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Male Pregnancy in the Seahorse (Hippocampus Abdominalis): Investigating the Genetic Regulation of a Complex Reproductive Trait

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Male Pregnancy in the Seahorse (Hippocampus Abdominalis): Investigating the Genetic Regulation of a Complex Reproductive Trait Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2010 Male pregnancy in the seahorse (Hippocampus abdominalis): investigating the genetic regulation of a complex reproductive trait Stölting, Kai N Abstract: Seahorses and pipefish are characterized by different forms of male pregnancy, a complex mor- phological and physiological process akin a mammalian pregnancy. The genetic regulation of this complex trait, however, is unknown, complicating our efforts to understand how this trait has evolved. To permit such studies, the processes of male pregnancy have been reviewed, and the genes of male pregnancy have been identified using cDNA-AFLP based differential displays and next generation sequencing technology. Initial efforts to identify gene expression differences during male pregnancy using a novel cDNA-AFLP endlabelling protocol proved unsuccessful, and an extensive eukaryote-wide computer-based optimization study was undertaken to optimize the cDNA-AFLP methodology for species in which genome data are unavailable. Next generation sequencing was ultimately used to identify the genes of male pregnancy. More than 38,000 cDNA fragments have been sequenced and annotated wherever possible. Hundreds of genes up- and downregulated during male pregnancy were identified, and major gene functions have been associated with these genes. As a result, a more circumspect picture of both processes and the genes involved in male pregnancy in the seahorse is available. This thesis is structured into four chapters. Chapters I and III have been published in peer reviewed international journals. Chapters II and IV are being prepared for submission. Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-43648 Dissertation Originally published at: Stölting, Kai N. Male pregnancy in the seahorse (Hippocampus abdominalis): investigating the genetic regulation of a complex reproductive trait. 2010, University of Zurich, Faculty of Science. Male Pregnancy in the Seahorse (Hippocampus abdominalis): Investigating the Genetic Regulation of a Complex Reproductive Trait Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultät der Universität Zürich von Kai Nikolas Stölting aus Deutschland Promotionskomitee Prof. Dr. Anthony B. Wilson (Vorsitz und Leitung der Promotion) Prof. Dr. Andreas Wagner Prof. Dr. Tadeusz Kawecki Zürich, 2010 2 TABLE OF CONTENTS SUMMARY 4 ZUSAMMENFASSUNG 7 GENERAL INTRODUCTION 11 CHAPTER I: Male Pregnancy in Seahorses and Pipefish: Beyond the Mammalian Model 20 CHAPTER II: Cost-Effective Fluorescent Amplified Fragment Length Polymorphism Analyses 52 CHAPTER III: Eukaryotic Transcriptomics in silico: Optimizing cDNA-AFLP Efficiency 68 CHAPTER IV: Comparative Transcriptomics of the Male Pregnant Seahorse Hippocampus abdominalis 111 ACKNOWLEDGEMENTS 158 CURRICULUM VITAE 160 3 SUMMARY SUMMARY Seahorses and pipefish are characterized by different forms of male pregnancy, a complex morphological and physiological process akin a mammalian pregnancy. The genetic regulation of this complex trait, however, is unknown, complicating our efforts to understand how this trait has evolved. To permit such studies, the processes of male pregnancy have been reviewed, and the genes of male pregnancy have been identified using cDNA-AFLP based differential displays and next generation sequencing technology. Initial efforts to identify gene expression differences during male pregnancy using a novel cDNA-AFLP endlabelling protocol proved unsuccessful, and an extensive eukaryote-wide computer-based optimization study was undertaken to optimize the cDNA-AFLP methodology for species in which genome data are unavailable. Next generation sequencing was ultimately used to identify the genes of male pregnancy. More than 38,000 cDNA fragments have been sequenced and annotated wherever possible. Hundreds of genes up- and downregulated during male pregnancy were identified, and major gene functions have been associated with these genes. As a result, a more circumspect picture of both processes and the genes involved in male pregnancy in the seahorse is available. This thesis is structured into four chapters. Chapters I and III have been published in peer reviewed international journals. Chapters II and IV are being prepared for submission. Chapter I We reviewed the processes of mammalian pregnancy and the male pregnancy of seahorses and pipefish (syngnathid fishes) as a basis for further studies on the evolution of male pregnancy. During male pregnancy, syngnathid males incubate developing embryos in a specialized brooding structure, the brood pouch, in which they are aerated, osmoregulated, protected and likely also provisioned during development. Direct comparisons of the syngnathid male pregnancy with other forms of viviparity strongly suggests parallels in physiology, morphology and genetic changes, and a review of recent advances on syngnathid pregnancy highlights similarities and differences between seahorse and 4 SUMMARY mammalian pregnancy. This comparison is the foundation to further studies on the evolution of a complex trait, the male pregnancy. Chapter II Amplified fragment length polymorphisms (AFLP) are a widely used fingerprinting tool, which can be used in high-throughput AFLP protocols which require the incorporation of fluorescently-labelled oligonucleotides. Large numbers of fragments can thus be rapidly screened on automated DNA sequencing machines. The per-marker costs are comparably low for AFLPs, but the key element for high-throughput approaches, the fluorescently-labelled oligonucleotide, remain costly. In reducing this fraction of the experimental setup by implementing fluorescent endlabelling of AFLPs, this tool will be even more accessible for laboratories with reduced budgets. The endlabelling alternative presented here benefits from statistical analyses which indicate that the standard fluorescent AFLPs and the novel endlabelled alternatives produce comparable results. However, given the differences in the size and numbers of fragments generated with the two methods, we do not recommend to combine partial data generated with both approaches. Given the considerably reduced setup costs and comparable performance, we suggest that researchers commencing a new AFLP project use endlabelled AFLPs instead of traditional fluorescent AFLPs. Chapter III Differentially expressed genes can be detected using the AFLP methodology on complementary DNA through the correlation of trait expression with cDNA expression profiles. However, given the methodological complexity of the AFLP approach and the taxonomic diversity of organisms typically studied with AFLPs, the optimal design of such approaches can vary from species to species. In modeling and optimizing the cDNA-AFLP assay design for all eukaryotic species, we identify factors which can substantially increase the quality of cDNA- AFLP experiments in any eukaryotic species. Factors revealed by in silico simulations on 92 species covering most major eukaryotic group include the choice of individual restriction enzymes substantially affecting screen quality. While some evidence of phylogenetic signal in the cDNA-pool coverage is present, this signal is largely mediated by organismal GC content, a second key factor 5 SUMMARY affecting the quality of a screen. In optimizing cDNA-AFLP on a broad sample, a strict linear relationship between the number of fragments screened per selective AFLP-PCR reaction and the size of the underlying cDNA pool is detected. This allows to estimate the number of genes expressed in a target tissue, an application that should be invaluable as next-generation sequencing technologies are adapted for differential display. Chapter IV Studies on the evolution of reproductive complexity have been complicated by an absence of transitional forms. Syngnathid fishes are an ideal model for such investigations, as extant species exhibit a wide diversity of rudimentary and more complex form of male pregnancy. Unfortunately, little is known about the genetic regulation of male pregnancy in syngnathid fishes, and knowledge on the genes associated with pregnancy is key to undertaking comparative evolutionary studies investigating the origins of this mode of reproduction. We assembled the first reference transcriptome for the seahorse, consisting of 38,419 contigs representing more than 30,000 different cDNAs. Functional annotations of approximately 27% of these contigs allow the first comprehensive view of seahorse gene functions, biological processes and cellular localizations during the pregnancy process. In a comparative transcriptome screen of pregnant and non- pregnant individuals, hundreds of genes were identified and annotated which are differentially expressed during male pregnancy. None of the different annotation classes however, indicate significant differences in the representation of genes from pregnant and non-pregnant brood pouch tissues. Our study also quantified the effects of cDNA normalization on gene discovery, and shows clearly that normalization is essential in studies that aim for a full representation of the transcriptome. The assembly of the seahorse transcriptome will be used in the construction of a microarray for the comparative analysis of gene expression during pregnancy in other syngnathids and represents a critical first key step towards understanding
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