Bioinformatics and Next Generation Sequencing: Applications of Arthropod Genomes

Over the past decade, the Next Generation Sequencing (NGS) technology has been broadly applied in many areas such as genomics, medical diagnosis, biotechnology, virology, biological systematics, forensic biology, and anthropology. Taken together, it has offered us brilliant insights into life sciences. Most of the work presented in this thesis describes NGS applications on genome assembly, genome annotation, and comparative genomics, using arthropods as case studies: (1) by sequencing and analyzing the genomes of three Tetranychus spider mites with three completely different feeding behaviors, we uncovered genomic signature variations and indicative of pest adaptations; (2) we sequenced, assembled and annotated five Brevipalpus flat mite genomes and their corresponding endosymbiont Cardinium genomes. Comparative genomics reveals herbivorous pest adaptations and parthenogenesis; (3) the complete genomic analysis of parasitoid wasp Copidosoma floridanum indicates the mechanism of polyembryony of such primary parasite of moths. By bioinformatics and genomics approaches, my study provides the genomic basis and establishes the hypotheses for the future biology in pest and arthropod researches. These NGS applications of arthropod genomes will offer new insights into arthropod evolution and plant-herbivore interactions, open unique opportunities to develop novel plant protection strategies, and additionally, provide arthropod genomic resources as well

ACARORUM CATALOGUS IX. Acariformes, Acaridida, Schizoglyphoidea (Schizoglyphidae), Histiostomatoidea (Histiostomatidae, Guanolichidae), Canestrinioidea (Canestriniidae, Chetochelacaridae, Lophonotacaridae, Heterocoptidae), Hemisarcoptoidea (Chaetodactylidae, Hyadesiidae, Algophagidae, Hemisarcoptidae, Carpoglyphidae, Winterschmidtiidae)

The 9th volume of the series Acarorum Catalogus contains lists of mites of 13 families, 225 genera and 1268 species of the superfamilies Schizoglyphoidea, Histiostomatoidea, Canestrinioidea and Hemisarcoptoidea. Most of these mites live on insects or other animals (as parasites, phoretic or commensals), some inhabit rotten plant material, dung or fungi. Mites of the families Chetochelacaridae and Lophonotacaridae are specialised to live with Myriapods (Diplopoda). The peculiar aquatic or intertidal mites of the families Hyadesidae and Algophagidae are also included.Publishe

Investigating relationships in the New Zealand alpine Ranunculus using RNA sequencing : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Manawatū, New Zealand

Whether the alpine flora of New Zealand is resilient enough to withstand the effects of climate change is an important and unanswered question. Conspicuous amongst the alpine flora are the species of Ranunculus in section Pseudadonis. This monophyletic group of species is hypothesised to have rapidly diversified into distinct mountain habitats, with some species convergently evolving into similar habitats. Investigating how cryptic physiologies have convergently evolved in some Ranunculus species may provide insight into the adaptive potential of this group of plants. It has been argued that hybridisation is an important evolutionary process explaining the morphological and ecological variation of New Zealand alpine Ranunculus species. Hybridisation, and in particular introgression, has also been hypothesised elsewhere as an effective means for closely-related species to share genetic material and undergo rapid adaptation through selection of standing genetic variation. This research aimed to use RNA sequencing technology to address questions of physiology and phylogeny amongst four taxa of the alpine Ranunculus group. Habitat characterisation was carried out before plants were sampled and grown under standardised conditions in a common garden experiment. Bioinformatic approaches were used to analyse high-throughput sequencing data of RNA extracted from these laboratory-grown plants. This research illustrates the potential of RNA sequencing for studying non-model plant species. However, the conservative analytical approaches adopted, and noise within the data, limited inferences of physiological traits and evolutionary relationships. Analyses of heterozygosity and issues with de novo transcriptome assembly suggested greater numbers of gene variants than expected for these small, isolated populations of alpine plants. These gene variants likely occur because of the polyploid genomes of the New Zealand alpine Ranunculus. Further work is needed, however, to confirm this genetic diversity. Overall, this work reinforces the difficulties in studying non-model polyploid systems. Yet, it does hint at a genetic richness within the alpine Ranunculus that might aid survival of this clade during a rapidly changing future

Desarrollo de técnicas bioinformáticas para el análisis de datos de secuenciación masiva en sistemática y genómica evolutiva: Aplicación en el análisis del sistema quimiosensorial en artrópodos

[spa] Las tecnologías de secuenciación de próxima generación (NGS) proporcionan datos potentes para investigar cuestiones biológicas y evolutivas fundamentales, como estudios relacionados con la genómica evolutiva de la adaptación y la filogenética. Actualmente, es posible llevar a cabo proyectos genómicos complejos analizando genomas completos y / o transcriptomas, incluso de organismos no modelo. En esta tesis, hemos realizado dos estudios complementarios utilizando datos NGS. En primer lugar, hemos analizado el transcriptoma (RNAseq) de los principales órganos quimiosensoriales del quelicerado Macrothele calpeiana, Walckenaer, 1805, la única araña protegida en Europa, para investigar el origen y la evolución del sistema quimiosensorial (SQ) en los artrópodos. El SQ es un proceso fisiológico esencial para la supervivencia de los organismos, y está involucrado en procesos biológicos vitales, como la detección de alimentos, parejas o depredadores y sitios de ovoposición. Este sistema, está relativamente bien caracterizado en hexápodos, pero existen pocos estudios en otros linajes de artrópodos. El análisis de nuestro transcriptoma permitió detectar algunos genes expresados en los supuestos órganos quimiosensoriales de los quelicerados, como cinco NPC2 y dos IR. Además, también detectamos 29 tránscritos adicionales después de incluir en los perfiles de HMM nuevos miembros del SQ de genomas de artrópodos recientemente disponibles, como algunos genes de las familias de los SNMP, ENaC, TRP, GR y una OBP-like. Desafortunadamente, muchos de ellos eran fragmentos parciales. En segundo lugar, también hemos desarrollado algunas herramientas bioinformáticas para analizar datos de RNAseq y desarrollar marcadores moleculares. Los investigadores interesados en la aplicación biológica de datos NGS pueden carecer de la experiencia bioinformática requerida para el tratamiento de la gran cantidad de datos generados. En este contexto, principalmente, es necesario el desarrollo de herramientas fáciles de usar para realizar todos los procesos relacionados con el procesamiento básico de datos NGS y la integración de utilidades para realizar análisis posteriores. En esta tesis, hemos desarrollado dos herramientas bioinformáticas con interfaz gráfica, que permite realizar todos los procesos comunes del procesamiento de datos NGS y algunos de los principales análisis posteriores: i) TRUFA (TRanscriptome User-Friendly Analysis), que permite analizar datos RNAseq de organismos que no modelos, incluyendo la anotación funcional y el análisis de expresión génica diferencial; y ii) DOMINO (Development Of Molecular markers In Non-model Organisms), que permite identificar y seleccionar marcadores moleculares apropiados para análisis de biología evolutiva. Estas herramientas han sido validadas utilizando simulaciones por ordenador y datos experimentales, principalmente de arañas.[eng] The Next Generation Sequencing (NGS) technologies are providing powerful data to investigate fundamental biological and evolutionary questions including phylogenetic and adaptive genomic topics. Currently, it is possible to carry out complex genomic projects analyzing the complete genomes and/or transcriptomes even in non-model organisms. In this thesis, we have performed two complementary studies using NGS data. Firstly, we have analyzed the transcriptome (RNAseq) of the main chemosensory organs of the chelicerate Macrothele calpeiana, Walckenaer, 1805, the only spider protected in Europe, to investigate the origin and evolution of the Chemosensory System (CS) in arthropods. The CS is an essential physiological process for the survival of organisms, and it is involved in vital biological processes, such as the detection of food, partners or predators and oviposition sites. This system, which has it relatively well characterized in hexapods, is completely unknown in other arthropod lineages. Our transcriptome analysis allowed to detect some genes expressed in the putative chemosensory organs of chelicerates, such as five NPC2s and two IRs. Furthermore, we detected 29 additional transcripts after including new CS members from recently available genomes in the HMM profiles, such as the SNMPs, ENaCs, TRPs, GRs and one OBP-like. Unfortunately, many of them were partial fragments. Secondly, we have also developed some bioinformatics tools to analyze RNAseq data, and to develop molecular markers. Researchers interested in the biological application of NGS data may lack the bioinformatic expertise required for the treatment of the large amount of data generated. In this context, the development of user-friendly tools for common data processing and the integration of utilities to perform downstream analysis is mostly needed. In this thesis, we have developed two bioinformatics tools with an easy to use graphical interface to perform all the basics processes of the NGS data processing: i) TRUFA (TRanscriptome User-Friendly Analysis), that allows analyzing RNAseq data from non-model organisms, including the functional annotation and differential gene expression analysis; and ii) DOMINO (Development of Molecular markers in Non-model Organisms), which allows identifying and selecting molecular markers appropriated for evolutionary biology analysis. These tools have been validated using computer simulations and experimental data, mainly from spiders

27th Fungal Genetics Conference

Program and abstracts from the 27th Fungal Genetics Conference Asilomar, March 12-17, 2013

27th Fungal Genetics Conference

Program and abstracts from the 27th Fungal Genetics Conference Asilomar, March 12-17, 2013