Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation

Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta—CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms.

[1]  M. Kirkpatrick,et al.  Chromosome Inversions, Local Adaptation and Speciation , 2017, Genetics.

[2]  Meganathan P. Ramakodi,et al.  Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs , 2014, Science.

[3]  Denis M Larkin,et al.  Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor , 2014, BMC Genomics.

[4]  W. Earnshaw,et al.  The Centromere: Chromatin Foundation for the Kinetochore Machinery , 2014, Developmental cell.

[5]  D. Badenhorst,et al.  Molecular Cytogenetic Search for Cryptic Sex Chromosomes in Painted Turtles Chrysemys picta , 2014, Cytogenetic and Genome Research.

[6]  Y. Uno,et al.  The Staurotypus Turtles and Aves Share the Same Origin of Sex Chromosomes but Evolved Different Types of Heterogametic Sex Determination , 2014, PloS one.

[7]  Stephen D. Sarre,et al.  Highly Differentiated ZW Sex Microchromosomes in the Australian Varanus Species Evolved through Rapid Amplification of Repetitive Sequences , 2014, PloS one.

[8]  J. Deakin,et al.  Tracing the evolution of amniote chromosomes , 2014, Chromosoma.

[9]  Y. Uno,et al.  Karyotype evolution in monitor lizards: cross-species chromosome mapping of cDNA reveals highly conserved synteny and gene order in the Toxicofera clade , 2013, Chromosome Research.

[10]  J. Logan,et al.  The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system , 2013, Proceedings of the National Academy of Sciences.

[11]  Drew R. Schield,et al.  The Burmese python genome reveals the molecular basis for extreme adaptation in snakes , 2013, Proceedings of the National Academy of Sciences.

[12]  E. Olmo,et al.  Karyological Characterization of the Endemic Iberian Rock Lizard, Iberolacerta monticola (Squamata, Lacertidae): Insights into Sex Chromosome Evolution , 2013, Cytogenetic and Genome Research.

[13]  Nerida Harley,et al.  Reconstruction of the ancestral marsupial karyotype from comparative gene maps , 2013, BMC Evolutionary Biology.

[14]  A. Georges,et al.  Molecular cytogenetic map of the central bearded dragon, Pogona vitticeps (Squamata: Agamidae) , 2013, Chromosome Research.

[15]  Bronwen L. Aken,et al.  The draft genomes of soft–shell turtle and green sea turtle yield insights into the development and evolution of the turtle–specific body plan , 2013, Nature Genetics.

[16]  Sonja J. Prohaska,et al.  Analysis of the African coelacanth genome sheds light on tetrapod evolution , 2013, Nature.

[17]  N. Valenzuela,et al.  Transcriptional evolution underlying vertebrate sexual development , 2013, Developmental dynamics : an official publication of the American Association of Anatomists.

[18]  D. Badenhorst,et al.  A ZZ/ZW microchromosome system in the spiny softshell turtle, Apalone spinifera, reveals an intriguing sex chromosome conservation in Trionychidae , 2013, Chromosome Research.

[19]  Alexander S. Garruss,et al.  Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution , 2013, Nature Genetics.

[20]  Victoria Svinti,et al.  New approaches for unravelling reassortment pathways , 2013, BMC Evolutionary Biology.

[21]  Kiyokazu Agata,et al.  Inference of the Protokaryotypes of Amniotes and Tetrapods and the Evolutionary Processes of Microchromosomes from Comparative Gene Mapping , 2012, PloS one.

[22]  F. Delsuc,et al.  Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria) , 2012, BMC Biology.

[23]  M. Ferguson-Smith,et al.  Extensive Homology of Chicken Macrochromosomes in the Karyotypes of Trachemys scripta elegans and Crocodylus niloticus Revealed by Chromosome Painting despite Long Divergence Times , 2012, Cytogenetic and Genome Research.

[24]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[25]  A. Desai,et al.  Structure, assembly and reading of centromeric chromatin. , 2012, Current opinion in genetics & development.

[26]  Jennifer C. Drew,et al.  Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes , 2012, Genome Biology.

[27]  S. Tishkoff,et al.  Genetic adaptation to high altitude in the Ethiopian highlands , 2012, Genome Biology.

[28]  K. Gull,et al.  Detailed interrogation of trypanosome cell biology via differential organelle staining and automated image analysis , 2012, BMC Biology.

[29]  Y. Uno,et al.  Chromosomal localization of the 18S-28S and 5S rRNA genes and (TTAGGG)n sequences of butterfly lizards (Leiolepis belliana belliana and Leiolepis boehmei, Agamidae, Squamata) , 2011, Genetics and molecular biology.

[30]  Jacob D. Jaffe,et al.  The genome of the green anole lizard and a comparative analysis with birds and mammals , 2011, Nature.

[31]  D. Adams,et al.  CHROMOSOME NUMBER AND SEX DETERMINATION COEVOLVE IN TURTLES , 2011, Evolution; international journal of organic evolution.

[32]  Lalji Singh.  The charms of sex chromosomes in snakes , 2011, Journal of Biosciences.

[33]  Tetsuya Hori,et al.  Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences. , 2010, Genome research.

[34]  Albert J. Vilella,et al.  Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis , 2010, PLoS biology.

[35]  D. O’Meally,et al.  The First Cytogenetic Map of the Tuatara, Sphenodon punctatus , 2010, Cytogenetic and Genome Research.

[36]  N. Valenzuela.  Multivariate Expression Analysis of the Gene Network Underlying Sexual Development in Turtle Embryos with Temperature-Dependent and Genotypic Sex Determination , 2010, Sexual Development.

[37]  H. Loxdale,et al.  Rapid genetic changes in natural insect populations , 2010 .

[38]  A. Georges,et al.  The ZW sex microchromosomes of an Australian dragon lizard share no homology with those of other reptiles or birds , 2009, Chromosome Research.

[39]  A. Sinclair,et al.  The avian Z-linked gene DMRT1 is required for male sex determination in the chicken , 2009, Nature.

[40]  Y. Uno,et al.  The ZW Micro-Sex Chromosomes of the Chinese Soft-Shelled Turtle (Pelodiscus sinensis, Trionychidae, Testudines) Have the Same Origin as Chicken Chromosome 15 , 2009, Cytogenetic and Genome Research.

[41]  N. Valenzuela.  The painted turtle, Chrysemys picta: a model system for vertebrate evolution, ecology, and human health. , 2009, Cold Spring Harbor protocols.

[42]  N. Valenzuela.  Egg incubation and collection of painted turtle embryos. , 2009, Cold Spring Harbor protocols.

[43]  P. Martinez,et al.  Karyotypic characterization of Trachemys dorbigni (Testudines: Emydidae) and Chelonoidis (Geochelone) donosobarrosi (Testudines: Testudinidae), two species of Cryptodiran turtles from Argentina , 2009, Genetica.

[44]  S. Teichmann,et al.  The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. , 2009, Genome research.

[45]  D. Cooper,et al.  Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution , 2009, BMC Evolutionary Biology.

[46]  Y. Matsuda,et al.  The ZW sex chromosomes of Gekko hokouensis (Gekkonidae, Squamata) represent highly conserved homology with those of avian species , 2009, Chromosoma.

[47]  A. Ruiz-Herrera,et al.  Telomeric repeats far from the ends: mechanisms of origin and role in evolution , 2009, Cytogenetic and Genome Research.

[48]  Loren H Rieseberg,et al.  Revisiting the Impact of Inversions in Evolution: From Population Genetic Markers to Drivers of Adaptive Shifts and Speciation? , 2008, Annual review of ecology, evolution, and systematics.

[49]  C. Organ,et al.  New resources inform study of genome size, content, and organization in nonavian reptiles. , 2008, Integrative and comparative biology.

[50]  N. Valenzuela.  Evolution of the gene network underlying gonadogenesis in turtles with temperature-dependent and genotypic sex determination. , 2008, Integrative and comparative biology.

[51]  E. Olmo.  Trends in the evolution of reptilian chromosomes. , 2008, Integrative and comparative biology.

[52]  A. Georges,et al.  An XX/XY heteromorphic sex chromosome system in the Australian chelid turtle Emydura macquarii: A new piece in the puzzle of sex chromosome evolution in turtles , 2008, Chromosome Research.

[53]  L. Gustafsson,et al.  A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution , 2008, Genetics.

[54]  N. Archidiacono,et al.  Primate chromosome evolution: Ancestral karyotypes, marker order and neocentromeres , 2008, Chromosome Research.

[55]  N. Valenzuela.  RELIC THERMOSENSITIVE GENE EXPRESSION IN A TURTLE WITH GENOTYPIC SEX DETERMINATION , 2007, Evolution; international journal of organic evolution.

[56]  Y. Kohara,et al.  Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. , 2007, Genome research.

[57]  Y. Matsuda,et al.  Different origins of bird and reptile sex chromosomes inferred from comparative mapping of chicken Z-linked genes , 2007, Cytogenetic and Genome Research.

[58]  H. Tempest,et al.  The evolution of the avian genome as revealed by comparative molecular cytogenetics , 2007, Cytogenetic and Genome Research.

[59]  Fumiko Ohta,et al.  The medaka draft genome and insights into vertebrate genome evolution , 2007, Nature.

[60]  Bronwen L. Aken,et al.  Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences , 2007, Nature.

[61]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[62]  Y. Matsuda,et al.  Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes , 2006, Proceedings of the National Academy of Sciences.

[63]  A. Bolzán,et al.  Telomeres, interstitial telomeric repeat sequences, and chromosomal aberrations. , 2006, Mutation research.

[64]  A. Helwak,et al.  High Guanine and Cytosine Content Increases mRNA Levels in Mammalian Cells , 2006, PLoS biology.

[65]  J. Graves,et al.  Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. , 2006, Trends in genetics : TIG.

[66]  A. Georges,et al.  An XX/XY sex microchromosome system in a freshwater turtle, Chelodina longicollis (Testudines: Chelidae) with genetic sex determination , 2006, Chromosome Research.

[67]  A. Georges,et al.  The dragon lizard Pogona vitticeps has ZZ/ZW micro-sex chromosomes , 2005, Chromosome Research.

[68]  E. Olmo.  Rate of Chromosome changes and Speciation in Reptiles , 2005, Genetica.

[69]  Kiyokazu Agata,et al.  Highly conserved linkage homology between birds and turtles: Bird and turtle chromosomes are precise counterparts of each other , 2005, Chromosome Research.

[70]  Shyam Prabhakar,et al.  Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. , 2005, Human molecular genetics.

[71]  F. Ayala,et al.  Chromosome speciation: Humans, Drosophila, and mosquitoes , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[72]  A. Ruiz-Herrera,et al.  Evolutionary breakpoints are co-localized with fragile sites and intrachromosomal telomeric sequences in primates , 2004, Cytogenetic and Genome Research.

[73]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[74]  J. Masabanda,et al.  Chromosome assignment of eight SOX family genes in chicken , 2003, Cytogenetic and Genome Research.

[75]  A. T. Sumner.  Chromosomes: Organization and Function , 2003 .

[76]  D. Burt,et al.  Origin and evolution of avian microchromosomes , 2002, Cytogenetic and Genome Research.

[77]  E. Olmo,et al.  Different genomic evolutionary rates in the various reptile lineages. , 2002, Gene.

[78]  C. Azzalin,et al.  Human intrachromosomal telomeric-like repeats: sequence organization and mechanisms of origin , 2001, Chromosoma.

[79]  M. Schartl,et al.  First report on chicken genes and chromosomes 2000 , 2000, Cytogenetic and Genome Research.

[80]  M. Schartl,et al.  Conserved synteny between the chicken Z sex chromosome and human chromosome 9 includes the male regulatory gene DMRT1: a comparative (re)view on avian sex determination , 2000, Cytogenetic and Genome Research.

[81]  K P Fung,et al.  Molecular cloning and characterization of FHL2, a novel LIM domain protein preferentially expressed in human heart. , 1998, Gene.

[82]  J. W. Foster,et al.  Mutations in SOX9, the gene responsible for Campomelic dysplasia and autosomal sex reversal. , 1995, American journal of human genetics.

[83]  D. Birnbaum,et al.  The human FGF9 gene maps to chromosomal region 13q11-q12. , 1995, Genomics.

[84]  A. Monaco,et al.  An unusual member of the nuclear hormone receptor superfamily responsible for X-linked adrenal hypoplasia congenita , 1994, Nature.

[85]  Sahar Mansour,et al.  Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene , 1994, Nature.

[86]  H. Williams,et al.  Healing of broken human chromosomes by the addition of telomeric repeats. , 1994, American journal of human genetics.

[87]  A. Baldini,et al.  Improved telomere detection using a telomere repeat probe (TTAGGG)n generated by PCR. , 1991, Nucleic acids research.

[88]  J. Bickham,et al.  Structure and variation of the Nucleolus Organizer Region in turtles , 1985, Genetica.

[89]  G. Smith.  Avian sex determination , 1983, Veterinary Record.

[90]  J. Bickham.  Two-hundred-million-year-old chromosomes: deceleration of the rate of karyotypic evolution in turtles. , 1981, Science.

[91]  S. Bloom,et al.  Visualization of nucleolar organizer regions in mammalian chromosomes using silver staining , 1975, Chromosoma.

[92]  A. T. Sumner.  A simple technique for demonstrating centromeric heterochromatin. , 1972, Experimental cell research.

[93]  M. Seabright.  A rapid banding technique for human chromosomes. , 1971, Lancet.

[94]  Nicholas G. Crawford,et al.  More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. , 2012, Biology letters.

[95]  Daniel E. Warren,et al.  The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage , 2013, Genome Biology.

[96]  Y. Matsuda,et al.  The origin and differentiation process of X and Y chromosomes of the black marsh turtle (Siebenrockiella crassicollis, Geoemydidae, Testudines) , 2011, Chromosome Research.

[97]  P. Shaw,et al.  The Structure of rDNA Chromatin , 2011 .

[98]  Miriam K. Konkel,et al.  Tumour invasion and metastasis initiated by microRNA-10b in breast cancer , 2008, Nature.

[99]  Horst Hameister,et al.  Reconstruction of the ancestral ferungulate karyotype by electronic chromosome painting (E-painting) , 2006, Chromosome Research.

[100]  B. Dutrillaux,et al.  Reconstruction of the ancestral karyotype of eutherian mammals , 2004, Chromosome Research.

[101]  J. Graves,et al.  Comparative Chromosome Painting Between Marsupial Orders: Relationships with a 2n = 14 Ancestral Marsupial Karyotype , 2004, Chromosome Research.