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

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Abstract

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.

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Acknowledgments

The authors thank Drs. Kiyoshi Ezawa, Hiroki Kokubo, Kazuho Ikeo, Toshihiko Shiroishi, and Hiroyuki Sasaki for their many helpful discussions, suggestions, and comments. The authors appreciate English polishing by Ms Rumiko Suzuki, Ms Mahoko Takahashi, and Mr. Tim Jinam. This study was supported partly by The Graduate University for Advanced Studies (Sokendai) to M.M. and by Grant-in-Aid for scientific research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan to N.S.

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Authors and Affiliations

  1. Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan

    Masatoshi Matsunami, Kenta Sumiyama & Naruya Saitou

  2. Division of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan

    Masatoshi Matsunami, Kenta Sumiyama & Naruya Saitou

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  1. Masatoshi Matsunami
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  2. Kenta Sumiyama
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  3. Naruya Saitou
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Correspondence to Naruya Saitou.

Electronic supplementary material

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239_2010_9396_MOESM1_ESM.xls

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

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

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

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

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

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)

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Matsunami, M., Sumiyama, K. & Saitou, N. Evolution of Conserved Non-Coding Sequences Within the Vertebrate Hox Clusters Through the Two-Round Whole Genome Duplications Revealed by Phylogenetic Footprinting Analysis. J Mol Evol 71, 427–436 (2010). https://doi.org/10.1007/s00239-010-9396-1

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