title: Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake.
abstract: BACKGROUND
  Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm lizards and snakes). Karyotypes of these sauropsidan groups generally consist of macrochromosomes and microchromosomes. In chicken, microchromosomes exhibit a higher GC-content than macrochromosomes. To examine the pattern of intra-genomic GC heterogeneity in lepidosaurian genomes, we constructed a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 183 cDNA clones by fluorescence in situ hybridization, and examined the correlation between the GC-content of exonic third codon positions (GC3) of the genes and the size of chromosomes on which the genes were localized.
  
  
  RESULTS
  Although GC3 distribution of snake genes was relatively homogeneous compared with those of the other amniotes, microchromosomal genes showed significantly higher GC3 than macrochromosomal genes as in chicken. Our snake cytogenetic map also identified several conserved segments between the snake macrochromosomes and the chicken microchromosomes. Cross-species comparisons revealed that GC3 of most snake orthologs in such macrochromosomal segments were GC-poor (GC3 < 50%) whereas those of chicken orthologs in microchromosomes were relatively GC-rich (GC3 ≥ 50%).
  
  
  CONCLUSIONS
  Our results suggest that the chromosome size-dependent GC heterogeneity had already occurred before the lepidosaur-archosaur split, 275 million years ago. This character was probably present in the common ancestor of lepidosaurs and but lost in the lineage leading to Anolis during the diversification of lepidosaurs. We also identified several genes whose GC-content might have been influenced by the size of the chromosomes on which they were harbored over the course of sauropsid evolution.
authors.affiliation: Department of Information and Biological Sciences, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan. kazumi.matsubara@canberra.edu.au
authors.forename: Kazumi
authors.initials: K
authors.lastname: Matsubara
authors.forename: Shigehiro
authors.initials: S
authors.lastname: Kuraku
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Tarui
authors.forename: Osamu
authors.initials: O
authors.lastname: Nishimura
authors.forename: Chizuko
authors.initials: C
authors.lastname: Nishida
authors.forename: Kiyokazu
authors.initials: K
authors.lastname: Agata
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Kumazawa
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Matsuda
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics*; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics*; D003062:Codon / Q000235:genetics; D020732:Cytogenetic Analysis; D018076:DNA, Complementary / Q000235:genetics; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D016678:Genome / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence; D012911:Snakes / Q000235:genetics*; D013045:Species Specificity
chemical_list: D003062:Codon; D018076:DNA, Complementary