The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology

The winter moth (Operophtera brumata) belongs to one of the most species-rich families in Lepidoptera, the Geometridae (approximately 23,000 species). This family is of great economic importance as most species are herbivorous and capable of defoliating trees. Genome assembly of the winter moth allows the study of genes and gene families, such as the cytochrome P450 gene family, which is known to be vital in plant secondary metabolite detoxification and host-plant selection. It also enables exploration of the genomic basis for female brachyptery (wing reduction), a feature of sexual dimorphism in winter moth, and for seasonal timing, a trait extensively studied in this species. Here we present a reference genome for the winter moth, the first geometrid and largest sequenced Lepidopteran genome to date (638 Mb) including a set of 16,912 predicted protein-coding genes. This allowed us to assess the dynamics of evolution on a genome-wide scale using the P450 gene family. We also identified an expanded gene family potentially linked to female brachyptery, and annotated the genes involved in the circadian clock mechanism as main candidates for involvement in seasonal timing. The genome will contribute to Lepidopteran genomic resources and comparative genomics. In addition, the genome enhances our ability to understand the genetic and molecular basis of insect seasonal timing and thereby provides a reference for future evolutionary and population studies on the winter moth

A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity

Background: The 16S rRNA gene is the gold standard in molecular surveys of bacterial and archaeal diversity, but it has the disadvantages that it is often multiple-copy, has little resolution below the species level and cannot be readily interpreted in an evolutionary framework. We compared the 16S rRNA marker with the single-copy, protein-coding rpoB marker by amplifying and sequencing both from a single soil sample. Because the higher genetic resolution of the rpoB gene prohibits its use as a universal marker, we employed consensus-degenerate primers targeting the Proteobacteria. <p/>Methodology/Principal Findings: Pyrosequencing can be problematic because of the poor resolution of homopolymer runs. As these erroneous runs disrupt the reading frame of protein-coding sequences, removal of sequences containing nonsense mutations was found to be a valuable filter in addition to flowgram-based denoising. Although both markers gave similar estimates of total diversity, the rpoB marker revealed more species, requiring an order of magnitude fewer reads to obtain 90% of the true diversity. The application of population genetic methods was demonstrated on a particularly abundant sequence cluster. <p/>Conclusions/Significance: The rpoB marker can be a complement to the 16S rRNA marker for high throughput microbial diversity studies focusing on specific taxonomic groups. Additional error filtering is possible and tests for recombination or selection can be employed

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization

Insights on dispersal and recruitment paradigms: sex- and age-dependent variations in a nomadic breeder

Correction DOI: 10.1007/s00442-017-4001-6 (WOS:000419477800010)International audienceSex- and age-dependence in recruitment and dispersal are often explained by costs arising from competition for holding a breeding territory over the years-a typical feature of species living in stable habitats. For instance, long-lived birds with male territoriality often exhibit large variation in recruitment age and higher dispersal in females and young individuals. As a corollary, we expected that species with ephemeral habitat suitability, and hence nomadic breeding, would show weak age- and sex-dependence in dispersal and low variation in recruitment age, because territory ownership is not maintained over the years. In addition, the higher cost of reproduction in females might not be (over)compensated for by costs of territoriality in males. Accordingly, females would recruit later than males. We explored these variations using multievent capture-recapture models over 13 years, 3479 (2392 sexed) slender-billed gulls (Chroicocephalus genei) and 45 colony sites along the French Mediterranean coast. As expected, variability in recruitment age was low with males recruiting earlier than females. Nonetheless, dispersal in and out of the study area decreased with age and was slightly higher in males than in females. Decreased dispersal with age might result from foraging benefits associated with increased spatial familiarity. Higher dispersal in males might be explained by a male-biased sex ratio or higher philopatry benefits in females (arising from their higher cost of reproduction). Sex- and age-dependent dispersal and recruitment may thus occur in the absence of year-to-year breeding territory ownership, which stresses the importance of considering other processes in shaping recruitment and dispersal patterns

Transcriptional regulation underlying the temperature response of embryonic development rate in the winter moth

Climate change will strongly affect the developmental timing of insects, as their development rate depends largely on ambient temperature. However, we know little about the genetic mechanisms underlying the temperature sensitivity of embryonic development in insects. We investigated embryonic development rate in the winter moth (Operophtera brumata), a species with egg dormancy which has been under selection due to climate change. We used RNA sequencing to investigate which genes are involved in the regulation of winter moth embryonic development rate in response to temperature. Over the course of development, we sampled eggs before and after an experimental change in ambient temperature, including two early development weeks when the temperature sensitivity of eggs is low and two late development weeks when temperature sensitivity is high. We found temperature-responsive genes that responded in a similar way across development, as well as genes with a temperature response specific to a particular development week. Moreover, we identified genes whose temperature effect size changed around the switch in temperature sensitivity of development rate. Interesting candidate genes for regulating the temperature sensitivity of egg development rate included genes involved in histone modification, hormonal signalling, nervous system development and circadian clock genes. The diverse sets of temperature-responsive genes we found here indicate that there are many potential targets of selection to change the temperature sensitivity of embryonic development rate. Identifying for which of these genes there is genetic variation in wild insect populations will give insight into their adaptive potential in the face of climate change

Number of OTUs as a function of fractional sequence difference (OTU cut-off) for the 16S rRNA marker gene (A) and the <i>rpoB</i> marker gene (B).

<p>OTU number is plotted for filtered and trimmed sequences (undenoised), denoised sequences and denoised- and reading frame corrected sequences (automated and manual correction). The latter treatments were only applicable to <i>rpoB</i>.</p

90% sampling effort, defined as number of reads required to observe 90% of the true diversity, for proteobacterial species.

<p>* = The parametric total diversity estimates are given as lower 95% confidence interval : median : upper 95% confidence interval.</p

Estimation of species richness for sequences classified as Proteobacteria.

<p>* = The parametric total diversity estimates are given as lower 95% confidence interval : median : upper 95% confidence interval.</p

Rarefaction curves showing mean expected OTU number for Proteobacteria as a function of sample size.

<p>The 1% and 2.3% cut-offs for 16S rRNA and <i>rpoB</i> are chosen to reflect species definitions (see text).</p