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Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate.

Hadrys H, Simon S, Kaune B, Schmitt O, Schöner A, Jakob W, Schierwater B - PLoS ONE (2012)

Bottom Line: Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera).We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics.Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.

View Article: PubMed Central - PubMed

Affiliation: ITZ, Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany. heike.hadrys@ecolevol.de

ABSTRACT
Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.

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Neighbor-Joining tree of the 25 new Hox gene sequences (lab, pb, Dfd, Ubx, abd-A, Abd-B) and known orthologs from other insects (GenBank accession numbers: Folsomia candida AF361326, AF361327, AF361329, AF361333, AF361334, AF361335; Drosophila melanogaster; NM_057265, X63728, X05136, X76210, X54453, X16134; Tribolium castaneum AF231104, AF187068, U81039, AF146649, AF017415, AF227923).Sequences from this study are in bold. Note that all new sequences group to expected homologs.
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pone-0034682-g002: Neighbor-Joining tree of the 25 new Hox gene sequences (lab, pb, Dfd, Ubx, abd-A, Abd-B) and known orthologs from other insects (GenBank accession numbers: Folsomia candida AF361326, AF361327, AF361329, AF361333, AF361334, AF361335; Drosophila melanogaster; NM_057265, X63728, X05136, X76210, X54453, X16134; Tribolium castaneum AF231104, AF187068, U81039, AF146649, AF017415, AF227923).Sequences from this study are in bold. Note that all new sequences group to expected homologs.

Mentions: Homolog identification of the isolated Hox genes is widely, but not completely non-problematic. All assignments shown in Table 2 are the immediate assignments according to BLAST searches. As it has been shown that caution should be taken when using the best BLAST hit to infer gene homology [31]–[33], we performed phylogenetic analyses to further test the assignments of the newly isolated Hox genes. In these analyses (Neighbor-Joining, NJ) with published homeobox sequences the new homeobox sequences for lab, pb, Dfd, Ubx, abd-A, Abd-B group into the expected clades. The genes Scr, ftz, and Antp are generally problematic. Even their full length homeodomain sequences do not allow an unambiguous assignment in a standard distance analysis (Fig. S1). A Neighbour Joining analysis of only the six potentially unambiguous new homeobox sequences (lab, pb, Dfd, Ubx, Abd-B) groups all new fragments into the expected clades of homologs from other insects and thus confirms the results of NCBI Blast (Fig. 2), except for abd-A which appears paraphyletic. Based on the partial homeobox sequences we cannot unambiguously distinguish between Scr and Antp homeobox fragments in Diplura, Archaeognatha, Ephemeroptera, Odonata, Plecoptera and Dermaptera. The isolated homeobox fragments differ between orders, but no amino acid substitutions are found in the short fragment spanning homeodomain positions 20 to 45 (Fig. 3). For these gene fragments more sequence information is required to distinguish between the two alternatives, since amino acid substitutions have been known to occur at positions 1, 4, 6, 7 and 60 only (Fig. 3). We believe that we have amplified both genes (different homeobox sequences) but we are reluctant to suggest an assignment to the Scr or Antp gene family in the absence of unambiguous differences in the homeodomain. For odonates we have verified the correct assignment of the new gene fragments to their Scr, Antp, and Ubx gene families also by RACE-PCR, amplifying full length homeobox sequences for developmental studies (data will be reported elsewhere).


Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate.

Hadrys H, Simon S, Kaune B, Schmitt O, Schöner A, Jakob W, Schierwater B - PLoS ONE (2012)

Neighbor-Joining tree of the 25 new Hox gene sequences (lab, pb, Dfd, Ubx, abd-A, Abd-B) and known orthologs from other insects (GenBank accession numbers: Folsomia candida AF361326, AF361327, AF361329, AF361333, AF361334, AF361335; Drosophila melanogaster; NM_057265, X63728, X05136, X76210, X54453, X16134; Tribolium castaneum AF231104, AF187068, U81039, AF146649, AF017415, AF227923).Sequences from this study are in bold. Note that all new sequences group to expected homologs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369913&req=5

pone-0034682-g002: Neighbor-Joining tree of the 25 new Hox gene sequences (lab, pb, Dfd, Ubx, abd-A, Abd-B) and known orthologs from other insects (GenBank accession numbers: Folsomia candida AF361326, AF361327, AF361329, AF361333, AF361334, AF361335; Drosophila melanogaster; NM_057265, X63728, X05136, X76210, X54453, X16134; Tribolium castaneum AF231104, AF187068, U81039, AF146649, AF017415, AF227923).Sequences from this study are in bold. Note that all new sequences group to expected homologs.
Mentions: Homolog identification of the isolated Hox genes is widely, but not completely non-problematic. All assignments shown in Table 2 are the immediate assignments according to BLAST searches. As it has been shown that caution should be taken when using the best BLAST hit to infer gene homology [31]–[33], we performed phylogenetic analyses to further test the assignments of the newly isolated Hox genes. In these analyses (Neighbor-Joining, NJ) with published homeobox sequences the new homeobox sequences for lab, pb, Dfd, Ubx, abd-A, Abd-B group into the expected clades. The genes Scr, ftz, and Antp are generally problematic. Even their full length homeodomain sequences do not allow an unambiguous assignment in a standard distance analysis (Fig. S1). A Neighbour Joining analysis of only the six potentially unambiguous new homeobox sequences (lab, pb, Dfd, Ubx, Abd-B) groups all new fragments into the expected clades of homologs from other insects and thus confirms the results of NCBI Blast (Fig. 2), except for abd-A which appears paraphyletic. Based on the partial homeobox sequences we cannot unambiguously distinguish between Scr and Antp homeobox fragments in Diplura, Archaeognatha, Ephemeroptera, Odonata, Plecoptera and Dermaptera. The isolated homeobox fragments differ between orders, but no amino acid substitutions are found in the short fragment spanning homeodomain positions 20 to 45 (Fig. 3). For these gene fragments more sequence information is required to distinguish between the two alternatives, since amino acid substitutions have been known to occur at positions 1, 4, 6, 7 and 60 only (Fig. 3). We believe that we have amplified both genes (different homeobox sequences) but we are reluctant to suggest an assignment to the Scr or Antp gene family in the absence of unambiguous differences in the homeodomain. For odonates we have verified the correct assignment of the new gene fragments to their Scr, Antp, and Ubx gene families also by RACE-PCR, amplifying full length homeobox sequences for developmental studies (data will be reported elsewhere).

Bottom Line: Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera).We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics.Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.

View Article: PubMed Central - PubMed

Affiliation: ITZ, Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany. heike.hadrys@ecolevol.de

ABSTRACT
Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.

Show MeSH