Genome assemblies of three closely related leaf beetle species (Galerucella spp)

Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla and G. tenella. The three assemblies have a genome size ranging from 460 Mbp to 588 Mbp, with N50 from 31,588 kbp to 79.674 kbp, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.

Genome assemblies of three closely related leaf beetle species (Galerucella spp).

Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla and G. tenella. The three assemblies have a genome size ranging from 460Mb to 588Mb, with N50 from 31,588kb to 79.674kb, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.

Molecular anatomy of the pre-primitive-streak chick embryo

The early stages of development of the chick embryo, leading to primitive streak formation (the start of gastrulation), have received renewed attention recently, especially for studies of the mechanisms of large-scale cell movements and those that position the primitive streak in the radial blastodisc. Over the long history of chick embryology, the terminology used to define different regions has been changing, making it difficult to relate studies to each other. To resolve this objectively requires precise definitions of the regions based on anatomical and functional criteria, along with a systematic molecular map that can be compared directly to the functional anatomy. Here, we undertake these tasks. We describe the characteristic cell morphologies (using scanning electron microscopy and immunocytochemistry for cell polarity markers) in different regions and at successive stages. RNAseq was performed for 12 regions of the blastodisc, from which a set of putative regional markers was selected. These were studied in detail by in situ hybridization. Together this provides a comprehensive resource allowing the community to define the regions unambiguously and objectively. In addition to helping with future experimental design and interpretation, this resource will also be useful for evolutionary comparisons between different vertebrate species.

Neuronal Innervation of the Subgenual Organ Complex and the Tibial Campaniform Sensilla in the Stick Insect Midleg

Mechanosensory organs in legs play are crucial receptors in the feedback control of walking and in the detection of substrate-borne vibrations. Stick insects serve as a model for the physiological role of chordotonal organs and campaniform sensilla. This study documents, by axonal tracing, the neural innervation of the complex chordotonal organs and groups of campaniform sensilla in the proximal tibia of the midleg in Sipyloidea sipylus. In total, 6 nerve branches innervate the different sensory structures, and the innervation pattern associates different sensilla types by their position. Sensilla on the anterior and posterior tibia are innervated from distinct nerve branches. In addition, the variation in innervation is studied for five anatomical branching points. The most common variation is the innervation of the subgenual organ sensilla by two nerve branches rather than a single one. The fusion of commonly separated nerve branches also occurred. However, a common innervation pattern can be demonstrated, which is found in >75% of preparations. The variation did not include crossings of nerves between the anterior and posterior side of the leg. The study corrects the innervation of the posterior subgenual organ reported previously. The sensory neuroanatomy and innervation pattern can guide further physiological studies of mechanoreceptor organs and allow evolutionary comparisons to related insect groups.

Spectrum of protein localization in proteomes captures evolutionary relation between species

The native subcellular localization or cellular compartment of a protein is the one in which it acts most often; it is one aspect of protein function. Do ten eukaryotic model organisms differ in their location spectrum, i.e. the fraction of its proteome in each of its seven major compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. To gauge the bias of prediction methods, we merged all available experimental annotations for the human proteome. In doing so, we found important values in both Swiss-Prot and the Human Protein Atlas (HPA). After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes: Homo sapiens, Gorilla gorilla, Pan troglodytes, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Anopheles gambiae, Caenorhabitis elegans, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Overall, the predicted location spectra were similar. However, the detailed differences were significant enough to plot trees and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states, corresponding to the seven studied localization classes. The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons.

Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks

SUMMARYMammals progress through similar physiological stages during life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects conserved molecular events is unclear. Here, we map common epigenetic changes experienced by mammalian genomes as they age, focusing on evolutionary comparisons of humans to dogs, an emerging model of aging. Using targeted sequencing, we characterize the methylomes of 104 Labrador retrievers spanning a 16 year age range, achieving >150X coverage within mammalian syntenic blocks. Comparison with human methylomes reveals a nonlinear relationship which translates dog to human years, aligns the timing of major physiological milestones between the two species, and extends to mice. Conserved changes center on specific developmental gene networks which are sufficient to capture the effects of anti-aging interventions in multiple mammals. These results establish methylation not only as a diagnostic age readout but as a cross-species translator of physiological aging milestones.

Chromosomal Evolution in Psittaciformes. Revisited

<p class="1Body">With colourful plumage, charismatic character and vocal learning abilities, parrots are one of the most striking and recognizable bird groups. Their attractiveness has drawn human attention for centuries, and members of the Psittaciformes order were, also, among the first avian species to be subject to cytogenetic studies which have contributed to understand their taxonomic and evolutionary relationships.</p><p class="1Body">We present here the karyological results collected by the study of thirteen parrot species new to karyology. These results are additionally supported by G banded preparations obtained in five species.</p><p class="1Body">The order Psittaciformes is an interesting example of a, typically, non migratory avian lineage with Gondwanaland origin, whose evolutionary radiation has been shaped by the Cenozoic geographic and climatic events that affected the land masses derived from the Gondwanaland continental split.</p><p class="1Body">We discuss the results of our studies, in conjunction with the previously compiled Psittaciformes cytogenetic data to delineate a picture of the chromosomal evolution of the order, concurrently with the biogeographic history of the lands in the southern Hemisphere.</p><p class="1Body">Considering the available data on parrot cytogenetics, a "standard parrot karyotype pattern" is proposed for evolutionary comparisons.</p><p class="1Body">Several biogeographic, and phylogenetically related "karyogram patterns" are also identified, and mechanisms of chromosome rearrangement that associate this patterns among them, and with the standard parrot karyotype pattern are proposed. These schemes on parrot chromosomal variation are discussed in relation to the general avian chromosome evolutionary theses proposed by cytogenetic and molecular genomic researchers.</p>

Intertwining phylogenetic trees and networks

The fields of phylogenetic tree and network inference have dramatically advanced in the last decade, but independently with few attempts to bridge them. Here we provide a framework, implemented in the phangorn library in R, to transfer information between trees and networks. This includes: 1) identifying and labelling equivalent tree branches and network edges, 2) transferring branch support to network edges, and 3) mapping bipartition support from a sample of trees (e.g. from bootstrapping or Bayesian inference) onto network edges. The ability to readily combine tree and network information should lead to more comprehensive evolutionary comparisons and conclusions.

Intertwining phylogenetic trees and networks

The fields of phylogenetic tree and network inference have dramatically advanced in the last decade, but independently with few attempts to bridge them. Here we provide a framework, implemented in the phangorn library in R, to transfer information between trees and networks. This includes: 1) identifying and labelling equivalent tree branches and network edges, 2) transferring branch support to network edges, and 3) mapping bipartition support from a sample of trees (e.g. from bootstrapping or Bayesian inference) onto network edges. The ability to readily combine tree and network information should lead to more comprehensive evolutionary comparisons and conclusions.