Metagenome skimming of insect specimen pools: potential for comparative genomics

Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from lowcoverage sequencing by “genome skimming,” which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and knownrepeatelementsof high and low complexity, includingnumerous copies ofrRNAandhistone genes.Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous “clusters” of scaffolds mapped to the same genomic site revealed intraand/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The “metagenome skimming” approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomic

The mitogenome of Hydropsyche pellucidula (Hydropsychidae): first gene arrangement in the insect order Trichoptera

International audienceWe describe the mitochondrial genome of Hydropsyche pellucidula Curtis 1834, which is first described for the suborder Annulipalpia and the first in the order Trichoptera to show a non-canonical gene order. The mitogenome was obtained by de novo assembly of shotgun sequenced total genomic DNA using Illumina Miseq technology, which produced an average coverage of 115× and a minimum coverage of 48×. The mitochondrial genome includes 13 protein-coding genes, 2 rRNAs and 22 tRNAs. The genome is characterized by a rearrangement in the relative position of protein-coding and ribosomal genes. This mitogenome sequence will be useful for studying the family Hydropsychidae, which is commonly used for freshwater pollution biomonitoring

A high resolution spatial population database of Somalia for disease risk mapping

The article investigates the possibility of creating a data collection system in an unstable environment like Somalia to estimate the incidence of infectious diseases in order to improve the reconstruction of the health sector.Maqaalku wuxuu baarayaa sidii lagu samayn lahaa nidaam lagu ururiyo daatooyinka meel aan xasillooneen sida Soomaaliya, si loo qiyaaso saamaynta cudurrada laysu gudbiyo, loona hagaajiyo qaybta caafimaadka.L'articolo indaga sulla possibilità di creare un sistema di raccolta dati in un contesto instabile come quello somalo per stimare l'incidenza di malattie infettive al fine di una migliore ricostruzione del settore sanitario

Uncovering trophic interactions in arthropod predators through DNA shotgun-sequencing of gut contents

Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives. We discuss caveats and some future prospects that could improve the use of direct DNA shotgun-sequencing to characterize arthropod trophic networks

Efeito do diluidor e da temperatura de congelação sobre o sêmen congelado de ovino da raça Santa Inês.

Objetivou-se verificar a influência do tipo de diluidor e da temperatura sobre motilidade do sêmen ovino. A coleta do sêmen foi efetuada uma vez por semana em cinco ovinos da raça Santa Inês, após feito um pool dos ejaculados e avaliado quanto ao volume, à motilidade, vigor, concentração e diluído no Leite e Tris. As amostras foram envasadas em palhetas de 0,25 ml e congeladas em três temperaturas (- 79o C, -90o C, -120o C) no equipamento TK 3000. Quando atingida a primeira temperatura, um grupo de palhetas foi transferido para o botijão criogênico e assim sucessivamente, para às demais temperaturas testadas. Após 30 dias, as palhetas foram descongeladas e o sêmen avaliado pelo método CASA. Procedeu-se a ANOVA para testar o efeito da temperatura de congelação sobre os diluidores. Para o diluidor leite, a motilidade progressiva e a percentagem de espermatozóide rápidos diferiu significativamente para temperatura de -79o C em relação às de -90o C e -120o C. No diluidor Tris não houve diferença significativa entre as temperaturas de congelação, entretanto foi significativo e superior ao diluidor a base leite em todas as temperaturas testadas. O diluidor Tris e a temperatura de congelação de -79o C mostraram ser o protocolo de congelação mais apropriado para sêmen de carneiros Santa Inês, entretanto estudos utilizando a inseminação artificial precisam ser conduzidos para validar sua qualidade. Abstract:: This study aimed to verify the influence of the temperature and the extender type on the motility of ram semen. The semen was collected a time per week in five ?Santa Inês? ram, after it was made one pool of the ejaculated and evaluated how much to the volume, motility, vigor, concentration and diluted with Milk and Tris.The samples were stored in straw of 0,25 mL to be frozen in three temperatures (-79°C,-90°C,-120°C) employing the TK 3000 equipment. When reached the first temperature, a group of straws was transferred to the cryogenic container and thus successively, for the the others tested temperatures. After 30 days, the straws had been thawed and the semen evaluated for the CASA method. It was used the ANOVA to test the effect of the temperature of freezing on the extenders. For the Milk, the progressive motility and the fast spermatozoid percentage for the temperature of -79°C differed significantly when compared to the temperatures of -90°C and -120°C. In the extender Tris did not have significant difference between the temperatures of freezing, however it was significant and superior to the extender milk in all tested temperatures. The extender Tris and the freezing temperature of -79°C showed to be the more appropriate freezing protocol for ?Santa Inês? ram semen. However more studies using the artificial insemination need to be lead to validate its quality

Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics.

DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR-based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross-reactions with the predator and related species genomes. Here, we use PCR-free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h 1, respectively). However, the facultative aphid symbionts Hamiltonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1?2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts

Efeito da concentração espermática sobre sêmen congelado de carneiros da raça Santa Inês.

Objetivou-se verificar o efeito da concentração final dos espermatozóide de ovinos sobre os parâmetros de motilidade do sêmen congelado. Foram coletados seis ejaculados de cinco carneiros Santa Inês, uma vez por semana feito um pool e avaliado o volume, motilidade, vigor, concentração espermática e, fracionado em três alíquotas para testar diluições diferentes (1000x106, 800x106, 600x106 espermatozóides por mL). As amostras foram envasadas em palhetas de 0,25 mL, congeladas no equipamento TK 3000 e conservadas no botijão criogênico. Decorridos 30 dias foram descongeladas e, o sêmen avaliado pelo método CASA. Procedeu-se a ANOVA para testar o resultado da concentração de espermatozóides sobre os parâmetros de motilidade. A concentração de 600 x 106 sptz/ mL para as variáveis percentagens de espermatozóides móveis, motilidade progressiva, percentagem de espermatozóides de velocidade rápida e média mostrou-se superior a de 800 x 106 sptz /mL e 1000 x 106 sptz /ml. Para a variável velocidade média da trajetória do espermatozóide rápido (VAPR) não foi observada diferença significativa entre as concentrações testadas. Neste estudo, a concentração de 600 x 106 sptz/ ml apresentou a melhor preservação dos parâmetros de motilidade após a congelação, tornandose adequada para o uso na inseminação artificial. No entanto necessita-se de mais estudos in vivo para avaliar a eficiência desta técnica

Population Distribution, Settlement Patterns and Accessibility across Africa in 2010

The spatial distribution of populations and settlements across a country and their interconnectivity and accessibility from urban areas are important for delivering healthcare, distributing resources and economic development. However, existing spatially explicit population data across Africa are generally based on outdated, low resolution input demographic data, and provide insufficient detail to quantify rural settlement patterns and, thus, accurately measure population concentration and accessibility. Here we outline approaches to developing a new high resolution population distribution dataset for Africa and analyse rural accessibility to population centers. Contemporary population count data were combined with detailed satellite-derived settlement extents to map population distributions across Africa at a finer spatial resolution than ever before. Substantial heterogeneity in settlement patterns, population concentration and spatial accessibility to major population centres is exhibited across the continent. In Africa, 90% of the population is concentrated in less than 21% of the land surface and the average per-person travel time to settlements of more than 50,000 inhabitants is around 3.5 hours, with Central and East Africa displaying the longest average travel times. The analyses highlight large inequities in access, the isolation of many rural populations and the challenges that exist between countries and regions in providing access to services. The datasets presented are freely available as part of the AfriPop project, providing an evidence base for guiding strategic decisions