RESUMO
Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.
RESUMO
Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7). We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences. Tree topology was congruent with previous phylogenies, all nodes being highly supported, suggesting that this marker is well-suited for deep phylogenies in Arcellinida and perhaps Amoebozoa. Furthermore, it enabled discrimination of close-related taxa. This short genetic marker (ca. 250bp) can therefore be used at different taxonomic levels, due to a fast-varying intergenic region presenting either a small intergenic sequence or an overlap, depending on the species.
Assuntos
Amebozoários/classificação , Amebozoários/genética , Código de Barras de DNA Taxonômico/normas , NADH Desidrogenase/genética , Filogenia , Amebozoários/enzimologia , Genes de Protozoários/genética , Marcadores Genéticos/genética , Especificidade da EspécieRESUMO
A checklist of the species of Hippoboscidae, Nycteribiidae and Streblidae and their hosts and localities in the state of Mato Grosso do Sul, based on literature and specimens deposited in scientific collections, is presented. Fifty-three species are recorded, being Xenotrichobius noctilionis Wenzel, 1976 reported for first time in Brazil.(AU)
Uma listagem das espécies de Hippoboscidae, Nycteribiidae e Streblidae, seus hospedeiros e localidades no estado de Mato Grosso do Sul, baseada em dados de literatura e no acervo de coleções científicas, é apresentada. Cinquenta e três espécies são registradas, sendo Xenotrichobius noctilionis Wenzel, 1976 reportada pela primeira vez no Brasil.(AU)
Assuntos
Animais , Dípteros , BrasilRESUMO
ABSTRACT A checklist of the species of Hippoboscidae, Nycteribiidae and Streblidae and their hosts and localities in the state of Mato Grosso do Sul, based on literature and specimens deposited in scientific collections, is presented. Fifty-three species are recorded, being Xenotrichobius noctilionis Wenzel, 1976 reported for first time in Brazil.
RESUMO Uma listagem das espécies de Hippoboscidae, Nycteribiidae e Streblidae, seus hospedeiros e localidades no estado de Mato Grosso do Sul, baseada em dados de literatura e no acervo de coleções científicas, é apresentada. Cinquenta e três espécies são registradas, sendo Xenotrichobius noctilionis Wenzel, 1976 reportada pela primeira vez no Brasil.
RESUMO
A checklist of the species of Hippoboscidae, Nycteribiidae and Streblidae and their hosts and localities in the state of Mato Grosso do Sul, based on literature and specimens deposited in scientific collections, is presented. Fifty-three species are recorded, being Xenotrichobius noctilionis Wenzel, 1976 reported for first time in Brazil.
Uma listagem das espécies de Hippoboscidae, Nycteribiidae e Streblidae, seus hospedeiros e localidades no estado de Mato Grosso do Sul, baseada em dados de literatura e no acervo de coleções científicas, é apresentada. Cinquenta e três espécies são registradas, sendo Xenotrichobius noctilionis Wenzel, 1976 reportada pela primeira vez no Brasil.