The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.This work was supported by the following grants: NHGRIU54HG003273 to R.A.G; EU Marie Curie ITN #215781 “Evonet” to M.A.; a Wellcome Trust Value in People (VIP) award to C.B. and Wellcome Trust graduate studentship WT089615MA to J.E.G; Marine rhythms of Life” of the University of Vienna, an FWF (http://www.fwf.ac.at/) START award (#AY0041321) and HFSP (http://www.hfsp.org/) research grant (#RGY0082/2010) to KT-­‐R; MFPL Vienna International PostDoctoral Program for Molecular Life Sciences (funded by Austrian Ministry of Science and Research and City of Vienna, Cultural Department -­‐Science and Research to T.K; Direct Grant (4053034) of the Chinese University of Hong Kong to J.H.L.H.; NHGRI HG004164 to G.M.; Danish Research Agency (FNU), Carlsberg Foundation, and Lundbeck Foundation to C.J.P.G.; U.S. National Institutes of Health R01AI55624 to J.H.W.; Royal Society University Research fellowship to F.M.J.; P.D.E. was supported by the BBSRC via the Babraham Institute;This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pbio.100200

The large-scale structure of the halo of the Andromeda galaxy II. Hierarchical structure in the Pan-Andromeda Archaeological Survey

The Pan-Andromeda Archaeological Survey is a survey of $>400$ square degrees centered on the Andromeda (M31) and Triangulum (M33) galaxies that has provided the most extensive panorama of a $L_\star$ galaxy group to large projected galactocentric radii. Here, we collate and summarise the current status of our knowledge of the substructures in the stellar halo of M31, and discuss connections between these features. We estimate that the 13 most distinctive substructures were produced by at least 5 different accretion events, all in the last 3 or 4 Gyrs. We suggest that a few of the substructures furthest from M31 may be shells from a single accretion event. We calculate the luminosities of some prominent substructures for which previous estimates were not available, and we estimate the stellar mass budget of the outer halo of M31. We revisit the problem of quantifying the properties of a highly structured dataset; specifically, we use the OPTICS clustering algorithm to quantify the hierarchical structure of M31's stellar halo, and identify three new faint structures. M31's halo, in projection, appears to be dominated by two `mega-structures', that can be considered as the two most significant branches of a merger tree produced by breaking M31's stellar halo into smaller and smaller structures based on the stellar spatial clustering. We conclude that OPTICS is a powerful algorithm that could be used in any astronomical application involving the hierarchical clustering of points. The publication of this article coincides with the public release of all PAndAS data products.Comment: Accepted for publication in the Astrophysical Journal. 51 pages, 24 figures, 5 tables. Some figures have degraded resolution. All PAndAS data products are available via the CADC at http://www.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/en/community/pandas/query.html where you can also find a version of the paper with full resolution figure

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA

The study of bacterial populations using whole genome sequencing is of considerable scientific and clinical interest. However, obtaining bacterial genomic information is not always trivial: the target bacteria may be difficult-to-culture or uncultured, and may be found within samples containing complex mixtures of other contaminating microbes and/or host cells, from which it is very difficult to derive robust sequencing data. Here we describe our procedure to generate sufficient target genomic DNA for whole bacterial genome sequencing, from clinical samples of the difficult-to-culture, obligate intracellular pathogen Chlamydia trachomatis, without the need for culture. Our protocol combines Immunomagnetic Separation (IMS) for targeted bacterial enrichment with Multiple Displacement Amplification (MDA) for whole genome amplification, followed by high throughput sequencing. Compared to other techniques which might be used to generate such data, IMS-MDA is an inexpensive, low-technology and highly transferable process, which provides amplified genomic DNA for sequencing from target bacteria in under 5 hours, with little hands-on time