Substantial Loss of Conserved and Gain of Novel MicroRNA Families in Flatworms

Abstract

Recent studies on microRNA (miRNA) evolution focused mainly on the comparison of miRNA complements between animal clades. However, evolution of miRNAs within such groups is poorly explored despite the availability of comparable data that in some cases lack only a few key taxa. For flatworms (Platyhelminthes), miRNA complements are available for some free-living flatworms and all major parasitic lineages, except for the Monogenea. We present the miRNA complement of the monogenean flatworm Gyrodactylus salaris that facilitates a comprehensive analysis of miRNA evolution in Platyhelminthes. Using the newly designed bioinformatics pipeline miRCandRef, the miRNA complement was disentangled from next-generation sequencing of small RNAs and genomic DNA without a priori genome assembly. It consists of 39 miRNA hairpin loci of conserved miRNA families, and 22 novel miRNAs. A comparison with the miRNA complements of Schmidtea mediterranea (Turbellaria), Schistosoma japonicum (Trematoda), and Echinococcus granulosus (Cestoda) reveals a substantial loss of conserved bilaterian, protostomian, and lophotrochozoan miRNAs. Eight of the 46 expected conserved miRNAs were lost in all flatworms, 16 in Neodermata and 24 conserved miRNAs could not be detected in the cestode and the trematode. Such a gradual loss of miRNAs has not been reported before for other animal phyla. Currently, little is known about miRNAs in Platyhelminthes, and for the majority of the lost miRNAs there is no prediction of function. As suggested earlier they might be related to morphological simplifications. The presence and absence of 153 conserved miRNAs was compared for platyhelminths and 32 other metazoan taxa. Phylogenetic analyses support the monophyly of Platyhelminthes (Turbellaria + Neodermata [Monogenea {Trematoda + Cestoda}]).

A critical appraisal of the use of microRNA data in phylogenetics

“…In all but the amniote study (19) (addressed below), secondary miRNA losses constitute between 27% and 54%, with an overall average of 38%, of the implied evolutionary changes. These phylogenetic results accord well with those of molecular evolutionary studies, in which prevalent secondary loss of miRNA families has been inferred for various taxa (14,(32)(33)(34)(35).…”

Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme

“…On the other hand, there has also been some debate on the utility of miRNA-based phylogenetics, which claimed that miRNAs are often lost from metazoan genomes and many early miRNA-based phylogenetic studies had numerous 'false negatives' because of the incorporation of taxa into their data matrix with a genome but no RNA sequencing data, or RNA sequencing date but no genome (Thomson et al, 2014). However, while miRNA loss certainly does exist (Fu et al, 2008;Fromm et al, 2013), it is not nearly as high as Thomson et al claimed. Furthermore, even if the data matrices used by early studies are recognized to contain 'false negatives', they simply cannot be used to track true patterns of miRNA gain/loss.…”

“…miRNA sequences, which have been successfully applied to many metazoan phylogenetic studies Heimberg et al, 2010;Sperling et al, 2010;Campbell et al, 2011;Philippe et al, 2011;Rota-Stabelli et al, 2011;Sperling et al, 2011;Wiegmann et al, 2011;Helm et al, 2012;Lyson et al, 2012;Pisani et al, 2012;Fromm et al, 2013;Peterson et al, 2013;Tarver et al, 2013), have five properties making them among the most reliable phylogenetic markers: (i) identification of novel miRNAs does not necessarily require fully sequenced genome sequence, (ii) new lineage-specific miRNA families are continually added to metazoan genomes through time which makes them ideal as phylogenetic markers, (iii) low levels of secondary miRNA loss, (iv) rarity of substitutions to the mature miRNA sequence, and (v) almost impossible scenario of convergent evolution of miRNAs Tarver et al, 2013). Therefore, miRNAs should provide an alternative and valuable evidence for the evolutionary position of Polypteriformes.…”

Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell

“…In some cases they have diverged beyond the point where homology is readily recognized (Schyth et al, 2015). Several clades, in particular Urochordata (Fu et al, 2008) and Platyhelminthes (Fromm et al, 2013), have undergone a massive restructuring of their microRNA repertoire. Recent quantitative studies (Thomson et al, 2014;Hertel and Stadler, 2015) show that loss of microRNAs, including loss of entire families, is not a rare process in metazoan evolution.…”