-15705. 10.1073/pnas.2535036100, 307631, 14673095.
40. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science 1996, 272(5265):1136-1144. 10.1126/science.272.5265.1136, 8638158.
41. Soto IC, Fontanesi F, Liu J, Barrientos A. Biogenesis and assembly of eukaryotic cytochrome c oxidase catalytic core. Biochim Biophys Acta 2012, 1817(6):883-897. 10.1016/j.bbabio.2011.09.005, 21958598.
42. Efremov RG, Sazanov LA. Respiratory complex I: 'steam engine' of the cell?. Curr Opin Struct Biol 2011, 21(4):532-540. 10.1016/j.sbi.2011.07.002, 21831629.
43. Bowes JB, Snyder KA, Segerdell E, Jarabek CJ, Azam K, Zorn AM, Vize PD. Xenbase: gene expression and improved integration. Nucleic Acids Res 2009, 38(Database issue):D607-D612. 2808955, 19884130.
44. Chevreux B. MIRA: An Automated Genome and EST Assembler 2006, Germany: Heidelberg University.
45. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-964. 146525, 9023104.
46. Laslett D, Canback B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24(2):172-175. 10.1093/bioinformatics/btm573, 18033792.
47. Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17(8):754-755. 10.1093/bioinformatics/17.8.754, 11524383.
48. Zhang Z, Li J, Yu J. Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evol Biol 2006, 6:44. 10.1186/1471-2148-6-44, 1552089, 16740169.