A PCR survey of Hox genes in the myzostomid Myzostoma cirriferum

Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans

The phylum Rotifera consists of minuscule, nonsegmented animals with a unique body plan and an unresolved phylogenetic position. The presence of pharyngeal articulated jaws supports an inclusion in Gnathifera nested in the Spiralia. Comparison of Hox genes, involved in animal body plan patterning, can be used to infer phylogenetic relationships. Here, we report the expression of five Hox genes during embryogenesis of the rotifer Brachionus manjavacas and show how these genes define different functional components of the nervous system and not the usual bilaterian staggered expression along the anteroposterior axis. Sequence analysis revealed that the lox5-parapeptide, a key signature in lophotrochozoan and platyhelminthean Hox6/lox5 genes, is absent and replaced by different signatures in Rotifera and Chaetognatha, and that the MedPost gene, until now unique to Chaetognatha, is also present in rotifers. Collectively, our results support an inclusion of chaetognaths in gnathiferans and Gnathifera as sister group to the remaining spiralians.

Rotifers are microscopic animals with an unusual, nonsegmented body plan consisting of a head, trunk and foot. Here, Fröbius and Funch investigate the role of Hox genes—which are widely used in animal body plan patterning—in rotifer embryogenesis and find non-canonical expression in the nervous system.

An Overview of Hox Genes in Lophotrochozoa: Evolution and Functionality

Hox genes are regulators of animal embryonic development. Changes in the number and sequence of Hox genes as well as in their expression patterns have been related to the evolution of the body plan. Lophotrochozoa is a clade of Protostomia characterized by several phyla which show a wide morphological diversity. Despite that the works summarized in this review emphasize the fragmentary nature of the data available regarding the presence and expression of Hox genes, they also offer interesting insight into the evolution of the Hox cluster and the role played by Hox genes in several phyla. However, the number of genes involved in the cluster of the lophotrochozoan ancestor is still a question of debate. The data presented here suggest that at least nine genes were present while two other genes, Lox4 and Post-2, may either have been present in the ancestor or may have arisen as a result of duplication in the Brachiopoda-Mollusca-Annelida lineage. Spatial and temporal collinearity is a feature of Hox gene expression which was probably present in the ancestor of deuterostomes and protostomes. However, in Lophotrochozoa, it has been detected in only a few species belonging to Annelida and Mollusca.

Phylogeny of Myzostomida (Annelida) and their relationships with echinoderm hosts

BACKGROUND

Myzostomids are marine annelids, nearly all of which live symbiotically on or inside echinoderms, chiefly crinoids, and to a lesser extent asteroids and ophiuroids. These symbionts possess a variety of adult body plans and lifestyles. Most described species live freely on the exterior of their hosts as adults (though starting life on the host inside cysts), while other taxa permanently reside in galls, cysts, or within the host's mouth, digestive system, coelom, or gonads. Myzostomid lifestyles range from stealing incoming food from the host's food grooves to consuming the host's tissue directly. Previous molecular studies of myzostomids have had limited sampling with respect to assessing the evolutionary relationships within the group; therefore molecular data from 75 myzostomid taxa were analyzed using maximum likelihood and maximum parsimony methods. To compare relationships of myzostomids with their hosts, a phylogeny was inferred for 53 hosts and a tanglegram constructed with 88 associations.

RESULTS

Gall- and some cyst-dwellers were recovered as a clade, while cyst-to-free-living forms were found as a grade including two clades of internal host-eaters (one infecting crinoids and the other asteroids and ophiuroids), mouth/digestive system inhabitants, and other cyst-dwellers. Clades of myzostomids were recovered that associated with asteroids, ophiuroids, and stalked or feather star crinoids. Co-phylogenetic analyses rejected a null-hypothesis of random associations at the global level, but not for individual associations. Event-based analyses relied most upon host-switching and duplication events to reconcile the association history.

CONCLUSION

Hypotheses were revised concerning the systematics and evolution of Myzostomida, as well their relationships to their hosts. We found two or three transitions between food-stealing and host-eating. Taxa that dwell within the mouth or digestive system and some cyst forms are arguably derived from cyst-to-free-living ancestors--possibly the result of a free-living form moving to the mouth and paedomorphic retention of the juvenile cyst. Phylogenetic conservatism in host use was observed among related myzostomid taxa. This finding suggests that myzostomids (which have a free-living planktonic stage) are limited to one or a few closely related hosts, despite most hosts co-occurring on the same reefs, many within physical contact of each other.

Mitochondrial genomes to the rescue--Diurodrilidae in the myzostomid trap

Diurodrilidae is a taxon of Lophotrochozoa comprising about six, exclusively interstitial species, which are up to 500μm long and dorsoventrally flattened. Traditionally, Diurodrilidae had been regarded as an annelid family. However, recently Diurodrilidae had been excluded from Annelida and been placed in closer relationship to platyzoan taxa based on both morphological and nuclear rRNA data. Since both, Diurodrilidae and platyzoan taxa, exhibit long branches in the molecular analyses, the close relationship might be due to a long branch attraction artifact. The annelid taxon Myzostomida had been trapped in a similar long branch attraction artifact with platyzoan taxa using nuclear rRNA data, but determination of the nearly complete mitochondrial genome of myzostomids revealed their annelid affinity. Therefore, we determined the nearly complete mitochondrial genome of Diurodrilus subterraneus as well as new nuclear rRNA data for D. subterraneus and some platyzoan taxa. All our analyses of nuclear rRNA and mitochondrial sequence and gene order data presented herein clearly place Diurodrilidae within Annelida and with strong nodal support values in some analyses. Therefore, the previously suggested exclusion of Diurodrilidae from Annelida and its close relationship with platyzoan taxa can be attributed to a long branch artifact. Morphological data do not unambiguously support a platyzoan affinity of Diurodrilidae, but instead would also be in line with a progenetic origin of Diurodrilidae within Annelida.

Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida

Myzostomida comprise a group of marine worms associated mainly with echinoderms since the Carboniferous. Due to their unusual morphology the phylogenetic position in relation to other Lophotrochozoa is discussed since their description. According to different morphological and molecular markers the Myzostomida are either close to Platyzoa or Annelida. Here we investigated small non-coding RNAs of Myzostoma cirriferum to infer the phylogenetic position of myzostomids. Based on transcriptomic data collected by Illumina Deep Sequencing we analyzed the microRNA (miRNA) families occurring in M. cirriferum. Phylogenetic analysis revealed the presence of 13 miRNA-families exclusively shared by Annelida (including Sipuncula) and Myzostomida, as such highly significantly supporting an annelid origin of myzostomids. Furthermore, using a mapping-approach and secondary structure models we predicted several miRNA-candidates unique for myzostomids.

Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data

BACKGROUND

In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms.

METHODOLOGY

Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony.

CONCLUSIONS

Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

BACKGROUND

Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa.

RESULTS

Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data.

CONCLUSION

We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.