Zardoya R, Meyer A: Complete mitochondrial genome suggests diapsid affinities of turtles. Proc Natl Acad Sci USA. 1998, 95: 14226-14231. 10.1073/pnas.95.24.14226.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hedges SB, Poling LL: A molecular phylogeny of reptiles. Science. 1999, 283: 998-1001. 10.1126/science.283.5404.998.
Article
CAS
PubMed
Google Scholar
Kumazawa Y, Nishida M: Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for archosaurian affinity of turtles. Mol Biol Evol. 1999, 16: 784-792. 10.1093/oxfordjournals.molbev.a026163.
Article
CAS
PubMed
Google Scholar
Cao Y, Sorenson MD, Kumazawa Y, Mindell DP, Hasegawa M: Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes. Gene. 2000, 259: 139-148. 10.1016/S0378-1119(00)00425-X.
Article
CAS
PubMed
Google Scholar
Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, Hay JM, Mindell DP: Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Mol Phylogenet Evol. 2003, 29: 289-297. 10.1016/S1055-7903(03)00108-8.
Article
CAS
PubMed
Google Scholar
Iwabe N, Hara Y, Kumazawa Y, Shibamoto K, Saito Y, Miyata T, Katoh K: Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins. Mol Biol Evol. 2005, 22: 810-813. 10.1093/molbev/msi075.
Article
CAS
PubMed
Google Scholar
Kumazawa Y: Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations. Gene. 2007, 388: 19-26. 10.1016/j.gene.2006.09.026.
Article
CAS
PubMed
Google Scholar
Benton MJ, Donoghue PCJ: Paleontological evidence to date the tree of life. Mol Biol Evol. 2007, 24: 26-53.
Article
CAS
PubMed
Google Scholar
Shedlock AM, Edwards SV: Amniotes (Amniota). The timetree of life. Edited by: Hedges SB, Kumar S. 2009, New York: Oxford University Press, 375-379.
Google Scholar
Beçak W, Beçak ML, Nazareth HRS, Ohno S: Close karyological kinship between the reptilian suborder Serpentes and the class Aves. Chromosoma. 1964, 15: 606-617. 10.1007/BF00319994.
Article
PubMed
Google Scholar
Bickham JW, Baker RJ: Chromosome homology and evolution of emydid turtles. Chromosoma. 1976, 54: 201-219. 10.1007/BF00293451.
Article
CAS
PubMed
Google Scholar
Bickham JW, Bull JJ, Legler JM: Karyotypes and evolutionary relationships of trinychoid turtles. Cytologia. 1983, 48: 177-183. 10.1508/cytologia.48.177.
Article
Google Scholar
Norris TB, Rickards GK, Daugherty CH: Chromosomes of tuatara, Sphenodon, a chromosome heteromorphism and an archaic reptilian karyotype. Cytogenet Genome Res. 2004, 105: 93-99. 10.1159/000078014.
Article
CAS
PubMed
Google Scholar
Takagi N, Sasaki M: A phylogenetic study of bird karyotypes. Chromosoma. 1974, 46: 91-120. 10.1007/BF00332341.
Article
CAS
PubMed
Google Scholar
Belterman RHR, de Boer LEM: A karyological study of 55 species of birds, including karyotypes of 39 species new to cytology. Genetica. 1984, 65: 39-82. 10.1007/BF00056765.
Article
Google Scholar
Shetty S, Griffin DK, Graves JAM: Comparative painting reveals strong chromosome homology over 80 million years of bird evolution. Chromosome Res. 1999, 7: 289-295. 10.1023/A:1009278914829.
Article
CAS
PubMed
Google Scholar
Nishida-Umehara C, Tsuda Y, Ishijima J, Ando J, Fujiwara A, Matsuda Y, Griffin DK: The molecular basis of chromosome orthologies and sex chromosomal differentiation in palaeognathous birds. Chromosome Res. 2007, 15: 721-734. 10.1007/s10577-007-1157-7.
Article
CAS
PubMed
Google Scholar
Cohen MM, Gans C: The chromosomes of the order Crocodylia. Cytogenetics. 1970, 9: 81-105. 10.1159/000130080.
Article
CAS
PubMed
Google Scholar
Kawagoshi T, Nishida C, Ota H, Kumazawa Y, Endo H, Matsuda Y: Molecular structures of centromeric heterochromatin and karyotypic evolution in the Siamese crocodile (Crocodylus siamensis) (Crocodylidae, Crocodylia). Chromosome Res. 2008, 16: 1119-1132. 10.1007/s10577-008-1263-1.
Article
CAS
PubMed
Google Scholar
International Chicken Genome Sequencing Consortium (ICGSC): Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004, 432: 695-716. 10.1038/nature03154.
Article
Google Scholar
Kuraku S, Ishijima J, Nishida-Umehara C, Agata K, Kuratani S, Yoichi M: cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. Chromosome Res. 2006, 14: 187-202. 10.1007/s10577-006-1035-8.
Article
CAS
PubMed
Google Scholar
Costantini M, Filippo MD, Auletta F, Bernardi G: Isochore pattern and gene distribution in the chicken genome. Gene. 2007, 400: 9-15. 10.1016/j.gene.2007.05.025.
Article
CAS
PubMed
Google Scholar
McQueen HA, Siriaco G, Bird AP: Chicken microchromosomes are hyperacetylated, early replicating, and gene rich. Genome Res. 1998, 8: 621-630.
PubMed Central
CAS
PubMed
Google Scholar
Smith J, Bruley CK, Paton IR, Dunn I, Jones CT, Windsor D, Morrice DR, Law AS, Masabanda J, Sazanov A, Waddington D, Fries R, Burt DW: Differences in gene density on chicken macrochromosomes and microchromosomes. Anim Genet. 2000, 31: 96-103. 10.1046/j.1365-2052.2000.00565.x.
Article
CAS
PubMed
Google Scholar
Habermann FA, Cremer M, Walter J, Kreth G, von Hase J, Bauer K, Wienberg J, Cremer C, Cremer T, Solovei I: Arrangements of macro- and microchromosomes in chicken cells. Chromosome Res. 2001, 9: 569-584. 10.1023/A:1012447318535.
Article
CAS
PubMed
Google Scholar
Axelsson E, Webster MT, Smith NG, Burt DW, Ellegren H: Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res. 2005, 15: 120-125. 10.1101/gr.3021305.
Article
PubMed Central
CAS
PubMed
Google Scholar
Federico C, Cantarella CD, Scavo C, Saccone S, Bed'Hom B, Bernardi G: Avian genomes: different karyotypes but a similar distribution of the GC-richest chromosome regions at interphase. Chromosome Res. 2005, 13: 785-793. 10.1007/s10577-005-1012-7.
Article
CAS
PubMed
Google Scholar
Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, Liu JS, Deschavanne PJ, Edwards SV: Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci USA. 2007, 104: 2767-2772. 10.1073/pnas.0606204104.
Article
PubMed Central
CAS
PubMed
Google Scholar
Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV: Genome evolution in Reptilia, the sister groups of mammals. Annu Rev Genomics Hum Genet. 2010, 11: 239-264. 10.1146/annurev-genom-082509-141646.
Article
CAS
PubMed
Google Scholar
Belle EM, Smith N, Eyre-Walker A: Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J Mol Evol. 2002, 55: 356-363. 10.1007/s00239-002-2333-1.
Article
CAS
PubMed
Google Scholar
Hamada K, Horiike T, Ota H, Mizuno K, Shinozawa T: Presence of isochore structures in reptile genomes suggested by the relationship between GC content of intron regions and those of coding regions. Genes Genet Syst. 2003, 78: 195-198. 10.1266/ggs.78.195.
Article
CAS
PubMed
Google Scholar
Chojnowski JL, Franklin J, Katsu Y, Iguchi T, Guillette LJ, Kimball RT, Braun EL: Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. J Mol Evol. 2007, 65: 259-266. 10.1007/s00239-007-9003-2.
Article
CAS
PubMed
Google Scholar
Chojnowski JL, Braun EL: Turtle isochore structure is intermediate between amphibians and other amniotes. Integr Comp Biol. 2008, 48: 454-462. 10.1093/icb/icn062.
Article
PubMed
Google Scholar
Elhaik E, Landan G, Graur D: Can GC content at third-codon positions be used as a proxy for isochore composition?. Mol Biol Evol. 2009, 26: 1829-1833. 10.1093/molbev/msp100.
Article
CAS
PubMed
Google Scholar
Clay OK, Bernardi G: GC3 of genes can be used as a proxy for isochore base composition: A reply to Elhaik et al. Mol Biol Evol. 2011, 28: 21-23. 10.1093/molbev/msq222.
Article
CAS
PubMed
Google Scholar
Romiguier J, Ranwez V, Douzery EJP, Galtier N: Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes. Genome Res. 2010, 20: 1001-1009. 10.1101/gr.104372.109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fujita MK, Edwards SV, Ponting CP: The Anolis lizard genome: an amniote genome without isochores. Genome Biol Evol. in press
Matsuda Y, Nishida-Umehara C, Tarui H, Kuroiwa A, Yamada K, Isobe T, Ando J, Fujiwara A, Hirao Y, Nishimura O, Ishijima J, Hayashi A, Saito T, Murakami T, Murakami Y, Kuratani S, Agata K: Highly conserved linkage homology between birds and turtles: Bird and turtle chromosomes are precise counterparts of each other. Chromosome Res. 2005, 13: 601-615. 10.1007/s10577-005-0986-5.
Article
CAS
PubMed
Google Scholar
Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, Ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K: The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011, 477: 587-591. 10.1038/nature10390.
Article
PubMed Central
PubMed
Google Scholar
Beçak W, Beçak ML: Cytotaxonomy and chromosomal evolution in Serpentes. Cytogenetics. 1969, 8: 247-262. 10.1159/000130037.
Article
PubMed
Google Scholar
Singh L: Evolution of karyotypes in snakes. Chromosoma. 1972, 38: 185-236. 10.1007/BF00326193.
Article
CAS
PubMed
Google Scholar
Matsubara K, Tarui H, Toriba M, Yamada K, Nishida-Umehara C, Agata K, Matsuda Y: Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes. Proc Natl Acad Sci USA. 2006, 103: 18190-18195. 10.1073/pnas.0605274103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.
Article
PubMed Central
CAS
PubMed
Google Scholar
Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987, 4: 406-425.
CAS
PubMed
Google Scholar
Katoh K, Kuma K, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005, 33: 511-518. 10.1093/nar/gki198.
Article
PubMed Central
CAS
PubMed
Google Scholar
Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704. 10.1080/10635150390235520.
Article
PubMed
Google Scholar
Matsuda Y, Chapman VM: Application of fluorescence in situ hybridization in genome analysis of the mouse. Electrophoresis. 1995, 16: 261-272. 10.1002/elps.1150160142.
Article
CAS
PubMed
Google Scholar
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002, 12: 1611-1618. 10.1101/gr.361602.
Article
PubMed Central
CAS
PubMed
Google Scholar
Castoe TA, de Koning AJ, Hall KT, Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor SM, Pollock DD: Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biol. 2011, 12: 406-10.1186/gb-2011-12-7-406. URL: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEQU
Article
PubMed Central
CAS
PubMed
Google Scholar
Wise2 - Intelligent algorithms for DNA searches. URL: http://www.ebi.ac.uk/Tools/Wise2/index.html
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E: Ensembl 2005. Nucleic Acids Res. 2005, 33: D447-453. 10.1093/nar/gki378. URL: http://www.ensembl.org/
Article
PubMed Central
CAS
PubMed
Google Scholar
NCBI Entrez Gene. URL: http://www.ncbi.nlm.nih.gov/gene/
Al-Shahrour F, Dîaz-Uriarte R, Dopazo J: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004, 20: 578-580. 10.1093/bioinformatics/btg455. URL: http://babelomics.bioinfo.cipf.es/functional.html
Article
CAS
PubMed
Google Scholar
Shibusawa M, Nishibori M, Nishida-Umehara C, Tsudzuki M, Masabanda J, Griffin DK, Matsuda Y: Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny. Cytogenet Genome Res. 2004, 106: 111-119. 10.1159/000078570.
Article
CAS
PubMed
Google Scholar
Holmquist GP: Chromosome bands, their chromatin flavors, and their functional features. Am J Hum Genet. 1992, 51: 17-37.
PubMed Central
CAS
PubMed
Google Scholar
Saccone S, De Sario A, Della Valle G, Bernardi G: The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes. Proc Natl Acad Sci USA. 1992, 89: 4913-4917. 10.1073/pnas.89.11.4913.
Article
PubMed Central
CAS
PubMed
Google Scholar
Saccone S, De Sario A, Wiegant J, Raap AK, Della Valle G, Bernardi G: Correlations between isochores and chromosomal bands in the human genome. Proc Natl Acad Sci USA. 1993, 90: 11929-11933. 10.1073/pnas.90.24.11929.
Article
PubMed Central
CAS
PubMed
Google Scholar
Saccone S, Cacciò S, Kusuda J, Andreozzi L, Bernardi G: Identification of the gene-richest bands in human chromosomes. Gene. 1996, 174: 85-94. 10.1016/0378-1119(96)00392-7.
Article
CAS
PubMed
Google Scholar
Nabholz B, Künstner A, Wang R, Jarvis ED, Ellegren H: Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Mol Biol Evol. 2011, 28: 2197-2210. 10.1093/molbev/msr047.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bucciarelli G, Di Filippo M, Costagliola D, Alvarez-Valin F, Bernardi G, Bernardi G: Environmental genomics: a tale of two fishes. Mol Biol Evol. 2009, 26: 1235-1243. 10.1093/molbev/msp041.
Article
CAS
PubMed
Google Scholar
Kasai F, O'Brien PC, Ferguson-Smith MA: Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken. Biol Lett. 2012, 8: 631-635. 10.1098/rsbl.2012.0141.
Article
PubMed Central
PubMed
Google Scholar
Benirschke K, Hsu TC: Chromosome atlas: fish, amphibians, reptiles and birds volume 1. 1971, New York: Springer
Google Scholar
Burt DW: Origin and evolution of avian microchromosomes. Cytogenet Genome Res. 2002, 96: 97-112. 10.1159/000063018.
Article
CAS
PubMed
Google Scholar
Nakatani Y, Takeda H, Kohara Y, Morishita S: Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res. 2007, 17: 1254-1265. 10.1101/gr.6316407.
Article
PubMed Central
CAS
PubMed
Google Scholar
Duret L, Eyre-Walker A, Galtier N: A new perspective on isochore evolution. Gene. 2006, 385: 71-74.
Article
CAS
PubMed
Google Scholar
Duret L, Galtier N: Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet. 2009, 10: 285-311. 10.1146/annurev-genom-082908-150001.
Article
CAS
PubMed
Google Scholar
Meunier J, Duret L: Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol. 2004, 21: 984-990. 10.1093/molbev/msh070.
Article
CAS
PubMed
Google Scholar
Costantini M, Cammarano R, Bernardi G: The evolution of isochore patterns in vertebrate genomes. BMC Genomics. 2009, 10: 146-10.1186/1471-2164-10-146.
Article
PubMed Central
PubMed
Google Scholar
Costantini M, Clay O, Auletta F, Bernardi1 G: An isochore map of human chromosomes. Genome Res. 2006, 16: 536-541. 10.1101/gr.4910606.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kai W, Kikuchi K, Tohari S, Chew AK, Tay A, Fujiwara A, Hosoya S, Suetake H, Naruse K, Brenner S, Suzuki Y, Venkatesh B: Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. Genome Biol Evol. 2011, 3: 424-442. 10.1093/gbe/evr041.
Article
CAS
PubMed
Google Scholar
Backström N, Forstmeier W, Schielzeth H, Mellenius H, Nam K, Bolund E, Webster MT, Ost T, Schneider M, Kempenaers B, Ellegren H: The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res. 2010, 20: 485-495. 10.1101/gr.101410.109.
Article
PubMed Central
PubMed
Google Scholar
Hildebrand F, Meyer A, Eyre-Walker A: Evidence of selection upon genomic GC-content in bacteria. PLoS Genet. 2010, 6: e1001107-10.1371/journal.pgen.1001107.
Article
PubMed Central
PubMed
Google Scholar
Bajic VB, Tan SL, Christoffels A, Schönbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y: Mice and men: their promoter properties. PLoS Genet. 2006, 2: e54-10.1371/journal.pgen.0020054.
Article
PubMed Central
PubMed
Google Scholar
D'Onofrio G, Ghosh TC, Saccone S: Different functional classes of genes are characterized by different compositional properties. FEBS Lett. 2007, 581: 5819-5824. 10.1016/j.febslet.2007.11.052.
Article
PubMed
Google Scholar
Ren L, Gao G, Zhao D, Ding M, Luo J, Deng H: Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation. Genome Biol. 2007, 8: R35-10.1186/gb-2007-8-3-r35.
Article
PubMed Central
PubMed
Google Scholar