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.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community‐led open‐source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL.

The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cellfate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50 = 222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.F latworms belong to the superphylum Lophotrochozoa, a vast assembly of protostome invertebrates (1, 2) (Fig. 1A). The evolutionary relationships within this clade are poorly resolved and the specific position of flatworms is currently debated (3, 4). Flatworms have attracted scientific attention for centuries because of their astonishing regenerative capabilities (5, 6), as well as their ability to "degrow" in a controlled way when starved (7). As far back as the early 1900s, Thomas Morgan recognized the potential of flatworms and conducted a number of fascinating regeneration experiments on planarian flatworms before his focus shifted to Drosophila genetics (8).Macrostomum lignano is (Fig. 1B), a free-living, regenerating flatworm isolated from the coast of the Mediterranean Sea. M. lignano is an obligatorily cross-fertilizing simultaneous hermaphrodite (9) that belongs to Macrostomorpha, whereas the other often-studied freeliving flatworms and human parasitic flatworms all belong to clades that are potentially more derived (less ancestral) in comparison with Macrostomorpha (2) (Fig. 1C).Many flatworms can regenerate nearly their entire body or amputated organs. This regenerative capacity is thought to be attributable to the presence of somatic stem cells, termed neoblasts (10, 11). In Schmidtea mediterranea (planarian flatworm), even a single transplanted neoblast has the ability to rescue, regenerate, and change the genotype of a fatally irradiated worm (12). M. lignano can regenerate every tissue, with the exception of the head region containing the brain (13,14).Neoblasts in M. lignano ( Fig. 1 D and E), in contrast to most vertebrate somatic stem cells, are plentiful, making up about ...

This is an accepted manuscript of an article published as Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Fortunato, S., Adamski, M., Mendivil Ramos, O., Leininger, S., Liu, J., Ferrier, D. E. K. & Adamska, M. 30 Oct 2014 In : Nature. 514, p. 620-623 doi: 10.1038 Likelihood (ML) analyses (Fig. 1, Extended Data Fig. 1). 86Given the importance of this potential assignment, we performed further phylogenetic 87 analyses of these putative Cdx orthologues. In addition to the ELEKEF motif which is Cdx genes from other species in NJ, ML and Bayesian analyses (Extended Data Figs. 3-5). 95We have also investigated the genomic neighbourhood of SciCdx to help resolve the 96 identity of this homeobox gene ( Fig. 2 humans. One of these, SAR1A/B also has a conserved neighbouring relationship with the 100 ParaHox cluster in the cnidarian, Nematostella vectensis (Fig. 2a, b). Although these gene neighbour genes into two distinct groups in the Sycon genome to statistically significant 106 levels ( Fig. 2c-e 115We studied the expression of Antp-class genes in Sycon using a combination of in situ 116 hybridization with quantitative transcriptome analysis (Fig. 3, Supplementary note 3 117and Extended Data Figs 7-9). For all Antp-class genes, except SciHex, expression can be 118 detected in oocytes and during cleavage (Fig. 3a and Extended Data Fig. 7a-g). During of SciHmx is also markedly elevated in these cells (Fig. 3e). SciNKC and NKD are uniquely 124 and strongly expressed in the cruciform cells of more advanced (pre-inversion stage) 125 embryos ( Fig. 3f-g). SciNKA is additionally detected in macromeres of embryos and 126 larvae, and along with SciNKG and SciNKB domains, forms a set of adjacent stripes along 127 the larval anterior-posterior axis (Fig. 3h-p). This pattern is reminiscent of "striped" (Fig. 3b, Extended Data Fig. 9) in sub-populations 136 of cells in all three cell layers (Extended Data Fig. 7). The clear expression of SciCdx in 137 the inner cell mass during formation of the choanocyte chamber (Fig .3q) predominantly detected within and around the oscular sphincter (Fig. 3r-w). Methods 156Genome and transcriptome assemblies will be described in detail elsewhere (Adamski, 157 Leininger and Adamska, unpublished results). Briefly, the high quality draft genome 158 assembly of S. ciliatum was generated using two (360bp and 530bp) paired-end libraries 159 and several mate-pair libraries ranging from 2.0 to 9.0 kb and the preliminary draft At least two independent experiments were carried for each probe.