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Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp).

ABSTRACT: MicroRNAs have been identified and analyzed in various model species, but an investigation of miRNAs in nonmodel species is required for a more complete understanding of miRNA evolution. In this study, we investigated the miRNAs of the nonmodel species Triops cancriformis (tadpole shrimp), a "living fossil," whose morphological form has not changed in almost 200 million years. Dramatic ontogenetic changes occur during its development. To clarify the evolution of miRNAs, we comparatively analyzed its miRNAs and the components of its RNAi machinery. We used deep sequencing to analyze small RNA libraries from the six different developmental stages of T. cancriformis (egg, first-fourth instars, and adult), and also analyzed its genomic DNA with deep sequencing. We identified 180 miRNAs (87 conserved miRNAs and 93 novel candidate miRNAs), and deduced the components of its RNAi machinery: the DICER1, AGO1-3, PIWI, and AUB proteins. A comparative miRNA analysis of T. cancriformis and Drosophila melanogaster showed inconsistencies in the expression patterns of four conserved miRNAs. This suggests that although the miRNA sequences of the two species are very similar, their roles differ across the species. An miRNA conservation analysis revealed that most of the conserved T. cancriformis miRNAs share sequence similarities with those of arthropods, although T. cancriformis is called a "living fossil." However, we found that let-7 and DICER1 of T. cancriformis are more similar to those of the vertebrates than to those of the arthropods. These results suggest that miRNA systems of T. cancriformis have evolved in a unique fashion.

SUBMITTER: Ikeda KT

PROVIDER: S-EPMC4338350 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp).

Ikeda Kahori T KT Hirose Yuka Y Hiraoka Kiriko K Noro Emiko E Fujishima Kosuke K Tomita Masaru M Kanai Akio A

RNA (New York, N.Y.) 20141218 2

MicroRNAs have been identified and analyzed in various model species, but an investigation of miRNAs in nonmodel species is required for a more complete understanding of miRNA evolution. In this study, we investigated the miRNAs of the nonmodel species Triops cancriformis (tadpole shrimp), a "living fossil," whose morphological form has not changed in almost 200 million years. Dramatic ontogenetic changes occur during its development. To clarify the evolution of miRNAs, we comparatively analyzed ...[more]

PMID: 25525151

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Project description:BackgroundThe Notostraca is a small but ancient crustacean order with a contrasting combination of a conservative morphology and a wide range of reproductive modes. The tadpole shrimp Triops cancriformis, includes bisexual - the putatively ancestral state -, androdioecious and hermaphrodite populations. As hermaphroditism and androdioecy confer a colonisation advantage, we expect the postglacial colonisation of northern Europe to have been effected by lineages with such reproductive modes. Therefore, N European populations should be composed of closely related lineages reflecting a recent range expansion. In contrast, glacial refugia in the south should contain bisexual populations with high haplotype diversity and more population structuring. To test these hypotheses, we analysed the geographic distribution of reproductive modes based on new and published sex ratio data. In addition, we investigated the European phylogeography of T. cancriformis by sequencing over a 1000 bp of mitochondrial DNA (mtDNA) in individuals from a large sample of populations of the three recognised subspecies.ResultsBisexual populations were only found in the Iberian Peninsula, with the rest of European populations showing low male proportions or no males. Androdioecious populations were found in Central and Eastern Europe. Regarding mtDNA diversity, Spanish and Moroccan populations of T. c. mauritanicus were highly divergent, and showed strong population structure. In contrast, Triops c. cancriformis and T. c. simplex formed a single mtDNA lineage with low haplotype diversity. This diversity was structured into two phylogenetic clades (A, B), coexisting in E Germany. Basal haplotypes of both lineages were found in the Iberian Peninsula. Most of the populations in clade A and B are either hermaphroditic or androdioecious, with the only bisexual population in these clades found in the Iberian Peninsula. The genetic divergence between these two clades suggests a split in the Late Pleistocene and their geographic distribution reflects a complex evolutionary history of European Triops populations, with possibly two episodes of range expansions - one of them by clade A - involving androdioecious and hermaphroditic populations.ConclusionAs we predicted, N European populations of T. cancriformis are closely related, with few widely distributed haplotypes and indications of a recent range expansion involving hermaphroditic/androdioecious lineages. A possible second range expansion or long distance colonisation may have created the secondary contact zone between T. c. cancriformis/simplex clades A and B. The large haplotype diversity and strong genetic subdivision in the Iberian Peninsula, which is known to contain only bisexual populations, strongly suggest that this area was a Pleistocene refugium for T. cancriformis, although the occurrence of additional eastern refugia cannot be ruled out. Our data support the status of T. c. mauritanicus as a separate species and the colonisation of N Africa from the Iberian Peninsula. We suggest that hermaphroditism/androdioecy has evolved recently in T. cancriformis and has facilitated the postglacial colonisation of northern Europe.

Dataset Information

Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp).

Publications

Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp).

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