Scienze Della Terra, Della Vita E Dell'ambiente
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Alma Mater Studiorum – Università di Bologna DOTTORATO DI RICERCA IN Scienze della Terra, della Vita e dell’Ambiente Ciclo 29 Settore Concorsuale di afferenza: 05/B1 Zoologia e Antropologia Settore Scientifico disciplinare: BIO/05 Zoologia TITOLO TESI Differential gene expression of dorsal pictorial ornaments and pigmentation in sKates (Rajidae, Chondrichthyes) Presentata da: Alice Ferrari Coordinatore Dottorato Relatore Prof. Barbara Mantovani Prof. Fausto Tinti Co-Relatori Prof. Walter Salzburger Alessia Cariani, PhD Esame finale anno 2017 ABSTRACT Approximately twenty years have passed since the beginning of concentrated investigations on the evolution and ecology of skates. The evidence generated thus far suggested that this monophyletic group have experienced multiple, parallel adaptive radiations at a regional scale, which contributed to the delineation of strong phylogeographical signal since the Cretaceous. This background represented the guiding light of the work described in this thesis, where two main themes were developed. The first one focused on the investigation of Raja miraletus L. species complex through the analysis of genetic variation derived from both mtDNA and nuDNA. The results presented herein assessed the presence of a restricted gene flow and different degree of divergence between the South African and Mediterranean samples, ascribing these patterns to oceanographic discontinuities. Despite the high species diversity characterising the Family, most Rajidae show a stable gross morphology and peculiar dorsal pigmentation patterns, which may have been implicated in cryptic speciation. Nonetheless, the adaptive value and the genetic basis of these traits remain poorly investigated. To fill this gap, this thesis also describes the application of RNA-sequencing technology on recently diverged skate species with sibling and sister phylogenetic relationships. Therefore, the second goal of this research consisted in investigating the molecular basis of pigmentation in five non-model species. To this end, the transcriptome profiling of different skin tissues was performed using the Illumina platform, whereas longer sequencing data were obtained from R. miraletus multiple organs using the Ion Torrent technology. After the assembly of a reference transcriptome and the mapping of Illumina reads, the Differential Gene Expression between skin tissues across species was performed, revealing the expression of transcripts mainly related to metabolic process and catalytic activity in which pigmentary genes appeared involved. This work could be considered the basis for future studies aiming to disentangle how pigmentary traits evolved in skates and other chondrichtyans, to evaluate whether the same or alternative traits have been used in parallel adaptations to similar environments and to understand if these traits follow species divergence or hybridisation. TABLE OF CONTENTS Chapter 1. General introduction 3 1.1. Thesis objectives and overview 3 1.2. Species and cryptic diversity 5 1.3. Cryptic lineages in chondrichthyans 10 Chapter 2. The name game: when evolution hides behind unchanging morphology 13 2.1. Introduction 13 2.2. Materials and methods 16 2.2.1. Sampling 16 2.2.2. DNA isolation and PCR amplification 16 2.2.3. mtDNA COI sequence 16 2.2.4. Expressed Sequence Tag-linked microsatellite loci 17 2.2.5. Data analysis 17 2.3. Results 21 2.3.1. Genetic diversity 21 2.3.2. Population connectivity 3 2.4. Discussion and conclusions 8 Chapter 3. Retrieving skates’ skin transcripts by Illumina sequencing 15 3.1. Introduction 15 3.1.1. Skin structure in elasmobranchs 17 3.1.3. Pigmentary genes 22 3.2. Materials and methods 23 3.2.1. The development of a sampling protocol and experimental scheme 23 3.2.2. RNA isolation 25 3.2.2.1. RNA extraction using TRIzol® Reagent 25 3.2.2.2. RNA extraction using the Direct-zol™ RNA MiniPrep Kit 25 3.2.2.3. RNA extraction using the Maxwell® 16MDx Instrument 26 3.2.2.4. RNA extraction using the BeadBeater 26 3.2.2.5. Combining RNA isolation protocols 26 3.2.3. Library preparation and sequencing 27 3.2.4. Raw reads quality check 28 3.3. Results 30 3.4. Discussion 31 Chapter 4. Retrieving a reference transcriptome for Raja miraletus by Ion Torrent sequencing 33 4.1. Introduction 33 4.2. Materials and methods 35 4.2.1. Sampling 35 4.2.2. RNA isolation 35 4.2.3. Ion Torrent library preparation and sequencing 36 4.2.4. The assembly 37 4.2.5. Functional annotation of transcripts 38 4.3. Results 38 4.4. Discussion 44 Chapter 5. Differentially expressed genes in skate skin 47 5.1. Introduction 47 5.2. Materials and methods 49 5.2.1. Differential gene expression analysis 49 5.3. Results 50 59 5.4. Discussion and conclusion 65 References 67 Appendix I Appendix II Appendix III Appendix IV 2 Chapter 1. General introduction 1.1. Thesis objectives and overview This dissertation focuses on Rajidae (Chondrichthyes), a family of cartilaginous fish inhabiting the continental shelf and slope of oceans worldwide and whose evolutionary history is far from being fully elucidated. The goals of this PhD research can be divided in two main, although interconnected, themes. First, the detection of genetic diversity, phylogeographic patterns and population structure of Raja miraletus L. complex aimed to highlight the cryptic evolution hidden under the differentiation of at least three lineages inhabiting the Mediterranean Sea and off the Atlantic coast of Africa. Second, this research aimed to identify the molecular basis underpinning skates’ pigmentation along with other genes connected to skin functions (i.e. collagen structures, metabolism, mucus production and immune response). Most of all, the work aimed to identify transcripts related to pigmentation, to perform the Differential Gene Expression (DGE) analysis of differently pigmented and non- pigmented skin and eventually compile a transcript catalogue for this tissue. The surplus value of this research was adding a tile to the genomic resources currently available for five non-model species and lastly, opening the door to the investigation on the evolution of pigmentary genes and their patterns of adaptation to specific ecological conditions (e.g. as an effect of convergence or the repeated evolution of similar phenotypes serving the same ecological function in two or more taxa). Specific research tasks and questions were separately addressed in each chapter. Chapter 1 begins with a brief introduction to the species concept and the undertones assumed within this thesis, putting in the spotlight those taxa which are hidden under the same nominal species and highly contribute to enrich the biodiversity inventory. Chapter 1 thus focuses on cryptic speciation in bony fish and chondrichthyans, reporting the most interesting and significant cases. In Chapter 2 the case of the brown skate Raja miraletus is described as an additional evidence of cryptic evolution within a species complex. The genetic variability and differentiation between different geographical populations was investigated at the mitochondrial and nuclear DNA level. The existence of at least three different lineages was discussed, supporting the identification of the South African brown skate as a resurrected species, Raja ocellifera, included in the nominal Raja miraletus 3 since 1967. Chapter 3 illustrated the path leading to the Illumina sequencing of different skin tissues belonging to five different species of genus Raja, which are phylogenetically related by sibling and sister relationships and display different dorsal patterning, ascribable to their adaptation to the benthic life. Chapter 4 focused on the production of long sequencing reads for the reconstruction of a draft transcriptome for R. miraletus, from the sampling phase to the library preparation and Ion Torrent sequencing. The transcriptome has been then used during the mapping of the Illumina reads obtained from skin tissues, to lastly perform the Differential Expression analysis (DE), as described in chapter 5. Chapter 5 introduced to the main critical points and issues especially related to RNA-seq data analysis. Details about the methods chosen are discussed. This final section includes the main results of DE analysis between different skin tissues across five target species and provides a first overview on the functional role of the identified genes. Finally, suggestions are given for future experiments that can validate and expand on the knowledge presented here. In fact, results of this work could be considered the starting point for a deeper and wider exploration of chondrichthyan pigmentary genes. 4 1.2. Species and cryptic diversity While reading ‘How many species are there on Earth?’ today, the 3 to 5 million species estimated in 1988 (May 1988) appear far from the most recent biodiversity inventory, where about 8.7 million eukaryotic species are predicted to be inhabiting the planet. It has also been appraised that 86% of terrestrial and 91% of marine species have not been described yet (Mora et al. 2011). How long should it take to fill this gap in our knowledge and how should we proceed in those under-sampled regions characterized by high species richness or simply not physically reachable? While answering these questions, Mora et al. (2011) raised an interesting paradox: considering 6,200 species described per year, 24.8 new species described per taxonomist and assuming that these values, together with the current rate of extinction, will remain constant in time and among taxa, characterizing new species may take as long as 1,200 years and the industry of 303,000 taxonomists, meaning that many species will become extinct before we would know they walked the earth or ‘swam the oceans’ (Mora et al.2011). Nonetheless, it is plausible that this filling-the-gap-issue would be simplified if considering the integration of DNA-based technologies to traditional taxonomy (Cariani et al. 2017; Landi et al. 2014; Costa et al. 2012). In general, underestimating diversity and overestimating species ranges are the main obstacles to the compilation of a comprehensive biodiversity inventory, especially if build on ‘taxonomic lumping’, i.e.