cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids

Kuraku, Shigehiro; Ishijima, Junko; Nishida‐Umehara, Chizuko; Agata, Kiyokazu; Kuratani, Shigeru; Matsuda, Yoichi

doi:10.1007/s10577-006-1035-8

Cited by 44 publications

(56 citation statements)

References 58 publications

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“…This is consistent with the results of genome sequencing in the green anole lizard (Anolis carolinensis, ACA) [11]. Chromosomal size-dependent GC compartmentalization is unique to birds and other reptiles whose karyotypes consist of macro-and microchromosomes [12]. However, crocodile chromosomes are different from those of birds and turtles that have numerous indistinguishable microchromosomes, and the chromosome GC content is unknown in CNI.…”

Section: Introductionsupporting

confidence: 83%

Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken

2012

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The genome size in turtles and crocodiles is thought to be much larger than the 1.2 Gb of the chicken ( Gallus gallus domesticus , GGA), according to the animal genome size database. However, GGA macrochromosomes show extensive homology in the karyotypes of the red eared slider ( Trachemys scripta elegans , TSC) and the Nile crocodile ( Crocodylus niloticus , CNI), and bird and reptile genomes have been highly conserved during evolution. In this study, size and GC content of all chromosomes are measured from the flow karyotypes of GGA, TSC and CNI. Genome sizes estimated from the total chromosome size demonstrate that TSC and CNI are 1.21 Gb and 1.29 Gb, respectively. This refines previous overestimations and reveals similar genome sizes in chicken, turtle and crocodile. Analysis of chromosome GC content in each of these three species shows a higher GC content in smaller chromosomes than in larger chromosomes. This contrasts with mammals and squamates in which GC content does not correlate with chromosome size. These data suggest that a common ancestor of birds, turtles and crocodiles had a small genome size and a chromosomal size-dependent GC bias, distinct from the squamate lineage.

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Section: Introductionsupporting

confidence: 83%

Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken

2012

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“…The chromosome homologies were investigated among the three species, and the numbers of homologous chromosome segments were found to be 25 and 49 for chromosomes 1-7 and the Z chromosomes between the snake and chicken and between the snake and human, respectively. We had constructed a cytogenetic map of the Chinese soft-shelled turtle (Pelodiscus sinensis) with 92 cDNA clones (4,20), which revealed that the chromosomes have been highly conserved between the chicken and the turtle, with the six largest chromosomes being almost equivalent to each other. All of the data collectively suggest that the number of chromosome rearrangements that occurred between the snake and chicken was much more than that between the turtle and chicken.…”

Section: Resultsmentioning

confidence: 99%

Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes

Matsubara

Tarui²,

Toriba

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

281

399

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All snake species exhibit genetic sex determination with the ZZ͞ZW type of sex chromosomes. To investigate the origin and evolution of snake sex chromosomes, we constructed, by FISH, a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 109 cDNA clones. Eleven of the 109 clones were localized to the Z chromosome. All human and chicken homologues of the snake Z-linked genes were located on autosomes, suggesting that the sex chromosomes of snakes, mammals, and birds were all derived from different autosomal pairs of the common ancestor. We mapped the 11 Z-linked genes of E. quadrivirgata to chromosomes of two other species, the Burmese python (Python molurus bivittatus) and the habu (Trimeresurus flavoviridis), to investigate the process of W chromosome differentiation. All and 3 of the 11 clones were localized to both the Z and W chromosomes in P. molurus and E. quadrivirgata, respectively, whereas no cDNA clones were mapped to the W chromosome in T. flavoviridis. Comparative mapping revealed that the sex chromosomes are only slightly differentiated in P. molurus, whereas they are fully differentiated in T. flavoviridis, and E. quadrivirgata is at a transitional stage of sex-chromosome differentiation. The differentiation of sex chromosomes was probably initiated from the distal region on the short arm of the protosex chromosome of the common ancestor, and then deletion and heterochromatization progressed on the sex-specific chromosome from the phylogenetically primitive boids to the more advanced viperids.comparative map ͉ chromosome homology ͉ FISH ͉ sex-determining gene ͉ reptile A ll snake species are subject to genetic sex determination with sex chromosomes, as are mammals and birds, and they have female heterogamety (ZZ males and ZW females). Comparative gene mapping between human and chicken revealed that human XX͞XY and chicken ZZ͞ZW sex chromosomes have no homologies (1, 2), suggesting that the sex chromosomes of mammals and birds were derived from different pairs of autosomes of the common ancestor. Beçak et al. (3) found that there is close karyological similarity between snakes and birds, such as distinct differentiation of macro-and microchromosomes and constant occurrence of ZW-type sex chromosomes. This finding leads us to predict the presence of homology between ophidian and avian sex chromosomes. However, no attempts have yet been made to investigate the conservation of the linkage homologies of snake chromosomes to human and chicken chromosomes by comparative gene mapping, although this approach would provide fundamental information on the genome evolution and the origin of sex-chromosome differentiation in amniotes. In another study (4), we constructed a preliminary cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 52 EST clones, which were isolated from the cDNA library of the brain tissue and were identified as snake homologues of human and chicken orthologous genes by a search of the DNA database. Of 52 EST clones, two genes, T...

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“…Alligator and turtle genome sizes are Ϸ30% smaller than human, Ϸ50% larger than chicken, and only Ϸ12% larger than Anolis, whose genome size is close to the mean for nonavian reptiles. Unlike alligator genomes, the anole, painted turtle, and chicken contain a significant number of microchromosomes (7), which we expect would be gene rich as reported for chickens (8) and the softshelled turtle (9). In general, it is unknown how the macrochromosomes of reptiles differ from those of mammals (10) and those of the nonavian reptiles investigated here.…”

mentioning

confidence: 79%

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

Shedlock

Botka

Zhao³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

129

159

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We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of Ϸ65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome.BAC ͉ Reptilia ͉ retroelement ͉ isochore ͉ intron

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cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids

Cited by 44 publications

References 58 publications

Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken

Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken

Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

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