High-quality genome assemblies of plant species using third generation genomic technologies and comprehensive genotypic characterization of Arabis inter-species introgression lines

Genomsequenzen sind für viele molekulare Studien von grundlegender Bedeutung. In den letzten Jahren wurden immer wieder neue kosten- und zeitsparende Lösungen gesucht, um Genomsequenzierung zu effizient und korrekt wie möglich zu gestalten. Die Entwicklung der DNA-Sequenzierungsverfahren ging dabei von der traditionellen Sanger-basierten Sequenzierung über die sogenannten Sequenzierungen der zweiten Generation bis zu den vor kurzem eingeführten Technologien der dritten Generation. Genom-Assemblierung mit der ursprünglichen Sanger-basierten Methode war zeitaufwändig und teuer, bzw führte basierend auf der zweiten Generation der Technologien zu fragmentierten Genomsequenzen. Die neuesten Technologien der dritten Generation, also Technologien, die lange DNA Moleküle auslesen können, versprechen schnelle, kostengünstige Assemblierung von nahezu vollständigen Genomsequenzen. Sequenzierungsmethoden wie PacBio’s Single Molecular Real-Time (SMRT) und Oxford Nanopore’s MINION Sequenzierungen generieren dabei DNA-Sequenzen mit einer durchschnittlichen Lese-Länge von etwa 10 kb. Darüber hinaus können Genomkartierungs-Technologien wie Optische Kartierung und Chromatin-Kontakt-Sequenzierung Strukturinformation über mehrere hundert kb oder mehrere Mb erstellen. In dieser Arbeit werde ich zunächst die genomischen Technologien der dritten Generation und ihre Anwendungen auf die Pflanzengenom-Assemblierung zusammenfassen und diskutieren, wie sie die besonderen Herausforderungen von heterozygoten und polyploiden Pflanzengenomen in Einleitung überwinden können. In meinem ersten Projekt, beschreibe ich, wie ich zwei der neuen Genomekartierungs-Technologien im Kontext von der Genomassemblierung von drei Verwandten der Modell-Pflanze Arabidopsis thaliana verglichen habe. Beide Technologien führten zu ähnlichen Verbesserungen der Assemblierungsqualität. Darüber hinaus habe ich Workflows entwickelt, um beide Technologien zu integrieren, umso die Assemblierung nochmals zu verbessern. Im zweiten Projekt stelle ich die Genomassemblierung und Annotation von Arabis montbretiana vor. A. montbretiana ist eine einjährige Schwester der mehrjährigen Pflanze A. alpina (deren Genomassemblierung in meinem ersten Projekt beschrieben ist). Die beiden hochwertigen Arabis-Genom-Assemblierungen ermöglichten es uns, die genomische Basis zu untersuchen, die der unterschiedlichen Evolutionen der beiden Pflanzen zugrunde liegt. Interessanterweise zeigte die vergleichende genomische Analyse zwischen A. montbretiana und A. alpina wesentliche genomische Umlagerungen, darunter über 1.200 translozierte Gene, die heterogene Variationen in den Nachkommen einer Kreuzung aus den beiden Arten erzeugt

드노보 전장유전체 조립 및 분석을 통한 해양 절지동물 진화 사례 연구

학위논문 (박사) -- 서울대학교 대학원 : 자연과학대학 생명과학부, 2020. 8. 김원.The de novo genome assembly has become an essential approach for studying non-model organisms since the post-genome era arrived. The reported cases of de novo genome assemblies of non-model arthropods have increased dramatically in recent days. The marine arthropod, however, is one of the least sequenced animal groups despite of their surprisingly high taxonomic and morphological diversity. The de novo genome studies on these marine arthropods remain mostly limited in terms of their cases and quality of assemblies up to now. This study therefore conducted the first case of de novo genome research focusing to the under-sampled marine arthropod groups, the Class Pycnogonida and the Infraorder Brachyura in Korea. In this study, one mitochondrial genome and four whole-genomes were de novo assembled and their genomic characteristics were discussed. While the two cases of de novo genomes assembled by using short read-length sequencing showed limited assembly quality, the long read-length based assemblies of Nymphon striatum and Chionoecetes opilio provided significantly informative, high-qualitied genomes. The preliminary phylogenomic research of this study which firstly included the representative genomes of pycnogonid and brachyuran decapod, also implied that recent hypothesis of xiphosuran nested in the most derived clade, Arachnopulmonate, is indeedly plausible. Furthermore, the limitations of de novo genome researches on the laboratory experiment lacking bioinformatics background were discussed to establish an optimized research workflow for the genomic study on non-model marine arthropod.포스트게놈 시대의 도래에 따라 드노보 유전체 조립은 비모델 생명체의 생명현상을 연구하는데 필수적인 과정이 되었다. 비모델 절지동물의 드노보 조립된 유전체의 사례는 근래에 들어 급격하게 증가했다. 그러나, 해양 절지동물은 놀라울 정도로 다양한 분류군과 형태를 가짐에도 불구하고, 가장 드노보 유전체 조립 연구가 미흡한 분류군 중 하나이다. 현재까지 보고된 해양 절지동물의 드노보 유전체 조립 연구는 대부분이 그 양과 질 모두가 제한적이다. 그러므로, 본 연구는 국내에서 최초로 선행 연구가 미흡한 해양 절지동물 분류군인 바다거미 강과 단미 하목에 초점을 맞춰 드노보 유전체 조립 및 분석을 실시하였다. 본 연구의 결과로, 1건의 미토콘드리아 유전체와 4건의 전장유전체가 드노보 조립되었으며, 조립된 유전체의 특징이 기술되었다. 단서열 염기서열결정법으로 조립된 두 건의 유전체의 품질은 비교적 낮았으나, 장서열 염기서열결정법을 주로하여 조립된 Nymphon striatum과 Chionoecetes opilio 유전체가 매우 풍부한 고품질 유전체 정보를 제공한다는 것이 밝혀졌다. 본 연구에서 수행된 기초적인 계통유전체학 연구는 바다거미 강과 십각 목을 각각 대표하는 드노보 조립된 유전체를 최초로 포함했으며, 이를 통해 최근 논란의 대상인 거미강에 속하는 투구게류 가설을 지지하는 결과를 나타내는 것으로 밝혀졌다. 더 나아가, 비생물정보학 연구실 환경에서 이루어지는 드노보 유전체 연구에서 발생하는 제한요인들을 분석함으로써 비모델 해양 절지동물의 드노보 유전체 연구에 최적화된 안정적인 연구방법론을 제시하였다.BACKGROUNDS 1 CHAPTER 1. THE PILOT RESEARCHES FOR EVOLUTIONARY STUDIES ON MARINE ARTHROPOD GENOMES 17 1.1. The preliminary genomic studies on Liparis tanakae and its genomic characteristics 19 1.1.1. Introduction 19 1.1.2. Materials and Methods 22 1.1.3. Results 29 1.1.4. Discussion 35 1.2. The de novo Mitochondrial genome assembly of Chionoecetes opilio : The manual curation of predicted genes and the phylogenomic analyses with large datasets 38 1.2.1. Introduction 38 1.2.2. Materials and Methods 40 1.2.3. Results 43 1.2.4. Discussion 49 CHAPTER 2. THE DE NOVO GENOME ASSEMBLIES OF THREE MARINE ARTHROPODS 53 2.1. The first de novo assembled genome of Portunus trituberculatus indicating the bottlenecks in researching non-model marine arthropods 55 2.1.1. Introduction 55 2.1.2. Materials and Methods 57 2.1.3. Results 63 2.1.4. Discussion 69 2.2. The high-qualitied marine arthropod assemblies : De novo assembled Chionoecetes opilio and Nymphon striatum genomes and their characteristics 71 2.2.1. Introduction 71 2.2.2. Materials and Methods 76 2.2.3. Results 86 2.3. General discussion 100 2.3.1. The ab initio prediction and annotation of marine arthropod Hox genes 100 2.3.2. The optimizied workflow of de novo whole-genome researches of marine arthropods 104 CHAPTER 3. THE CASE STUDY OF THE ARTHROPOD EVOLUTION THROUGH THE COMPARATIVE WHOLE-GENOME ANALYSES 111 3.1. The preliminary chelicerate phylogenomic analyses incorporating under-sampled taxa 113 3.1.1. Introduction 113 3.1.2. Materials and Methods 120 3.1.3. Results and Discussion 125 CONCLUSION 131 REFERENCES 135 APPENDIX 157 Appendix 1. Detailed list of sequenced animal genomes with their Scientific names visible 159 ABSTRACT (In Korean) 180Docto

The great Africanised family of humankind : securing and undoing the human through Africa in literature and film

Abstract : The Poisonwood Bible (Barbara Kingsolver, 1998), Amaryllis in Blueberry (Christina Meldrum, 2011), The Garden of Burning Sand (Corban Addison, 2013) and The Constant Gardener (dir. Fernando Mereilles, 2005) can be characterised as critical of the West’s political and humanitarian interventions in Africa. They are also, however, instances of that pervasive but much-maligned genre of literature and film: texts ostensibly about Africa but written by Westerners and reflective of Western lives and norms. Recognising the problems of representations of Africa and Africans, this study, nevertheless, also attempts to take the sincerity of these texts seriously. Though three of the texts offer criticisms of colonialism, imperialism and neo-imperialism, such criticisms are not their true impetus. In fact, the absence of such criticisms in Addison’s novel throws into relief the fact that the central concern in all four texts is the division between Africa and the West in so far as it represents human disunity. In other words, a crisis of human community underpins each of these texts. Their solution to this disunity is deceptively simple: human unity based on and legitimised by an essential human sameness. Africa plays a special role in making what is a grey, abstract universalist humanism expressible: it provides ‘colour’ and ‘texture’ but also, as the origin of the species, it provides a singular, stable origin which, in turn, offers the transcendence of difference. The threat that Africa’s contradictory position—provider of difference, guarantor of human sameness—poses to these texts’ projections of a universally inclusive human community are sublimated by their idealisation of Africa. The crucial difference that Africa provides is that of a heightened and essential humanity, not a denigrated one. I argue that these texts’ idealisations of Africa betray an ontological anxiety within Western subjecthood, that there is a crisis of humanism rather than only a tiresome reiteration of problematic tropes. By taking the sincerity of these texts seriously, therefore, I attempt to move beyond the Us/Them paradigm that has dominated literary analyses of texts about Africa but written by Westerners, without ignoring or dismissing the representational inequities that persist.Ph.D. (English

“We are white”: oral tradition, documented history and molecular biology of Xhosa clans descended from non-African forebears and their expression of this ancestry through the idiom of ancestor religion

Xhosa clan membership is symbolised by a clan-name (isiduko) and passed along the male line from father to son. This social indicator has a biological counterpart in Y chromosome DNA that passes through successive generations in the patriline. Both relate specifically to a distant patrilineal forebear or apical ancestor. The present study has involved the collection and documentation of oral-historical information relating to the descent of certain Cape Nguni clans from non-African forebears and (where possible) a review of documented accounts of such origins. The research has also included collection of buccal cells from male research participants and analysis of their Y chromosome DNA. This method indicates whether a man’s patrilineal forebear lived in Africa. Otherwise, it indicates the broad geographical region from which he originated, hence providing an additional, independent source of information relating to ancestry that can confirm or challenge claims made based on oral history. Ethnographic research into the performance of distinctive ancestor rituals by clan members explores the continuing relevance of foreign ancestry in the contemporary context of rural communities in the Eastern Cape, South Africa. The study heeds calls for the decolonisation of scholarship in various ways: methodologically, through transdisciplinary research; ontologically, by questioning the utility of the nature: culture and related dichotomies; and epistemologically, because instead of relying entirely on the western academic tradition, it takes account of other modes of knowledge production. In rejection of the notion that only one side of history is true, it records multiple voices – those of the powerful but also the ordinary. The study deals with race and racial identification, but confirms the superficiality of these constructed differences by offering evidence of their submergence in the unifying power of kinship and descent

Laws of the Sea

Laws of the Sea assembles scholars from law, geography, anthropology, and environmental humanities to consider the possibilities of a critical ocean approach in legal studies. Unlike the United Nations’ monumental Convention on the Law of the Sea, which imagines one comprehensive constitutional framework for governing the ocean, Laws of the Sea approaches oceanic law in plural and dynamic ways. Critically engaging contemporary concerns about the fate of the ocean, the collection’s twelve chapters range from hydrothermal vents through the continental shelf and marine genetic resources to coastal communities in France, Sweden, Florida, and Indonesia. Documenting the longstanding binary of land and sea, the chapters pose a fundamental challenge to European law’s “terracentrism” and its pervasive influence on juridical modes of knowing and making the world. Together, the chapters ask: is contemporary Eurocentric law—and international law in particular—capable of moving away from its capitalist and colonial legacies, established through myriad oceanic abstractions and classifications, toward more amphibious legalities? Laws of the Sea will appeal to legal scholars, geographers, anthropologists, cultural and political theorists, as well as scholars in the environmental humanities, political ecology, ocean studies, and animal studies

On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction

International audienc