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An insight into the phylogenetic history of HOX linked gene families in vertebrates.

Abbasi AA, Grzeschik KH - BMC Evol. Biol. (2007)

Bottom Line: A topology comparison approach revealed four discrete co-duplicated groups: group 1 involves the genes from GLI, HH, INHB, IGFBP (cluster-1), and SLC4A families; group 2 involves ERBB, ZNFN1A, and IGFBP (cluster-2) gene families; group 3 involves the HOX clusters and the SP gene family; group 4 involves the integrin beta chain and myosine light chain families.We conclude that co-duplicated groups may themselves be remnants of ancient small-scale duplications (involving chromosomal segments or gene-clusters) which occurred at different time points during chordate evolution.Whereas the recent combination of genes from distinct co-duplicated groups on different chromosomal regions (human chromosomes 2q, 7, 12q, and 17q) is probably the outcome of subsequent rearrangement of genomic segments, including syntenic groups of genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Human Genetics, Philipps-University, Bahnhofstrasse 7 D35037 Marburg, Germany. abbasiam@staff.uni-marburg.de

ABSTRACT

Background: The human chromosomes 2q, 7, 12q and 17q show extensive intra-genomic homology, containing duplicate, triplicate and quadruplicate paralogous regions centered on the HOX gene clusters. The fact that two or more representatives of different gene families are linked with HOX clusters is taken as evidence that these paralogous gene sets might have arisen from a single chromosomal segment through block or whole chromosome duplication events. This would imply that the constituent genes including the HOX clusters reflect the architecture of a single ancestral block (before vertebrate origin) where all of these genes were linked in a single copy.

Results: In the present study we have employed the currently available set of protein data for a wide variety of vertebrate and invertebrate genomes to analyze the phylogenetic history of 11 multigene families with three or more of their representatives linked to human HOX clusters. A topology comparison approach revealed four discrete co-duplicated groups: group 1 involves the genes from GLI, HH, INHB, IGFBP (cluster-1), and SLC4A families; group 2 involves ERBB, ZNFN1A, and IGFBP (cluster-2) gene families; group 3 involves the HOX clusters and the SP gene family; group 4 involves the integrin beta chain and myosine light chain families. The distinct genes within each co-duplicated group share the same evolutionary history and are duplicated in concert with each other, while the constituent genes of two different co-duplicated groups may not share their evolutionary history and may not have duplicated simultaneously.

Conclusion: We conclude that co-duplicated groups may themselves be remnants of ancient small-scale duplications (involving chromosomal segments or gene-clusters) which occurred at different time points during chordate evolution. Whereas the recent combination of genes from distinct co-duplicated groups on different chromosomal regions (human chromosomes 2q, 7, 12q, and 17q) is probably the outcome of subsequent rearrangement of genomic segments, including syntenic groups of genes.

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Consistencies in phylogenies of families having members on at least three of the HOX-bearing chromosomes (A) schematic topology of GLI, INHB, IGFBP, HH and SLC4A families (B) schematic topology of ERBB, ZNFN1A and IGFBP family members (C) schematic topology of HOX clusters and SP gene family (D) schematic topology of integrin beta chain and myosin light chain gene families. In each case the percentage bootstrap support of the internal branches is given in parentheses. The connecting bars on the left depict the close physical linkage of relevant genes.
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Figure 9: Consistencies in phylogenies of families having members on at least three of the HOX-bearing chromosomes (A) schematic topology of GLI, INHB, IGFBP, HH and SLC4A families (B) schematic topology of ERBB, ZNFN1A and IGFBP family members (C) schematic topology of HOX clusters and SP gene family (D) schematic topology of integrin beta chain and myosin light chain gene families. In each case the percentage bootstrap support of the internal branches is given in parentheses. The connecting bars on the left depict the close physical linkage of relevant genes.

Mentions: To test whether the four-fold paralogy seen on human HOX-bearing chromosomes (Figure 1) is an outcome of doubling events of a single ancestral block, we employed the topology comparison approach to check the consistencies among the phylogenies of 12 gene families including the HOX clusters. We recovered four independent co-duplicated groups involving the members from total 11 gene families. The largest co-duplicated group suggests the simultaneous duplication of members of five gene families (Figure 9A) where the order and close physical linkage of constituent genes is largely disrupted, except GLI and INHB genes which are tightly bound to each other on each of the relevant chromosomes (Figure 1). The second co-duplicated group involves the members from ERBB, ZNFN1A, and IGFBP families and indicates a conservation of linkage and gene order following co-duplication events (Figure 9B). The HOX clusters and members of the SP gene family represent the third co-duplicated group (Figure 9C); again the constituent genes remained closely linked on each of the relevant chromosomal segments. The fourth co-duplicated group involves the members from two gene families (Figure 9D) where the linkage between the co-duplicated genes is largely disrupted, except on Hsa17 where MYL4 is closely linked to ITGB3 gene (Figure 1).


An insight into the phylogenetic history of HOX linked gene families in vertebrates.

Abbasi AA, Grzeschik KH - BMC Evol. Biol. (2007)

Consistencies in phylogenies of families having members on at least three of the HOX-bearing chromosomes (A) schematic topology of GLI, INHB, IGFBP, HH and SLC4A families (B) schematic topology of ERBB, ZNFN1A and IGFBP family members (C) schematic topology of HOX clusters and SP gene family (D) schematic topology of integrin beta chain and myosin light chain gene families. In each case the percentage bootstrap support of the internal branches is given in parentheses. The connecting bars on the left depict the close physical linkage of relevant genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2235844&req=5

Figure 9: Consistencies in phylogenies of families having members on at least three of the HOX-bearing chromosomes (A) schematic topology of GLI, INHB, IGFBP, HH and SLC4A families (B) schematic topology of ERBB, ZNFN1A and IGFBP family members (C) schematic topology of HOX clusters and SP gene family (D) schematic topology of integrin beta chain and myosin light chain gene families. In each case the percentage bootstrap support of the internal branches is given in parentheses. The connecting bars on the left depict the close physical linkage of relevant genes.
Mentions: To test whether the four-fold paralogy seen on human HOX-bearing chromosomes (Figure 1) is an outcome of doubling events of a single ancestral block, we employed the topology comparison approach to check the consistencies among the phylogenies of 12 gene families including the HOX clusters. We recovered four independent co-duplicated groups involving the members from total 11 gene families. The largest co-duplicated group suggests the simultaneous duplication of members of five gene families (Figure 9A) where the order and close physical linkage of constituent genes is largely disrupted, except GLI and INHB genes which are tightly bound to each other on each of the relevant chromosomes (Figure 1). The second co-duplicated group involves the members from ERBB, ZNFN1A, and IGFBP families and indicates a conservation of linkage and gene order following co-duplication events (Figure 9B). The HOX clusters and members of the SP gene family represent the third co-duplicated group (Figure 9C); again the constituent genes remained closely linked on each of the relevant chromosomal segments. The fourth co-duplicated group involves the members from two gene families (Figure 9D) where the linkage between the co-duplicated genes is largely disrupted, except on Hsa17 where MYL4 is closely linked to ITGB3 gene (Figure 1).

Bottom Line: A topology comparison approach revealed four discrete co-duplicated groups: group 1 involves the genes from GLI, HH, INHB, IGFBP (cluster-1), and SLC4A families; group 2 involves ERBB, ZNFN1A, and IGFBP (cluster-2) gene families; group 3 involves the HOX clusters and the SP gene family; group 4 involves the integrin beta chain and myosine light chain families.We conclude that co-duplicated groups may themselves be remnants of ancient small-scale duplications (involving chromosomal segments or gene-clusters) which occurred at different time points during chordate evolution.Whereas the recent combination of genes from distinct co-duplicated groups on different chromosomal regions (human chromosomes 2q, 7, 12q, and 17q) is probably the outcome of subsequent rearrangement of genomic segments, including syntenic groups of genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Human Genetics, Philipps-University, Bahnhofstrasse 7 D35037 Marburg, Germany. abbasiam@staff.uni-marburg.de

ABSTRACT

Background: The human chromosomes 2q, 7, 12q and 17q show extensive intra-genomic homology, containing duplicate, triplicate and quadruplicate paralogous regions centered on the HOX gene clusters. The fact that two or more representatives of different gene families are linked with HOX clusters is taken as evidence that these paralogous gene sets might have arisen from a single chromosomal segment through block or whole chromosome duplication events. This would imply that the constituent genes including the HOX clusters reflect the architecture of a single ancestral block (before vertebrate origin) where all of these genes were linked in a single copy.

Results: In the present study we have employed the currently available set of protein data for a wide variety of vertebrate and invertebrate genomes to analyze the phylogenetic history of 11 multigene families with three or more of their representatives linked to human HOX clusters. A topology comparison approach revealed four discrete co-duplicated groups: group 1 involves the genes from GLI, HH, INHB, IGFBP (cluster-1), and SLC4A families; group 2 involves ERBB, ZNFN1A, and IGFBP (cluster-2) gene families; group 3 involves the HOX clusters and the SP gene family; group 4 involves the integrin beta chain and myosine light chain families. The distinct genes within each co-duplicated group share the same evolutionary history and are duplicated in concert with each other, while the constituent genes of two different co-duplicated groups may not share their evolutionary history and may not have duplicated simultaneously.

Conclusion: We conclude that co-duplicated groups may themselves be remnants of ancient small-scale duplications (involving chromosomal segments or gene-clusters) which occurred at different time points during chordate evolution. Whereas the recent combination of genes from distinct co-duplicated groups on different chromosomal regions (human chromosomes 2q, 7, 12q, and 17q) is probably the outcome of subsequent rearrangement of genomic segments, including syntenic groups of genes.

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