Recently we published a paper using genome skimming to generate markers for phylogenetic analysis of glycerid annelids (Richter et al. 2015). We are interested in this group, as we are also working on the evolution of venom system of these annelids (e.g. von Reumont et al. 2014). Genome skimming basically means low coverage genome sequencing using NGS techniques. E.g., in the case of a coverage of 5x, it is expected that every part of the genome is (on average) sequenced 5 times. This is far from enough to assemble the nuclear genome. However, sequences which are present in higher copy number within the cell will have also a higher coverage than the average. E.g., we can easily expect 100 or more mitochondria per cell and consequently they will be also represented in a much higher coverage after sequencing. Using this method, complete mitochondria can be reconstructed quite easily from shallowly sequenced nuclear genomes. So we did this for 19 glycerid specimens and one outgroup (Goniadidae). After assembling the data, we were able to recover complete mitochondria for 14 species. For the other cases, several large contigs containing the mitochondrial genes could be found. Moreover, we also retrieved the ribosomal cluster (18S, ITS1, 5.8S, ITS2, 28S), which is also presented in many (tandemly repeated) copies per genome. Using the sequence data, we were able to reconstruct a fairly supported phylogeny of glycerids (Fig. 1), which will help us in the future to understand venom evolution in this group. Continue reading Mitogenomics is not dead… an example from glycerid annelids
In 2010 when I still had my lab in Leipzig (Germany) we started noticing that a species of syllid annelids can be frequently found in our warm water aquariums. As we were working on annelid phylogenomics, we were quite happy having easy access to these animals in Leipzig, a place that is at least several hundreds kilometers away from any access to the sea. We sequenced the transcriptome, but couldn’t identify the animal (neither by morphology nor barcoding) to the species level. The following years, the population remained stable. Ovbviously they were reproducing quite well and we usually had a peak of individuals in late spring. We realized that this so far undescribed species has the potential to be our lab rat for different research questions, e.g., on syllid reproduction and regeneration. Consequently, we decided to formally describe this animal (Aguado et al. 2014). Even though we could not indicate its native geographical range of occurrence, we described it in such detail that it should be recognized when found outside our aquariums. In honor of the newborn son (Anton Helm) of one member of our research team we named the species Typosyllis antoni (Fig. 1). Continue reading A worm called Anton
Inspired by a blog post of Christopher Mah I started to compile a list of polychaetologists who are active on twitter. Polychaetologists are researchers interested in polychaete biology, taxonomy and evolution. Polychaetes are those (mostly marine) Annelida which are not clitellates. Phylogenetic analyses convincingly support that also echiurans, sipunculans, siboglinids and myzostomids are part of Annelida. We (Anne Weigert and myself) reviewed the current state of annelid phylogeny here. I did not include clitellatetologists (is this an even existing term?), as I do not have a good overview whats going on in research in this field and who is on twitter. I broadly considered everybody who could show up at the International Polychaete Conference (IPC) as potential polychaetologist. This meeting takes place every three years. The last one ended just in August in Cardiff (check for talks and twitter storify here), the next one will be in Long Beach, Los Angeles in 2019. Moreover, I included some tweeting scientists who from time to time end up working with polychaetes. I also tried to sort the twitter accounts into different research fields. But this is mostly to put some order and I am aware that many of them could easily fit in two or more of the categories. It is also likely that I overlooked several tweeting polychaetologists. Just leave a comment in case I forgot you (or somebody you know) – or if you are super unhappy ending in the wrong category or on the list at all. Continue reading A list of tweeting polychaetologists
After spending one and a half year on twitter (https://twitter.com/C_Blei) I decided that its finally time to at least arrange a blog for posting comments, news or random thoughts which need more than 140 characters. I will try to stay away from rants… Instead, you will find here from time to time some news about my research, other peoples research or whatever thoughts I think I should share with everybody. Blogs will usually focus on evolutionary biology and genomics of invertebrates (mostly Annelida and Hymenoptera) and bacterial endosymbionts (Wolbachia and friends!). Phylogenetic and genomic methods will be also of interest. So, stay tuned for updates at this place. For those who are curious, but afraid to google it, Bembecinus is a genus of apoid wasps (Hymenoptera, Aculeata).