|Supplementary File 1: Methodological descriptions for the in silico identification of conserved syntenic segmental associations and the multispecies comparative chromosome architecture of human chromosomes.
(i) In silico identification of conserved syntenic segmental associations at deeper nodes of the vertebrate tree.
The SyntenyTracker application (Donthu et al., 2009) was used to established homologous synteny blocks (HSBs) between human and the genomes of thirteen mammalian species (chimpanzee, orangutan, rhesus macaque, mouse, rat, cow, dog, armadillo, elephant,
tenrec, opossum and platypus) plus the chicken and the frog. The blocks of homologous
synteny are based on the position of orthologous genes in the genomes of the respective species.
Regions with three or more genes conserved in position (without disruption) were considered as single HSBs. Orthologous genes in all pair-wise comparison, except human-frog, were downloaded from the Ensembl genome browser v61 using the Biomart platform. In the case of the human-frog comparison the recently published frog genome (Hellsten et al., 2010) was used in which the homologous regions between human and the different linkage groups in frog are provided. The files were sorted by linkage group and examined for position against the frog scaffolds so as to obtain an ordered list of the HSBs in the human genome. All HSBs detected in the species are detailed in Supplementary File 2. For each species we established the start and end (in bp) of the homologous segment in the human genome. Where possible, we also determined the positions (start and end) of the conserved segments in all the species analysed. We then used the “Evolutionary Highway” (http://eh-demo.ncsa.uiuc.edu/) to plot the coordinates of the HSBs onto the human chromosomes thus permitting a comprehensive visualization of the chromosomal syntenies (Supplementary File 3); these were mapped to the chicken, platypus and opossum genomes to show the composition of the HSBs in the three outgroup species to Placentalia (Figure 3).
The armadillo and the tenrec assemblies are incomplete and, as a consequence, it was only possible to identify HSBs <0.1Mbp in size. This meant that < 2% of the genomes
could be scanned for homology with human leading to their exclusion from the subsequent analysis of ancestral conserved syntenies. Improved assembly of the elephant and platypus genomes allowed us to establish that 54.66% and 37.15% of the human genome is homologous to elephant and platypus genomes, respectively. The major portion of the platypus genome is assembled into chromosomes (1-7, 10-12, 14, 15, 17, 18, 20, X1, X2, X3 and X5) but there are still 441 contings and 351 ultracontings without chromosomal assignment and several platypus chromosomes remain unassembled (8, 9, 13, 16, 19, 21-23 and X4 and are therefore absent in Figure 3). A total of 142 nonassembled scaffolds, on the other hand, currently represent the elephant genome. These unassigned regions are, in part, responsible of the low homology coverage with human genome.
Xenopus tropicalis, on the other hand, is estimated to possess a genome comprising 1.7
Gbp distributed over 10 chromosomes or linkage groups (Hellsten et al., 2010). Of this, 769Mb has been placed onto 691 scaffolds based on genetic markers. This paucity of information is further underscored by 200Mbp being assigned to linkage groups based on inference but without genetic markers (Hellsten et al., 2010). In contrast, the coverage provided by chicken, opossum and the boreoeutherian genomes (i.e., chimpanzee, orangutan, rhesus macaque, mouse, rat, cow and dog) is vastly improved permitting the identification of larger regions of homology with the human genome. When considered in their entirety, the number and median length (bp) of the detected HSBs reflect the extent of genome reshuffling among species. Put differently, these data show the degree to which inversions, fusions and fissions alter the gene order between contiguous HSBs. Therefore, pairwise comparisons of primate (chimpanzee, orangutan and macaque) genomes with human show the conservation of large (between 60Mbp and 30Mbp of average size) but relatively few HSBs, followed by the dog, cow and rodents (mouse and rat) with smaller but increasing numbers of HSBs.
(ii) Multispecies comparative chromosome architecture of human chromosomes.
The “Evolutionary Highway” (http://eh-demo.ncsa.uiuc.edu/) was used to plot the coordinates of the HSBs obtained by the Synteny Tracker in all human chromosomes (Supplementary File 3). Gray blocks indicate HSBs, with the chromosomal identity indicated by either a number or an uppercase letter and a number. Lowercase letters indicate order of the HSB in that species’ chromosome or scaffold (in the case of the frog and elephant genomes). A detailed listed of the HSBs is provided in the Supplementary File 2. Although analyzed, the armadillo and tenrec HSBs are not shown due to extremely low coverage results.
Donthu R, Lewin HA, Larkin DM (2009). SyntenyTracker: a tool for defining homologous
synteny blocks using radiation hybrid maps and whole-genome sequence. BMC Res
Notes 2: 148.
Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, et al. (2010). The
genome of the Western clawed frog Xenopus tropicalis. Science 328: 633-636.