Limits...
The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa.

Ryan JF, Pang K, NISC Comparative Sequencing ProgramMullikin JC, Martindale MQ, Baxevanis AD - Evodevo (2010)

Bottom Line: However, these comparisons require complete genomes that, until now, did not exist for the ctenophore lineage.We have characterized the full complement of Mnemiopsis homeodomains from this species and have compared them to species from other early branching lineages.Our results suggest that Porifera and Ctenophora were the first two extant lineages to diverge from the rest of animals.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. andy@nhgri.nih.gov.

ABSTRACT

Background: The much-debated phylogenetic relationships of the five early branching metazoan lineages (Bilateria, Cnidaria, Ctenophora, Placozoa and Porifera) are of fundamental importance in piecing together events that occurred early in animal evolution. Comparisons of gene content between organismal lineages have been identified as a potentially useful methodology for phylogenetic reconstruction. However, these comparisons require complete genomes that, until now, did not exist for the ctenophore lineage. The homeobox superfamily of genes is particularly suited for these kinds of gene content comparisons, since it is large, diverse, and features a highly conserved domain.

Results: We have used a next-generation sequencing approach to generate a high-quality rough draft of the genome of the ctenophore Mnemiopsis leidyi and subsequently identified a set of 76 homeobox-containing genes from this draft. We phylogenetically categorized this set into established gene families and classes and then compared this set to the homeodomain repertoire of species from the other four early branching metazoan lineages. We have identified several important classes and subclasses of homeodomains that appear to be absent from Mnemiopsis and from the poriferan Amphimedon queenslandica. We have also determined that, based on lineage-specific paralog retention and average branch lengths, it is unlikely that these missing classes and subclasses are due to extensive gene loss or unusually high rates of evolution in Mnemiopsis.

Conclusions: This paper provides a first glimpse of the first sequenced ctenophore genome. We have characterized the full complement of Mnemiopsis homeodomains from this species and have compared them to species from other early branching lineages. Our results suggest that Porifera and Ctenophora were the first two extant lineages to diverge from the rest of animals. Based on this analysis, we also propose a new name - ParaHoxozoa - for the remaining group that includes Placozoa, Cnidaria and Bilateria.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic relationship of early-branching animal lineages. Given the conflicting results of several recent studies and the current existing phylogenomic evidence presented in this study, we have constructed an animal phylogeny that includes two polytomies. It is uncertain whether Porifera or Ctenophora branched at the base. The evidence from this study (and others) unites Placozoa, Cnidaria and Bilateria into the subkingdom ParaHoxozoa. The origins of class and subclass founders are indicated along major branches of the tree.
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Figure 6: Phylogenetic relationship of early-branching animal lineages. Given the conflicting results of several recent studies and the current existing phylogenomic evidence presented in this study, we have constructed an animal phylogeny that includes two polytomies. It is uncertain whether Porifera or Ctenophora branched at the base. The evidence from this study (and others) unites Placozoa, Cnidaria and Bilateria into the subkingdom ParaHoxozoa. The origins of class and subclass founders are indicated along major branches of the tree.

Mentions: There is strong evidence suggesting that Mnemiopsis has homeodomains belonging to six of the 11 defined homeodomain classes (ANTP, PRD, LIM, POU, SINE and TALE). Mnemiopsis appears to be missing the other five homeodomain classes (HNF, CUT, PROS, ZF and CERS). It is also missing ¬the Hox/ParaHox and extended Hox subclasses of the ANTP class, as well as the S50 and K50 subclass of the PRD class. Given that Trichoplax, Nematostella and the bilaterians examined in our study clearly possess all of these classes and subclasses, the most parsimonious animal tree would involve Ctenophora and Porifera branching off the main animal trunk prior to the Placozoa, Cnidaria and Bilateria (Figure 6). This configuration is congruent with most of the previously published 18 S phylogenies and results from several of the EST-based phylogenomic studies [12,15].


The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa.

Ryan JF, Pang K, NISC Comparative Sequencing ProgramMullikin JC, Martindale MQ, Baxevanis AD - Evodevo (2010)

Phylogenetic relationship of early-branching animal lineages. Given the conflicting results of several recent studies and the current existing phylogenomic evidence presented in this study, we have constructed an animal phylogeny that includes two polytomies. It is uncertain whether Porifera or Ctenophora branched at the base. The evidence from this study (and others) unites Placozoa, Cnidaria and Bilateria into the subkingdom ParaHoxozoa. The origins of class and subclass founders are indicated along major branches of the tree.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2959044&req=5

Figure 6: Phylogenetic relationship of early-branching animal lineages. Given the conflicting results of several recent studies and the current existing phylogenomic evidence presented in this study, we have constructed an animal phylogeny that includes two polytomies. It is uncertain whether Porifera or Ctenophora branched at the base. The evidence from this study (and others) unites Placozoa, Cnidaria and Bilateria into the subkingdom ParaHoxozoa. The origins of class and subclass founders are indicated along major branches of the tree.
Mentions: There is strong evidence suggesting that Mnemiopsis has homeodomains belonging to six of the 11 defined homeodomain classes (ANTP, PRD, LIM, POU, SINE and TALE). Mnemiopsis appears to be missing the other five homeodomain classes (HNF, CUT, PROS, ZF and CERS). It is also missing ¬the Hox/ParaHox and extended Hox subclasses of the ANTP class, as well as the S50 and K50 subclass of the PRD class. Given that Trichoplax, Nematostella and the bilaterians examined in our study clearly possess all of these classes and subclasses, the most parsimonious animal tree would involve Ctenophora and Porifera branching off the main animal trunk prior to the Placozoa, Cnidaria and Bilateria (Figure 6). This configuration is congruent with most of the previously published 18 S phylogenies and results from several of the EST-based phylogenomic studies [12,15].

Bottom Line: However, these comparisons require complete genomes that, until now, did not exist for the ctenophore lineage.We have characterized the full complement of Mnemiopsis homeodomains from this species and have compared them to species from other early branching lineages.Our results suggest that Porifera and Ctenophora were the first two extant lineages to diverge from the rest of animals.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. andy@nhgri.nih.gov.

ABSTRACT

Background: The much-debated phylogenetic relationships of the five early branching metazoan lineages (Bilateria, Cnidaria, Ctenophora, Placozoa and Porifera) are of fundamental importance in piecing together events that occurred early in animal evolution. Comparisons of gene content between organismal lineages have been identified as a potentially useful methodology for phylogenetic reconstruction. However, these comparisons require complete genomes that, until now, did not exist for the ctenophore lineage. The homeobox superfamily of genes is particularly suited for these kinds of gene content comparisons, since it is large, diverse, and features a highly conserved domain.

Results: We have used a next-generation sequencing approach to generate a high-quality rough draft of the genome of the ctenophore Mnemiopsis leidyi and subsequently identified a set of 76 homeobox-containing genes from this draft. We phylogenetically categorized this set into established gene families and classes and then compared this set to the homeodomain repertoire of species from the other four early branching metazoan lineages. We have identified several important classes and subclasses of homeodomains that appear to be absent from Mnemiopsis and from the poriferan Amphimedon queenslandica. We have also determined that, based on lineage-specific paralog retention and average branch lengths, it is unlikely that these missing classes and subclasses are due to extensive gene loss or unusually high rates of evolution in Mnemiopsis.

Conclusions: This paper provides a first glimpse of the first sequenced ctenophore genome. We have characterized the full complement of Mnemiopsis homeodomains from this species and have compared them to species from other early branching lineages. Our results suggest that Porifera and Ctenophora were the first two extant lineages to diverge from the rest of animals. Based on this analysis, we also propose a new name - ParaHoxozoa - for the remaining group that includes Placozoa, Cnidaria and Bilateria.

No MeSH data available.


Related in: MedlinePlus