Open Access Highly Accessed Research article

Evolution of coding and non-coding genes in HOX clusters of a marsupial

Hongshi Yu12, James Lindsay3, Zhi-Ping Feng45, Stephen Frankenberg12, Yanqiu Hu12, Dawn Carone3, Geoff Shaw12, Andrew J Pask123, Rachel O’Neill3, Anthony T Papenfuss46 and Marilyn B Renfree12*

Author Affiliations

1 ARC Centre of Excellence in Kangaroo Genomics, The University of Melbourne, Melbourne, Victoria, 3010, Australia

2 Department of Zoology, The University of Melbourne, Melbourne, Victoria, 3010, Australia

3 Department of Molecular and Cell Biology, College of Liberal Arts and Sciences, University of Connecticut, Connecticut, CT, 06269, USA

4 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia

5 Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, 3010, Australia

6 Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, 3010, Australia

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BMC Genomics 2012, 13:251  doi:10.1186/1471-2164-13-251

Published: 18 June 2012

Additional files

Additional file 1:

The length of exon and intron of tammar 39HOXgenes (bp).

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Additional file 2:

The sequences of 39 tammarHOX genes.

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Additional file 3:

Repetitive elements in tammarHOXclusters.

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Additional file 4:

Phylogenetic footprinting analyses ofHOXA cluster with mVISTA. mVISTA plot generated with HOXA genomic sequences from tammar, human (chr7:27131531–27244164), mouse (chr6:52104079–52216539) and frog (scaffold_56:1381000–1485000) with tammar as a reference. Conserved regions above the level of 70%/100 bp are highlighted under the curve, with red indicating conserved non-coding regions, blue representing conserved coding-protein exons, and turquoise representing microRNAs or long non-coding protein exons. HOTAIRM1 and HOXA11AS representing the long non-coding RNAs are conserved in all mammals and have much lower similarity in frog. microRNA miR-196b is highly conserved in all species. Arrow stands for the transcription orientation.

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Additional file 5:

Phylogenetic footprinting analyses ofHOXB cluster with mVISTA. mVISTA plot generated with HOXB genomic sequences from tammar, human (chr17: 43960868–44165742), mouse (chr11: 96024912–96229585) and frog (scaffold_334: 483000–620000) with tammar as a reference. microRNAs miR-10a located between HOXB4 and HOXB5 is highly conserved in all species. miR-196a1 is also conserved in all mammals. Other details as in figure Additional file 4.

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Additional file 6:

Phylogenetic footprinting analyses ofHOXC cluster with mVISTA. mVISTA plot generated with HOXC genomic sequences from tammar, human (chr12: 52605461–52742874), mouse (chr15: chr15:102750000–102892969) and frog (scaffold_226: 269568–557892) with tammar as a reference. The information of long ncRNAs and microRNAs is same as in Figure  3. Other details as in figure Additional file 4.

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Additional file 7:

Phylogenetic footprinting analyses ofHOXD cluster with mVISTA. mVISTA plot generated with HOXD genomic sequences from tammar, human (chr2: 176656359–176768195), mouse (chr2: 74497085–74613489) and frog (scaffold_163: 534804–660354) with tammar as a reference. Other details as in figure Additional file 4.

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Additional file 8:

The sequences of lncRNAs and microRNAs in tammar.

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Additional file 9:

Valid target positions of known miRNAs in tammar HOXclusters.

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Additional file 10:

Newly discovered target positions of putative miRNAs in tammarHOXclusters.

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Additional file 11:

Phylogenetic relationships and high-order grouping ofHOX families from tammar and human. A representative an unrooted tree with rooting that should be considered arbitrary. Phylogenetic analysis was based on the homeodomain regions with an extension of extra 20 amino acids on both sides from human and tammar. The phylogenetic tree was constructed using neighbor-joining method with 100 bootstrap replicates showing bootstrap support values on the nodes. 13 monophyletic groups were shown to form HOX1 to HOX13. Three big branches according to their functions during the developmental events are shown: anterior, central and posterior.

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Additional file 12:

Primers for RT-PCR.

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