XB-ART-46522PLoS One. January 1, 2012; 7 (12): e53027.
Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping.
Comparative genome analysis of non-avian reptiles and amphibians provides important clues about the process of genome evolution in tetrapods. However, there is still only limited information available on the genome structures of these organisms. Consequently, the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes in tetrapods remain poorly understood. We constructed chromosome maps of functional genes for the Chinese soft-shelled turtle (Pelodiscus sinensis), the Siamese crocodile (Crocodylus siamensis), and the Western clawed frog (Xenopus tropicalis) and compared them with genome and/or chromosome maps of other tetrapod species (salamander, lizard, snake, chicken, and human). This is the first report on the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes inferred from comparative genomic analysis of vertebrates, which cover all major non-avian reptilian taxa (Squamata, Crocodilia, Testudines). The eight largest macrochromosomes of the turtle and chicken were equivalent, and 11 linkage groups had also remained intact in the crocodile. Linkage groups of the chicken macrochromosomes were also highly conserved in X. tropicalis, two squamates, and the salamander, but not in human. Chicken microchromosomal linkages were conserved in the squamates, which have fewer microchromosomes than chicken, and also in Xenopus and the salamander, which both lack microchromosomes; in the latter, the chicken microchromosomal segments have been integrated into macrochromosomes. Our present findings open up the possibility that the ancestral amniotes and tetrapods had at least 10 large genetic linkage groups and many microchromosomes, which corresponded to the chicken macro- and microchromosomes, respectively. The turtle and chicken might retain the microchromosomes of the amniote protokaryotype almost intact. The decrease in number and/or disappearance of microchromosomes by repeated chromosomal fusions probably occurred independently in the amphibian, squamate, crocodilian, and mammalian lineages.
PubMed ID: 23300852
PMC ID: PMC3534110
Article link: PLoS One.
Genes referenced: kidins220 tbx2
Article Images: [+] show captions
|Figure 2. Comparative cytogenetic map of macrochromosomes of the Chinese soft-shelled turtle (Pelodiscus sinensis).Homologous chicken and human chromosomes are shown to the left of each turtle chromosome (see Table S1). Genetic linkages that are homologous to chicken macrochromosomal arms and/or macrochromosomes (GGA1p, 1q, 2p, 2q, 3, 4q, and GGA5–8) are represented by 10 differently colored bars, and segments drawn with diagonal lines indicate the chicken Z chromosome. The G-banded ideograms of the turtle chromosomes, which were constructed using Hoechst 33258-stained band patterns obtained by the replication banding method, were taken from our previous report . Solid bars to the right of the turtle chromosomes indicate the chromosomal segments in which intrachromosomal rearrangements occurred that resulted in differences between the turtle and chicken chromosomes.|
|Figure 3. Comparative cytogenetic map of the eight largest chromosomes of the Siamese crocodile (Crocodylus siamensis).Homologous chicken and human chromosomes are shown to the left of each crocodile chromosome (see Table S2). Genetic linkages of chicken macrochromosomal arms and/or macrochromosomes are represented by the same colored bars as those in Figure 2. The G-banded ideograms of the crocodile chromosomes were constructed in the present study by the same method as that used for the turtle chromosomes . Solid bars to the right of the crocodile chromosomes indicate the chromosomal segments in which intrachromosomal rearrangements occurred between the crocodile and chicken. un, chromosomal location is unknown in chicken. no, no homologs were found.|
|Figure 4. Comparative cytogenetic map of Xenopus (Silurana) tropicalis.Homologous chicken and human chromosomes are shown to the left of each X. tropicalis chromosome (see Table S3). Genetic linkages of chicken macrochromosomal arms and/or macrochromosomes are represented by the same colored bars as those in Figure 2. The G-banded ideograms of X. tropicalis chromosomes were taken from our previous report . Chromosomes are ordered in accordance with Hellsten et al. . Numbers in parentheses indicate chromosome numbers from our previous report . Solid bars to the right of the X. tropicalis chromosomes indicate the chromosomal segments in which intrachromosomal rearrangements occurred between X. tropicalis and chicken. Gene symbols and chicken chromosome numbers enclosed in boxes indicate the chromosomal segments that corresponded to chicken microchromosomes in which intrachromosomal rearrangements had occurred. un, chromosomal location is unknown.|
|Figure 6. Comparison of chromosomal locations of chicken microchromosomal linkages among vertebrate species.The chromosomal locations of chicken microchromosomal linkages on X. tropicalis chromosome 3 (A) and E. quadrivirgata chromosome 2 (B) are compared among four tetrapod species, X. tropicalis, salamander (A. mexicanum/A. tigrinum), lizard (A. carolinensis), and snake (E. quadrivirgata), and ancestral teleost fish. Genetic linkages of chicken macro- and microchromosomes are represented by the same colored bars as those in Figure 5, and each conserved genetic linkage was defined when two or more genes were located on each of chicken chromosomes. The chromosome numbers of the chicken microchromosomes are shown to the left of each chromosome. Information on the genetic linkages for the ancestral teleost fish, salamander, snake, lizard, and chicken was taken from Kasahara et al.  and Nakatani et al. , Voss et al. , Matsubara et al. , , Alföldi et al.  and the Ensembl Anole Lizard Genome Browser (http://www.ensembl.org/Anolis_carolinensis), and the Ensembl Chicken Genome Browser (http://www.ensembl.org/Gallus_gallus), respectively. The lizard chromosome that is homologous to GGA10 has not been identified yet. The genetic linkages of GGA10, 13, and 22 on X. tropicalis chromosome 3 and GGA12, 13, and 18 on snake chromosome 2 were localized to nonhomologous chromosomes in the other species, except for GGA13 and GGA18 on salamander chromosome 3. The salamander linkage 8 and 12 were contained in the same linkage group , , .|