Supplementary MaterialsSupplementary Info Supplementary Numbers 1-28, Supplementary Tables 1-31, Supplementary Notes 1-4 and Supplementary References ncomms9301-s1. the fossil record, Darwin first described lingulid brachiopods as living fossils,’ because PRI-724 biological activity their shell morphology offers changed little because the Silurian1. Predicated on molecular phylogeny, brachiopods comprise three subphyla, Linguliformea, Craniiformea and Rhynchonelliformea2. The Linguliformea, like the extant genus, DNAJC15 may have utilized calcium phosphate, as the phosphorus focus in seawater was saturated in the Cambrian7. Actually, some Cambrian PRI-724 biological activity arthropods, tommottids and different additional problematica also utilized calcium phosphate for his or her exoskeletons, whereas additional extant invertebrates such as for example corals, molluscs and echinoderms make use of calcium carbonate. Research of mollusc mantle transcriptomes and shell proteomes claim that gene models responsible for development of calcium carbonate-centered biominerals such as for example calcite or aragonite possess evolved rapidly. As a result, mineral homology among molluscs could basically represent parallel development8. As opposed to mollusc shells and additional invertebrate calcified cells, shells comprises calcium phosphate, laminated, versatile and abundant with organic components1. Despite their palaeontological importance, the evolutionary origin of shells continues to be unclear. Even more interestingly, although can be a protostome, its embryogenesis exhibits radial cleavage and enterocoelic coelom formation, normal of basal deuterostomes9. Despite such exclusive features, the phylogeny of brachiopods can be under debate. Prior to the 1980s, brachiopods had been categorized as deuterostomes, predicated on their setting of development. They had been grouped within protostomes pursuing an evaluation of 18S ribosomal RNAs10. This classification was additional backed by an evaluation of genes in brachiopods and priapulids11. Nevertheless, the phylogenetic placement of brachiopods continues to be controversial, regardless of intensive palaeontological12 and molecular phylogenetic research (Supplementary Note 2). For instance, whether brachiopods are monophyletic or polyphyletic2,13 and whether Brachiopoda can be near Phoronida, Nemertea, Mollusca, Annelida or additional lophotrochozoan phyla, continues to be to become resolved14,15,16. Here we present the first brachiopod genome of the lingulid, Our whole-genome phylogenetic analyses support a close relationship between and molluscs. Unexpectedly, we find that contrary to its reputation as a living fossil,’ the genome has been actively evolving, with a disorganized Hox cluster and recently expanded gene families. In addition, we show that although shares shell formation-related genes and mechanisms with molluscs, such as chitin synthase (CHS) and bone morphogenetic protein (BMP) signalling, it uses several domain combinations to produce lineage-specific shell matrix collagens, alanine-rich fibres and novel shell matrix proteins (SMPs). We propose that gene family expansion, domain shuffling and co-option of genes appear to comprise the genomic basis of (Fig. 1aCi) with 226-fold coverage using four next-generation sequencers (that is, Roche 454 GS FLX+, Illumina MiSeq and HiSeq 2500, and PacBio RS II). This effort yielded an assembly with a scaffold N50 size of 294?kb, comparable to those of other lophotrochozoan genomes17,18,19 (Supplementary Note 1, Supplementary Figs 1C3 and Supplementary Tables 1C3). The genome exhibits comparatively high heterozygosity (1.6%) and a low level of repetitive sequences (22.2%) (Supplementary Table 16). Together with a large quantity of transcriptome data from adult tissues and embryonic stages (Supplementary Fig. 4 and Supplementary Table 4), we estimated that contains 34,105 protein-coding gene models, 91% of which are supported by transcriptomes. The mean size of the genes is 6.7?kb with an average of 6.6 introns per gene. These numbers are closer to those of the sea snail, genes are most similar to mollusc genes, but only 12% to annelids, whereas 21% of PRI-724 biological activity the genes show no similarity to any known sequence, suggesting that these are unique to.