BaitFisher: A software package for multispecies target DNA enrichment probe design

Christoph Urs Mayer [et al.]Target DNA enrichment combined with high-throughput sequencing technologies is a powerful approach to probing a large number of loci in genomes of interest. However, software algorithms that explicitly consider nucleotide sequence information of target loci in multiple reference species for optimizing design of target enrichment baits to be applicable across a wide range of species have not been developed. Here we present an algorithm that infers target DNA enrichment baits from multiple nucleotide sequence alignments. By applying clustering methods and the combinatorial 1-center sequence optimization to bait design, we are able to minimize the total number of baits required to efficiently probe target loci in multiple species. Consequently, more loci can be probed across species with a given number of baits. Using transcript sequences of 24 apoid wasps (Hymenoptera: Crabronidae, Sphecidae) from the 1KITE project and the gene models of Nasonia vitripennis, we inferred 57,650, 120-bp-long baits for capturing 378 coding sequence sections of 282 genes in apoid wasps. Illumina reduced-representation library sequencing confirmed successful enrichment of the target DNA when applying these baits to DNA of various apoid wasps. The designed baits furthermore enriched a major fraction of the target DNA in distantly related Hymenoptera, such as Formicidae and Chalcidoidea, highlighting the baits' broad taxonomic applicability. The availability of baits with broad taxonomic applicability is of major interest in numerous disciplines, ranging from phylogenetics to biodiversity monitoring. We implemented our new approach in a software package, called BaitFisher, which is open source and freely available at https://github.com/cmayer/BaitFisher-package.git.C.B. is a “Ramon y Cajal” fellow supported by the Spanish Ministry of Science and Education (MEC) (RYC-2014-15615).Peer Reviewe

Phylogeny of "Sphecidae" (Hymenoptera: Apoidea) based on molecular data

Die Grabwespen (Sphecidae sensu Bohart & Menke 1976; Sphecidae sensu lato in neueren, phylogenetischen Arbeiten), zu denen nach Day (1984) und späteren Autoren auch die Heterogynaidae zählen, umfassen derzeit 266 Gattungen mit 9559 beschriebene Arten (Pulawski 2006). Zusammen mit den Bienen (= Apiformes nach Michener 2000, bzw. Anthophila nach Engel 2005) bilden die Grabwespen ein gut begründetes Monophylum, das nach Michener (1986) den Namen Apoidea trägt und eine der drei Hauptlinien innerhalb der aculeaten Hymenoptera ist. Die Monophylie der aculeaten Hymenoptera, der Apoidea sowie die der Bienen ist jeweils gut begründet (z.B. Brothers 1975, Königsmann 1978, Lomholdt 1982, Alexander 1992, Brothers & Carpenter 1993). Anders verhält es sich mit den Grabwespen. Neben der phylogenetischen Untersuchung von Brothers & (1993), die die Monophylie der Grabwespen unterstützt, haben andere morphologische als auch molekularsystematische Analysen starken Zweifel an dieser Hypothese aufkommen lassen (z.B. Königsmann 1978, Lomholdt 1982, Alexander 1992, Prentice 1998, Melo 1999, Ohl & Bleidorn 2006).Sequences from the nuclear long-wavelength-rhodopsin and the mitochondrial cytochrom-c-oxidase (subunit I) from different representatives of the Apoidea, with special emphasis on digger wasps (Sphecidae sensu lat), were analysed using maximum parsimony, maximum likelihood and Baysian inference methods. Compared with previous phylogenetic studies based on morphology, the results of the molecular analyses are controversial but correspond in the absence of support for the Sphecidae s. l (sensu Bohart & Menke). The relationships within the Sphecidae sensu stricto correspond largely with recent morphological studies. There is circumstantial evidence that the Ampulicidae and Sphecidae s. str. together form a monophyletic group, whereas the relationships within this taxon are still uncertain. Although there is no evidence for a definitive phylogenetic position of the Heterogynaidae; it can be excluded that they are the sistertaxon to all other Apoidea. Instead, they are probably a derived group within the Crabronidae. In conflict to the majority of current morphological studies, the molecular analyses provide no support for the Crabronidae and Bembicinae. Some molecular analyses imply a close relationship between Philanthinae and bees

On the role of the proventricle region in reproduction and regeneration in Typosyllis antoni (Annelida: Syllidae)

Background: Syllids are a species rich annelid family possessing remarkable regenerative ability, which is not only the response after traumatic injury, but also a key step during the life cycle of several syllid taxa. In these animals the posterior part of the body becomes an epitoke and is later detached as a distinct unit named stolon. Such a sexual reproductive mode is named schizogamy or stolonization. The prostomium and the proventricle, a modified foregut structure, have been proposed to have a control function during this process, though the concrete mechanisms behind it have never been elucidated. Results: By using different experimental set-ups, histology and immunohistochemistry combined with subsequent cLSM analyzes, we investigate and document the regeneration and stolonization in specimens of Typosyllis antoni that were amputated at different levels throughout the antero-posterior body axis. The removal of the anterior end including the proventricle implies an incomplete anterior regeneration as well as severe deviations from the usual reproductive pattern, i.e. accelerated stolonization, masculinization and the occurrence of aberrant stolons. The detailed anatomy of aberrant stolons is described. A histological study of the proventricle revealed no signs of glandular or secretory structures. The ventricle and the caeca are composed of glandular tissue but they are not involved in the reproductive and regenerative processes. Conclusions: As in other investigated syllids, the proventricle region has a significant role during stolonization and reproduction processes in Typosyllis antoni. When the proventricle region is absent, anterior and posterior regeneration are considerably deviated from the general patterns. However, proventricle ultrastructure does not show any glandular component, thereby questioning a direct involvement of this organ itself in the control of reproduction and regeneration. Our findings offer a comprehensive starting point for further studies of regeneration and reproductive control in syllids as well as annelids in general

Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida

<p>Abstract</p> <p>Background</p> <p>Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida.</p> <p>Results</p> <p>The first complete mitochondrial genome of a member of Sipuncula, <it>Sipunculus nudus</it>, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida <it>sensu lato</it>, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida.</p> <p>Conclusion</p> <p>The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.</p

The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata

Ramisyllis multicaudata is a member of Syllidae (Annelida, Errantia, Phyllodocida) with a remarkable branching body plan. Using a next-generation sequencing approach, the complete mitochondrial genomes of R. multicaudata and Trypanobia sp. are sequenced and analysed, representing the first ones from Syllidae. The gene order in these two syllids does not follow the order proposed as the putative ground pattern in Errantia. The phylogenetic relationships of R. multicaudata are discerned using a phylogenetic approach with the nuclear 18S and the mitochondrial 16S and cox1 genes. Ramisyllis multicaudata is the sister group of a clade containing Trypanobia species. Both genera, Ramisyllis and Trypanobia, together with Parahaplosyllis, Trypanosyllis, Eurysyllis, and Xenosyllis are located in a long branched clade. The long branches are explained by an accelerated mutational rate in the 18S rRNA gene. Using a phylogenetic backbone, we propose a scenario in which the postembryonic addition of segments that occurs in most syllids, their huge diversity of reproductive modes, and their ability to regenerate lost parts, in combination, have provided an evolutionary basis to develop a new branching body pattern as realised in Ramisyllis

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

<p>Abstract</p> <p>Background</p> <p>Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa.</p> <p>Results</p> <p>Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data.</p> <p>Conclusion</p> <p>We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.</p

Infection patterns and fitness effects of Rickettsia and Sodalis symbionts in the green lacewing Chrysoperla carnea

Endosymbionts are widely distributed in insects and can strongly affect their host ecology. The common green lacewing (Chrysoperla carnea) is a neuropteran insect which is widely used in biological pest control. However, their endosymbionts and their interactions with their hosts have not been very well studied. Therefore, we screened for endosymbionts in natural and laboratory populations of Ch. carnea using diagnostic PCR amplicons. We found the endosymbiont Rickettsia to be very common in all screened natural and laboratory populations, while a hitherto uncharacterized Sodalis strain was found only in laboratory populations. By establishing lacewing lines with no, single or co-infections of Sodalis and Rickettsia, we found a high vertical transmission rate for both endosymbionts (>89%). However, we were only able to estimate these numbers for co-infected lacewings. Sodalis negatively affected the reproductive success in single and co-infected Ch. carnea, while Rickettsia showed no effect. We hypothesize that the fitness costs accrued by Sodalis infections might be more tolerable in the laboratory than in natural populations, as the latter are also prone to fluctuating environmental conditions and natural enemies. The economic and ecological importance of lacewings in biological pest control warrants a more profound understanding of its biology, which might be influenced by symbionts