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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

Homeobox linkage in Mnemiopsis. These four pairs of homeoboxes are linked on four pairs of genomic scaffold. The distance between homeoboxes is noted in between each pair. Arrowheads applied to one side or the other represent the orientation of the linkage.
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Figure 5: Homeobox linkage in Mnemiopsis. These four pairs of homeoboxes are linked on four pairs of genomic scaffold. The distance between homeoboxes is noted in between each pair. Arrowheads applied to one side or the other represent the orientation of the linkage.

Mentions: There are four pairs of linked homeoboxes in our current Mnemiopsis genome assembly (Figure 5). The tightest linkage is between two ANTP class homeoboxes (MlANTP19 and MlANTP47), which are 4.7 KB apart. A different ANTP class homeobox (MlANTP68) is situated 5.0 KB downstream from the SINE class homeobox MLSIX36. The HOXL-related ANTP class homeobox MlANTP03a is separated by 26.0 KB from the PRD class homeobox MLPRD16. The ANTP class MlANTP21 and the SINE class homeobox MLSIX59 are on the same contig, 148.9 KB apart. None of the linked homeoboxes are obvious paralogs, suggesting that these pairs are not the result of recent duplication events.


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)

Homeobox linkage in Mnemiopsis. These four pairs of homeoboxes are linked on four pairs of genomic scaffold. The distance between homeoboxes is noted in between each pair. Arrowheads applied to one side or the other represent the orientation of the linkage.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Homeobox linkage in Mnemiopsis. These four pairs of homeoboxes are linked on four pairs of genomic scaffold. The distance between homeoboxes is noted in between each pair. Arrowheads applied to one side or the other represent the orientation of the linkage.
Mentions: There are four pairs of linked homeoboxes in our current Mnemiopsis genome assembly (Figure 5). The tightest linkage is between two ANTP class homeoboxes (MlANTP19 and MlANTP47), which are 4.7 KB apart. A different ANTP class homeobox (MlANTP68) is situated 5.0 KB downstream from the SINE class homeobox MLSIX36. The HOXL-related ANTP class homeobox MlANTP03a is separated by 26.0 KB from the PRD class homeobox MLPRD16. The ANTP class MlANTP21 and the SINE class homeobox MLSIX59 are on the same contig, 148.9 KB apart. None of the linked homeoboxes are obvious paralogs, suggesting that these pairs are not the result of recent duplication events.

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