Journal of Molecular Evolution

, Volume 71, Issue 5, pp 427–436

Evolution of Conserved Non-Coding Sequences Within the Vertebrate Hox Clusters Through the Two-Round Whole Genome Duplications Revealed by Phylogenetic Footprinting Analysis

  • Masatoshi Matsunami
  • Kenta Sumiyama
  • Naruya Saitou

DOI: 10.1007/s00239-010-9396-1

Cite this article as:
Matsunami, M., Sumiyama, K. & Saitou, N. J Mol Evol (2010) 71: 427. doi:10.1007/s00239-010-9396-1


As a result of two-round whole genome duplications, four or more paralogous Hox clusters exist in vertebrate genomes. The paralogous genes in the Hox clusters show similar expression patterns, implying shared regulatory mechanisms for expression of these genes. Previous studies partly revealed the expression mechanisms of Hox genes. However, cis-regulatory elements that control these paralogous gene expression are still poorly understood. Toward solving this problem, the authors searched conserved non-coding sequences (CNSs), which are candidates of cis-regulatory elements. When comparing orthologous Hox clusters of 19 vertebrate species, 208 intergenic conserved regions were found. The authors then searched for CNSs that were conserved not only between orthologous clusters but also among the four paralogous Hox clusters. The authors found three regions that are conserved among all the four clusters and eight regions that are conserved between intergenic regions of two paralogous Hox clusters. In total, 28 CNSs were identified in the paralogous Hox clusters, and nine of them were newly found in this study. One of these novel regions bears a RARE motif. These CNSs are candidates for gene expression regulatory regions among paralogous Hox clusters. The authors also compared vertebrate CNSs with amphioxus CNSs within the Hox cluster, and found that two CNSs in the HoxA and HoxB clusters retain homology with amphioxus CNSs through the two-round whole genome duplications.


Hox clusterTwo-round whole genome duplicationsConserved non-coding sequencesPhylogenetic footprintingRetinoic acid response elementAmphioxus

Supplementary material

239_2010_9396_MOESM1_ESM.xls (68 kb)
Supplementary Table 1: Feature of each CNS. Table shows location, conservation, length and feature of each CNS. Especially HoxA cluster, we compared our CNSs with footprinting results of Prohaska et al. (2004) and available transcript data. (XLS 68 kb)
239_2010_9396_MOESM2_ESM.xls (100 kb)
Supplementary Table 2: Conservation level of each CNS. Table shows existence or nonexistence of each CNS among 19 species. The CNSs which conserve among only placental mammalians are highlighted by purple. (XLS 100 kb)
239_2010_9396_MOESM3_ESM.ppt (169 kb)
Supplementary Figure 1: The guide tree The phylogenetic tree shows vertebrate phylogeny drawn upon Murphy et al. (2004). The scale bar is one million years ago (MYA). All species in this figure have four Hox clusters. On the right of the tree, higher taxonomic groupings are shown in colors. The same coloring is used in Figure 4 and Supplementary Figure 2. (PPT 169 kb)
239_2010_9396_MOESM4_ESM.ppt (530 kb)
Supplementary Figure 2: The phylogenetic footprinting analysis of the TP and DP CNSs The results of phylogenetic footprinting analysis of each TP (A) - (C) and each DP (D) – (K) are shown. Graphs are the results of sliding window analysis on each multiple alignment. X-axis represents base positions. Y-axis represents substitution number of each window. In the graph, substitution numbers within placental mammalians, amniotes and vertebrates are colored in blue, red and green, respectively. Orange boxes show paralogous conserved sequences. It is noted that paralogous conserved regions are also highly conserved at the orthologous comparison. (PPT 530 kb)
239_2010_9396_MOESM5_ESM.ppt (678 kb)
Supplementary Figure 3: Multiple alignments of each DP CNS. (A) - (H) are results of multiple alignments of paralogous conserved regions derived from each DP CNS. Construction of each alignment is same as Figure 2. (PPT 678 kb)
239_2010_9396_MOESM6_ESM.ppt (1 mb)
Supplementary Figure 4: Multiple alignments of each amphiCNS. Figures show multiple alignments of CNSs which are (A) conserved among all vertebrates and (B) not conserved among all vertebrates from comparison between vertebrate CNSs and amphiCNSs. Construction of each alignment is same as Figure 2. (PPT 1064 kb)

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Masatoshi Matsunami
    • 1
    • 2
  • Kenta Sumiyama
    • 1
    • 2
  • Naruya Saitou
    • 1
    • 2
  1. 1.Department of Genetics, School of Life ScienceThe Graduate University for Advanced Studies (SOKENDAI)MishimaJapan
  2. 2.Division of Population GeneticsNational Institute of GeneticsMishimaJapan