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Abstract: The clam Meretrix meretrix is an important commercial bivalve distributed in the coastal areas of South and Southeast Asia. In this study, marker–trait association analyses were performed based on the stock materials of M. meretrix with different vibrio-resistance profile obtained by selective breeding. Forty-eight EST-SSR markers were screened and 27 polymorphic SSRs of them were genotyped in the clam stocks with different resistance to Vibrio parahaemolyticus (11-R and 11-S) and to Vibrio harveyi (09-R and 09-C). Allele frequency distributions of the SSRs among different stocks were compared using Pearson's Chi-square test, and three functional EST-SSR markers (MM959, MM4765 and MM8364) were found to be associated with vibrio-resistance trait. The 140-bp allele of MM959 and 128-bp allele of MM4765 had significantly higher frequencies in resistant groups (11-R and 09-R) than in susceptive/control groups (11-S and 09-C) (P < 0.01), which suggested that the clams carrying these two alleles have stronger resistance against vibrio. Clam individuals of 11-S were divided into three subgroups based on the survival time post-challenge, and the multi-dimensional scaling (MDS) analysis showed that clusters generated by genetic similarity revealed by the three SSR markers were consistent with the three subgroups distinctions. The putative functions of contig959, contig4765 and contig8364 also suggested that the three SSR-involved genes might play important roles in immunity of M. meretrix. All these results supported that EST-SSR markers MM959, MM4765 and MM8364 were associated with vibrio-resistance and would be useful for marker-assisted selection (MAS) in M. meretrix genetic breeding. [Copyright &y& Elsevier]

Aim Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. Location Indo-Pacific, Red Sea, Arabian/Persian Gulf. Methods Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. Results Between five and eight genetically distinct lineages comparable to species were identified with minimal or no hybridization between them. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (about seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. Main conclusions The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the identification of Pocillopora species for future ecological and experimental work should rely on genetic characters that will improve research and aid in conservation strategies for these and other reef-building corals, including the detection of real and mistaken endemic populations. [ABSTRACT FROM AUTHOR]

Histocompatibility is the basis by which multicellular organisms of the same species distinguish self from nonself. Relatively little is known about the mechanisms underlying histocompatibility reactions in lower organisms. Botryllus schlössen is a colonial urochordate, a sister group of vertebrates, that exhibits a genetically determined natural transplantation reaction, whereby self-recognition between colonies leads to formation of parabionts with a common vasculature, whereas rejection occurs between incompatible colonies. Using genetically defined lines, whole-transcriptome sequencing, and genomics, we identified a single gene that encodes self-nonself and determines "graft" outcomes in this organism. This gene is significantly up-regulated in colonies poised to undergo fusion and/or rejection, is highly expressed in the vasculature, and is functionally linked to histocompatibility outcomes. These findings establish a platform for advancing the science of allorecognition. [ABSTRACT FROM AUTHOR]

Abstract: Ubiquitin-conjugating enzymes (UBE2s or E2s) are characterized by the presence of a highly conserved ubiquitin-conjugating (UBC) domain, which predominantly determines the type of ubiquitin chains and directly controls the cellular fate of the substrate. In this study, an E2 homolog was identified and functionally characterized in abalone, which we named ab-UBE2D. The full-length cDNA consists of 1005 bp with an ORF encoding a protein of 147 amino acids. The deduced amino acid sequence shows ab-UBE2D shares conserved UBC domain with other E2 proteins and belongs to class I E2 enzyme family, which are further confirmed by phylogenetic tree analysis. Real-time PCR and western blot analyses showed that ab-UBE2D was ubiquitously expressed in abalone and the expression level of ab-UBE2d was significantly induced by LPS and Poly (I:C). Immunofluorescence microscopy staining demonstrated that native ab-UBE2D was mainly distributed in the cytoplast. Ubiquitination assay showed that ab-UBE2D had ubiquitin conjugating activity to form the enzyme-(Ub)n conjugates. Taken together, these results strongly suggest that ab-UBE2D is an E2 homolog and it may be involved in the immune response of abalone, Haliotis diversicolor supertexta. [Copyright &y& Elsevier]

The Drosophila protein Turtle and the vertebrate proteins immunoglobulin superfamily (IgSF), member 9 (IGSF9/Dasm1) and IGSF9B are members of an evolutionarily ancient protein family. A bioinformatics analysis of the protein family revealed that invertebrates contain only a single IGSF9 family gene, whereas vertebrates contain two to four genes. In cnidarians, the gene appears to encode a secreted protein, but transmembrane isoforms of the protein have also evolved, and in many species, alternative splicing facilitates the expression of both transmembrane and secreted isoforms. In most species, the longest isoforms of the proteins have the same general organization as the neural cell adhesion molecule family of cell adhesion molecule proteins, and like this family of proteins, IGSF9 family members are expressed in the nervous system. A review of the literature revealed that Drosophila Turtle facilitates homophilic cell adhesion. Moreover, IGSF9 family proteins have been implicated in the outgrowth and branching of neurites, axon guidance, synapse maturation, self-avoidance, and tiling. However, despite the few published studies on IGSF9 family proteins, reports on the functions of both Turtle and mammalian IGSF9 proteins are contradictory. [ABSTRACT FROM AUTHOR]

Genetic diversity has emerged as an important source of variation in the ecological properties of populations, but there are few studies of genetic diversity effects on colonisation processes. This relative scarcity of studies is surprising given the influence of colonisation on species coexistence, invasion, and population persistence. Here, we manipulated relatedness in experimental populations of colonising larvae in four sessile marine invertebrates. We then examined the influence of coloniser relatedness on the number, spatial arrangement and phenotype of colonisers following permanent settlement. Overall, relatedness influenced colonisation in all four species, but the effects of relatedness on colonisation differed among species. The variable responses of species to manipulations of relatedness likely reflect differences in intensity of inter- and intra-specific competition among adults, as well as the differential consequences of larval behaviours for each species. Relatedness appears to play an underappreciated role in the colonisation process, and we recommend that future studies of genetic diversity effects consider not only adult stages - the focus of most work to date - but also the importance of genetic diversity in early life history stages. [ABSTRACT FROM AUTHOR]

The analysis of genetic structure is an important tool for the management of harvested and threatened species. Individual clustering methods and tests of Isolation by Distance (IBD) are currently used in this context. They have been applied to the red coral Corallium rubrum but some questions remained due to contrasted results among studies and limits in their interpretations. In this study, we used simulated and empirical data for a better understanding of the genetic structure in this species. We tested the impact of IBD between demes, sampling scheme and of clustering methods (BAPS, STRUCTURE or DAPC) on the inferred structure. By matching simulated scenarios to the empirical data, we first confirm that the genetic structure of the red coral is characterized by a combination between IBD and weak genetic breaks. Then, we demonstrate how the sampling scheme influences the results of the clustering methods. We also reveal the contrasted efficiencies of these methods to recover real demes or groups of demes in a context of IBD. Overall, our study underline the interest of comparing the results of different clustering methods and of using simulated data for interpreting empirical genetical data. [ABSTRACT FROM AUTHOR]

How morphological diversity arises is a key question in evolutionary developmental biology. As a long-term approach to address this question, we are developing the water bear Hypsibius dujardini (Phylum Tardigrada) as a model system. We expect that using a close relative of two well-studied models, Drosophila (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda), will facilitate identifying genetic pathways relevant to understanding the evolution of development. Tardigrades are also valuable research subjects for investigating how organisms and biological materials can survive extreme conditions. Methods to disrupt gene activity are essential to each of these efforts, but no such method yet exists for the Phylum Tardigrada. We developed a protocol to disrupt tardigrade gene functions by double-stranded RNA-mediated RNA interference (RNAi). We showed that targeting tardigrade homologs of essential developmental genes by RNAi produced embryonic lethality, whereas targeting green fluorescent protein did not. Disruption of gene functions appears to be relatively specific by two criteria: targeting distinct genes resulted in distinct phenotypes that were consistent with predicted gene functions and by RT-PCR, RNAi reduced the level of a target mRNA and not a control mRNA. These studies represent the first evidence that gene functions can be disrupted by RNAi in the phylum Tardigrada. Our results form a platform for dissecting tardigrade gene functions for understanding the evolution of developmental mechanisms and survival in extreme environments. [ABSTRACT FROM AUTHOR]

A large number of invasive marine invertebrates are recognized from Elkhorn Slough (ES), California. One of these species in the slough is treated as Hymeniacidon sinapium (Family Halichondriidae) but its species identity is in doubt pending molecular confirmation. The purpose of this investigation was to confirm the presence of H. sinapium in ES, determine its distribution in the slough, and compare its genetic diversity to others in California and worldwide. To address these goals, 23 specimens of Hymeniacidon were analyzed using DNA sequences of the nuclear rDNA internal transcribed spacers (ITS1 + ITS2) and the 5.8S exon. The sequences were compared against those of H. sinapium from: San Diego and Tomales Bay in California; Japan; and South Korea. All ES sequences were found to be nearly identical to the other H. sinapium sequences, differing by only 1-3 nucleotides. ES specimens displayed five unique genotypes: three showed intragenomic polymorphisms (IGPs) in the ITS1 region (positions 155, 181, and 195). These data conclusively document the presence of H. sinapium in ES as well as define the species to a relatively narrow portion of its eastern shores (~4 km long). Since the genetic diversity of H. sinapium in ES is higher than that reported worldwide, its presence in ES is likely the result of multiple introductions. One of the IGPs in ES was found to be the most abundant and was widely distributed in the slough: an indication that it may be spreading. [ABSTRACT FROM AUTHOR]

Abstract: Corals exhibit circadian behaviors, but little is known about the molecular mechanisms underlying the regulation of these behaviors. We surveyed the recently decoded genome of the coral, Acropora digitifera, for photoreceptor and circadian genes, using molecular phylogenetic analyses. Our search for photoreceptor genes yielded seven opsin and three cryptochrome genes. Two genes from each family likely underwent tandem duplication in the coral lineage. We also found the following A. digitifera orthologs to Drosophila and mammalian circadian clock genes: four clock, one bmal/cycle, three pdp1-like, one creb/atf, one sgg/zw3, two ck2alpha, one dco (csnk1d/cnsk1e), one slim/BTRC, and one grinl. No vrille, rev-ervα/nr1d1, bhlh2, vpac2, adcyap1, or adcyaplr1 orthologs were found. Intriguingly, in spite of an extensive survey, we also failed to find homologs of period and timeless, although we did find one timeout gene. In addition, the coral genes were compared to orthologous genes in the sea anemone, Nematostella vectensis. Thus, the coral and sea anemone genomes share a similar repertoire of circadian clock genes, although A. digitifera contains more clock genes and fewer photoreceptor genes than N. vectensis. This suggests that the circadian clock system was established in a common ancestor of corals and sea anemones, and was diversified by tandem gene duplications and the loss of paralogous genes in each lineage. It will be interesting to determine how the coral circadian clock functions without period. [Copyright &y& Elsevier]

Human-made structures are increasingly built in marine coastal habitats for a variety of purposes. Offshore oil and gas production platforms are among the largest examples. Yet, biological effects of these increasing density artificial substrata are under evaluated. The objective of our study is to investigate the possible role of offshore platforms in modifying the genetic composition of populations of natural rocky shores species. The serpulid Pomatoceros triqueter was used as a model, and genetic variation was assessed using a 419 bp fragment of the mtDNA COI gene in samples collected on eleven offshore gas platforms, on one coastal buoy on the sandy shore and in four sites located on natural rocky shores in the Adriatic Sea. Deep phylogenetic lineages were uncovered over all samples. Nucleotide diversity and mean number of pairwise differences among haplotypes were significantly smaller in offshore platform samples compared to rocky shores samples. No significant genetic structure was observed over all samples. We found direct evidence of lower genetic diversity on platforms confirming that, although artificial structures attract and support species typical of hard bottoms, they are not analogues of natural rocky habitats. [ABSTRACT FROM AUTHOR]

Microsatellites are simple sequence repeats with a high degree of polymorphism in the genome; they are used as DNA markers in many molecular genetic studies. Using traditional methods such as the magnetic beads enrichment method, only a few microsatellite markers have been isolated from the Chinese mitten crab Eriocheir sinensis, as the crab genome sequence information is unavailable. Here, we have identified a large number of microsatellites from the Chinese mitten crab by taking advantage of Solexa genomic surveying. A total of 141,737 SSR (simple sequence repeats) motifs were identified via analysis of 883 Mb of the crab genomic DNA information, including mono-, di-, tri-, tetra-, penta- and hexa-nucleotide repeat motifs. The number of di-nucleotide repeat motifs was 82,979, making this the most abundant type of repeat motif (58.54%); the second most abundant were the tri-nucleotide repeats (42,657, 30.11%). Among di-nucleotide repeats, the most frequent repeats were AC motifs, accounting for 67.55% of the total number. AGG motifs were the most frequent (59.32%) of the tri-nucleotide motifs. A total of 15,125 microsatellite loci had a flanking sequence suitable for setting the primer of a polymerase chain reaction (PCR). To verify the identified SSRs, a subset of 100 primer pairs was randomly selected for PCR. Eighty two primer sets (82%) produced strong PCR products matching expected sizes, and 78% were polymorphic. In an analysis of 30 wild individuals from the Yangtze River with 20 primer sets, the number of alleles per locus ranged from 2-14 and the mean allelic richness was 7.4. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in four of the 20 microsatellite loci after sequential Bonferroni corrections. This method is cost- and time-effective in comparison to traditional approaches for the isolation of microsatellites. [ABSTRACT FROM AUTHOR]

This study investigates the genetic structure and phylogeography of a broadcast spawning bivalve mollusc, Pinctada maxima, throughout the Indo- West Pacific and northern Australia. DNA sequence variation of the mitochondrial cytochrome oxidase subunit I ( COI) gene was analysed in 367 individuals sampled from nine populations across the Indo- West Pacific. Hierarchical AMOVA indicated strong genetic structuring amongst populations (ΦST = 0.372, P < 0.001); however, sequence divergence between the 47 haplotypes detected was low (maximum 1.8% difference) and no deep phylogenetic divergence was observed. Results suggest the presence of genetic barriers isolating populations of the South China Sea and central Indonesian regions, which, in turn, show patterns of historical separation from northern Australian regions. In P. maxima, historical vicariance during Pleistocene low sea levels is likely to have restricted planktonic larval transport, causing genetic differentiation amongst populations. However, low genetic differentiation is observed where strong ocean currents are present and is most likely due to contemporary larval transport along these pathways. Geographical association with haplotype distributions may indicate signs of early lineage sorting arising from historical population separations, yet an absence of divergent phylogenetic clades related to geography could be the consequence of periodic pulses of high genetic exchange. We compare our results with previous microsatellite DNA analysis of these P. maxima populations, and discuss implications for future conservation management of this species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••-••. [ABSTRACT FROM AUTHOR]

Abstract: Madrepora is one of the most ecologically important genera of reef-building scleractinians in the deep sea, occurring from tropical to high-latitude regions. Despite this, the taxonomic affinities and relationships within the genus Madrepora remain unclear. To clarify these issues, we sequenced the mitochondrial (mt) genome of the most widespread Madrepora species, M. oculata, and compared this with data for other scleractinians. The architecture of the M. oculata mt genome was very similar to that of other scleractinians, except for a novel gene rearrangement affecting only cox2 and cox3. This pattern of gene organization was common to four geographically distinct M. oculata individuals as well as the congeneric species M. minutiseptum, but was not shared by other genera that are closely related on the basis of cox1 sequence analysis nor other oculinids, suggesting that it might be unique to Madrepora. [Copyright &y& Elsevier]

Iso-enzymatic polymorphism analysis was carried out on Tunisian populations of Porcellionides pruinosus to clarify their confused taxonomic status, previously revealed by reproductive and morphological approaches. Seventeen allozyme loci were studied, using horizontal starch gel electrophoresis, in 230 adult specimens belonging to nine populations of P. pruinosus located in north, central and south Tunisia, to assess the levels of their intra-genetic and inter-genetic diversity, and to analyse their genetic structure. Our results indicate a low genetic variability with a polymorphism ratio ranging from 29.4% in Tabarka to 47.1% in the Garat Nâam and Raccada populations, and the mean number of alleles per locus was estimated at 1.51 ± 0.15. The direct-count of heterozygosity ranged between 8.1% and 15%. Substantial estimates of demic structuring were found at the total population (FST = 0.198), with a generalized and significant heterozygote deficiency detected in every population (with a mean value for all populations of FIS = 0.372). Genetic distances between the studied populations were low, indicating that they belong to the same species. Nevertheless, the genetic analyses showed the divergence of the population of Tabarka from all the other studied populations, with the lowest mean gene flow, 0.58, and the highest mean genetic distance, (0.182) obtained also by the morphological and reproductive approaches. [ABSTRACT FROM PUBLISHER]

The structures of some cryptogenes of previously unstudied species of homoxenous trypanosomatids that belong to different phylogenetic groups has been analyzed. New examples of the editing domain length reduction for A6 and COIII were found. A comparative analysis of the sequences allowed us to divide the cryptogenes into three groups (patterns) according to not only the evolutionary variations in the length of the edited domain, but also the degree of conservation of the nucleotide sequence. The potential factors that determine variants of the cryptogene structure are discussed. In addition, the alternative editing of the rps12 transcript of Wallaceina sp. Wsd has been demonstrated. [ABSTRACT FROM AUTHOR]

The genus Nais is a group of oligochaetous clitellates, common in eutrophic freshwater habitats. About 30 species are described. Species identification is based primarily on chaetal characters, which are often subtle, inconsistent, and even overlapping between nominal species. We investigated the correlation between genetic variation and chaetal morphology in this genus. Eighty-one individuals from Europe, North America, and China were included in the study. Seventy-five of these were preserved as vouchers. They were scrutinized with regard to chaetal morphology, and ten different morphotypes were identified. Three molecular markers, two mitochondrial (the COI gene and 16S rDNA) and one nuclear (the ITS region), were used to establish the genetic lineages in the material. Genetic variation was found to be largely congruent with chaetal character patterns. However, at least nine separately evolving lineages (all supported by mitochondrial as well as nuclear data) correspond to at most six nominal species. Four morphotypes/lineages are recognized as Nais barbata, Nais christinae, Nais elinguis, and Nais stolci, respectively, whereas five, or possibly more, lineages represent a morphological continuum covering the variation of the Nais communis/variabilis complex. Thus, cryptic speciation is revealed. Our results indicate that a taxonomic revision of the genus will be needed in the future. [ABSTRACT FROM AUTHOR]

Both the core JAK-STAT pathway components and their in vivo roles have been widely conserved between vertebrates and invertebrate models such as Drosophila melanogaster. Misregulation of JAK-STAT pathway activity has also been identified as a key factor in the development of multiple human malignancies. Recently, whole genome RNA interference (RNAi) screens in cultured Drosophila cells have identified both positively and negatively acting JAK-STAT pathway regulators. Here, we describe the analysis of 73 human genes representing homologs of 56 Drosophila genes originally identified by genome-wide RNAi screening as regulators of JAK-STAT signaling. Using assays for human STAT1 and STAT3 protein levels and phosphorylation status, as well as assays measuring the expression of endogenous STAT1 and STAT3 transcriptional targets, we have tested siRNAs targeting these 73 human genes and have identified potential JAK-STAT pathway regulatory roles in 69 (95%) of these. The genes identified represent a wide range of human JAK-STAT pathway regulators and include genes not previously known to modulate this signaling cascade. These results underline the value of model system based approaches for the identification of pathway regulators and have led to the identification of loci whose misregulation may ultimately be implicated in JAK-STAT pathway-mediated human disease. [ABSTRACT FROM AUTHOR]

Pax genes are a group of critical developmental transcriptional regulators in both invertebrates and vertebrates, characterized by the presence of a paired DNA-binding domain. Pax proteins also often contain an octapeptide motif and a C-terminal homeodomain. The genome of Nasonia vitripennis (Hymenoptera) has recently become available, and analysis of this genome alongside Apis mellifera allowed us to contribute to the phylogeny of this gene family in insects. Nasonia, a parasitic wasp, has independently evolved a similar mode of development to that of the well-studied Drosophila, making it an excellent model system for comparative studies of developmental gene networks. We report the characterization of the seven Nasonia Pax genes. We describe their genomic organization, and the embryonic expression of three of them, and uncover wider conservation of the octapeptide motif than previously described. [ABSTRACT FROM AUTHOR]

The complete mitogenome sequences of the intestinal flukeFasciolopsis buskiare presented for the first time in this study. It is 14,119 bp long and is thus the shortest trematode mitochondrial genome sequenced to date. TheF. buskimtDNA genome has a close resemblance withF. hepaticaand has a similar gene order tallying with that of other trematodes. The overall base composition ofF. buskimitogenome is 17.89% for A, 9.16% for C, 27.59% for G and 45.36% for T, and has a GC content of 36.75%. The assembled mitogenome (GenBank accession number KX449331) consists of 12 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNA genes. The mtDNA for the intestinal fluke reported herein would help investigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data. [ABSTRACT FROM PUBLISHER]

Complete mitochondrial genome sequence of the giant mud wormParaleonnates uschakovi(Polychaeta: Nereididae) was determined in this study for the first time. The mitogenome ofP. uschakoviis 15,540 bp in length. It has 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a non-coding region. Mitogenome analysis ofP. uschakovishowed inversion in the positions of three tRNAs compared to the mitogenome sequences ofPerinereis aibuhitensis,P. nuntiaandPlatynereis dumerilii. The phylogenetic position ofP. uschakovicompared to 15 selected polychaetes was investigated.P. uschakoviwas grouped into the family of Nereididae. It is closely related to the clade containingTylorrhynchus heterochaetusandNamalycastis abiuma. [ABSTRACT FROM PUBLISHER]

In this study, we found out the complete mitochondrial genome ofHalichondria(Halichondria) sp., a common demosponge in China. This is the first complete mitochondrial report on the genusHalichondria. The mitochondrial genome ofHalichondria(Halichondria) sp. is 20 746 bp in length, with 14 protein-coding genes, two rRNA genes and 25 tRNA genes. When compared with the complete mitochondrial genome ofHymeniacidon sinapium, our phylogenetic result suggested thatHalichondria(Halichondria) sp. converged well according to morphological result. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome ofTethyasp. was studied. This is the second complete mitochondrial report on the family Tethyidae. The mitochondrial genome ofTethyasp. is 20,582 bp in length, containing 14 protein-coding genes and 25 tRNA genes, with 2 rRNA genes. Our phylogenetic result suggested thatTethyasp. converged well withTethya actinia, which further verified the morphological result. We anticipate our study to shed light on future molecular studies of demosponges. [ABSTRACT FROM PUBLISHER]

In the past decade, the planarian has become an increasingly tractable invertebrate model for the investigation of regeneration and stem cell biology. Application of a variety of techniques and development of genomic reagents in this system have enabled exploration of the molecular mechanisms by which pluripotent somatic stem cells called neoblasts replenish, repair, and regenerate planarian tissues and organs. Recent investigations have implicated evolutionarily conserved signaling pathways in the re-establishment of anterior–posterior (A–P), dorsal–ventral (D–V), and medial–lateral (M–L) polarity after injury. These studies have significantly advanced our understanding of early events during planarian regeneration and have raised new questions about the mechanisms of stem cell-based tissue repair and renewal. [Copyright &y& Elsevier]

Abstract: Hedgehog signaling is an important component of cell–cell communication during bilaterian development, and abnormal Hedgehog signaling contributes to disease and birth defects. Hedgehog genes are composed of a ligand (“hedge”) domain and an autocatalytic intein (“hog”) domain. Hedgehog (hh) ligands bind to a conserved set of receptors and activate downstream signal transduction pathways terminating with Gli/Ci transcription factors. We have identified five intein-containing genes in the anthozoan cnidarian Nematostella vectensis, two of which (NvHh1 and NvHh2) contain definitive hedgehog ligand domains, suggesting that to date, cnidarians are the earliest branching metazoan phylum to possess definitive Hh orthologs. Expression analysis of NvHh1 and NvHh2, the receptor NvPatched, and a downstream transcription factor NvGli (a Gli3/Ci ortholog) indicate that these genes may have conserved roles in planar and trans-epithelial signaling during gut and germline development, while the three remaining intein-containing genes (NvHint1,2,3) are expressed in a cell-type-specific manner in putative neural precursors. Metazoan intein-containing genes that lack a hh ligand domain have previously only been identified within nematodes. However, we have identified intein-containing genes from both Nematostella and in two newly annotated lophotrochozoan genomes. Phylogenetic analyses suggest that while nematode inteins may be derived from an ancestral true hedgehog gene, the newly identified cnidarian and lophotrochozoan inteins may be orthologous, suggesting that both true hedgehog and hint genes may have been present in the cnidarian-bilaterian ancestor. Genomic surveys of N. vectensis suggest that most of the components of both protostome and deuterostome Hh signaling pathways are present in anthozoans and that some appear to have been lost in ecdysozoan lineages. Cnidarians possess many bilaterian cell–cell signaling pathways (Wnt, TGFβ, FGF, and Hh) that appear to act in concert to pattern tissues along the oral–aboral axis of the polyp. Cnidarians represent a diverse group of animals with a predominantly epithelial body plan, and perhaps selective pressures to pattern epithelia resulted in the ontogeny of the hedgehog pathway in the common ancestor of the Cnidaria and Bilateria. [Copyright &y& Elsevier]

The fibroblast growth factor (FGF) signal transduction pathway serves as one of the key regulators of early metazoan development, displaying conserved roles in the specification of endodermal, mesodermal, and neural fates during vertebrate development. FGF signals also regulate gastrulation, in part, by triggering epithelial to mesenchymal transitions in embryos of both vertebrates and invertebrates. Thus, FGF signals coordinate gastrulation movements across many different phyla. To help understand the breadth of FGF signaling deployment across the animal kingdom, we have examined the presence and expression of genes encoding FGF pathway components in the anthozoan cnidarian Nematostella vectensis. We isolated three FGF ligands ( NvFGF8A, NvFGF8B, and NvFGF1A), two FGF receptors ( NvFGFRa and NvFGFRb), and two orthologs of vertebrate FGF responsive genes, Sprouty ( NvSprouty), an inhibitor of FGF signaling, and Churchill ( NvChurchill), a Zn finger transcription factor. We found these FGF ligands, receptors, and response gene expressed asymmetrically along the oral/aboral axis during gastrulation and in a developing chemosensory structure of planula stages known as the apical tuft. These results suggest a conserved role for FGF signaling molecules in coordinating both gastrulation and neural induction that predates the Cambrian explosion and the origins of the Bilateria. [ABSTRACT FROM AUTHOR]

POU genes play a prominent role in the nervous system differentiation of several organism models, and in particular, they are involved in the differentiation of sensory neurons in numerous invertebrate and vertebrate species. In the present report, cloning and expression profile of a class IV POU gene in amphioxus was assessed for understanding its role in the sensory systems development. A single class IV gene, AmphiPOU-IV was isolated from the amphioxus Branchiostoma floridae. From a phylogenetic point of view, AmphiPOU-IV appears to be strictly related to the vertebrate one, sharing a high homology ratio especially with all vertebrate POU-IV proteins Brn-3a, Brn-3b, and Brn-3c. AmphiPOU-IV was found in the most anterior neural plate and in scattered ectodermic cells on the flanks of neurula, such ectodermic cells resemble the characteristic morphology and position of AmphiCoe and AmphiTrk developing sensory cells. Later on, the expression was confined in some motoneurons at level of the PMC and in some segmental arranged motoneurons in the hindbrain. Such expression is also maintained in larvae, and a new site of AmphiPOU-IV expression was also found in rostrum and mouth edge epidermal sensory cells of the larva. In conclusion, our data suggest an evolutionary conserved role of POU-IV transcription factors in the specification and differentiation of the sensory system in both vertebrates and invertebrates and underline the importance of amphioxus as linking step between them. [ABSTRACT FROM AUTHOR]

Summary: Cnidarians (corals, sea anemones, hydroids, and jellyfish) are a basal taxon closely related to bilaterally symmetrical animals and have been characterized as diploblastic and as radially symmetrical around their longitudinal axis. We show that some orthologs of key bilaterian dorso/ventral (D/V) patterning genes, including the TGFβ signaling molecules NvDpp and NvBMP5-8 and their antagonist NvChordin, are initially expressed asymmetrically at the onset of gastrulation in the anthozoan sea anemone Nematostella vectensis. Surprisingly, unlike flies and vertebrates, the TGFβ ligands and their antagonist are colocalized at the onset of gastrulation but then segregate by germ layer as gastrulation proceeds. TGFβ ligands, their extracellular enhancer, NvTolloid, and components of their downstream signaling pathway (NvSmad1/5 and NvSmad4) are all coexpressed in presumptive endoderm, indicating that only planar TGFβ signaling operates at these stages. NvChordin expression forms a boundary between TGFβ-expressing endodermal cells and aboral ectoderm. Manipulation of nuclear β-catenin localization affects TGFβ ligand and antagonist expression, suggesting that the ancestral role of the dpp/chordin antagonism during gastrulation may have been in germ-layer segregation and/or epithelial patterning rather than dorsal/ventral patterning. [Copyright &y& Elsevier]

The arthropods display a wide range of morphological diversity, varying tagmosis, as well as other aspects of the body plan, such as appendage and cuticular morphology. Here we review the roles of developmental regulatory genes in the evolution of arthropod morphology, with an emphasis on what is known from morphologically diverse species. Examination of tagmatic evolution reveals that these changes have been accompanied by changes in the expression patterns of Hox genes. In contrast, review of the modifications to wing morphology seen in insects shows that these body plan changes have generally favored alterations in downstream target genes. These and other examples are used to discuss the evolutionary implications of comparative developmental genetic data. [ABSTRACT FROM AUTHOR]

Hox genes play a key role in animal body plan development. These genes tend to occur in tightly linked clusters in the genome Vertebrates and invertebrates differ in their Hox cluster number, with vertebrates having multiple clusters and invertebrates usually having only one. Recent evidence shows that vertebrate Hox clusters are structurally more constrained than invertebrate Hox clusters; they exclude transposable elements, do not undergo tandem duplications, and conserve their intergenic distances and gene order. These constraints are only relaxed after a cluster duplication. In contrast, invertebrate Hox clusters are structurally more tandem duplications are common, the linkage of Hox genes can change quickly, or they can lose their structural integrity completely. We propose that the constraints on vertebrate Hox cluster structure lead to an association between the retention of duplicated Hox clusters and adaptive radiations. After a duplication the constraints on Hox cluster structure are temporarily lifted, which opens a window of evolvability for the Hox clusters. If this window of evolvability coincides with an adaptive radiation, chances are that a modified Hox cluster becomes recruited in an evolutionary novelty and then both copies of duplicated Hox clusters are retained. [ABSTRACT FROM AUTHOR]

Opisthorchis viverrini is highly prevalent throughout Southeast Asia. Chronic infection of this parasite leads to cholangiocarcinoma (CCA), a fatal bile duct cancer. The early and accurate detection of this parasite is very important; therefore, new PCR methods targeting cytochrome c oxidase subunit one and NADH dehydrogenase subunit one gene to detect O. viverrini in fecal specimens have been developed. Ninety O. viverrini-positive human fecal samples were used in this study. The PCR sensitivity of both genes was compared with internal transcribe spacer 2 (ITS2)-PCR. The sensitivity of cox1-PCR and nad1-PCR was 66.7 and 50 %, respectively. The sensitivity of cox1-PCR and nad1-PCR achieved 89.1 and 71.7 % in specimens containing O. viverrini eggs of >100 eggs per gram (EPG). Additionally, these primers can be used to provide the information on genetic diversity from mitochondrial genes of O. viverrini. [ABSTRACT FROM AUTHOR]

Examination of levels of inter- and intra-individual variation for a number of characters across 11 invertebrate species revealed a significant concordance of character coefficients of variation among samples within a species, suggesting that some characters are consistently more (or less) variable than others. In addition a significant positive correlation between character CV and asymmetry values was observed, suggesting that the underlying genetic mechanisms responsible for buffering character development against both external and internal environmental variation are either the same or inter-related. These results are discussed in relation to associations between character variation and individual fitness. [ABSTRACT FROM AUTHOR]

In this commentary, Qun Zheng and Michael L. Nonet examine Edwards et al.'s article in which they provide evidence for a domain in invertebrate neurons similar to the vertebrate axonal initial segment that serves to restrict certain organelles from entering the axonal compartment. In their article published in this month's GENETICS, Edwards et al. (2013) implicate the UNC-16/JIP3/SYD as a critical regulator of organelle entry into the axonal compartment: "An Organelle Gatekeeper Function for Caenorhabditis elegans UNC-16 (JIP3) at the Axon Initial Segment." [ABSTRACT FROM AUTHOR]

The 'species' is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The 'Porites lobata species complex' consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāneʻohe Bay Hawaiʻi during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated. [ABSTRACT FROM AUTHOR]

The peanut worm Sipunculus nudus is an economic important species in the fishery and aquaculture in Indo-West Pacific. However, it is a species complex consisting of cryptic species, which can be difficult to identify based on morphology. Here, we report the complete mitochondrial genome sequence of S. nudus from Beibu Bay. The mitogenome has 15,375 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs, and two ribosomal RNAs), and a putative control region. There were 5948 mutations sites between Chinese and French populations. This study adds a distinct mitogenome of S. nudus, and will provide useful genetic information for future genetic variation identification and genetic diversity evaluation of this economic valuable marine benthic invertebrate. [ABSTRACT FROM AUTHOR]

In this study, we sequenced the complete mitochondrial genome of Porites harrisoni using ezRAD and Illumina technology. Genome length consisted of 18,630 bp, with a base composition of 25.92% A, 13.28% T, 23.06% G, and 37.73% C. Consistent with other hard corals, P. harrisoni mitogenome was arranged in 13 protein-coding genes, 2 rRNA, and 2 tRNA genes. nad5 and cox1 contained embedded Group I Introns of 11,133 bp and 965 bp, respectively. [ABSTRACT FROM AUTHOR]

We have determined the mitochondrial DNA of Semisulcospira coreana. The complete mitogenome was 15,398 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic analysis showed that the mitochondrial DNA of S. coreana was much closely related to other Semisulcospira species. This mitogenome could be helpful information for a variety of biodiversity researches in Korean freshwater snail. [ABSTRACT FROM AUTHOR]

Corals in the genus Porites are among the major framework builders of reef structures worldwide, yet the genus has been challenging to study due to a lack of informative molecular markers. Here, we used ezRAD sequencing to reconstruct the complete mitochondrial genome of Porites fontanesii (GenBank accession number MG754069), a widespread coral species endemic to the Red Sea and Gulf of Aden. The gene arrangement of P. fontanesii did not differ from other Scleractinia and consisted of 18,658 bp, organized in 13 protein-coding genes, 2 rRNA genes, and 2 tRNA genes. This mitochondrial genome contributes essential data to work towards a better understanding of evolutionary relationships within Porites. [ABSTRACT FROM AUTHOR]

In this study a Sipuncula species Phascolosoma sp. was collected from seagrass area from Chuuk lagoon Micronesia and its complete mitochondrial genome analyzed. This is the second complete mitochondrial genome record from the genus after Phascolosoma esculenta. The total length of mitochondrial genome of the species is 16,571 bp, which is longer than P. esculenta record. Also, locations of tRNA-Gly and putative control region are different between two records. Furthermore, phylogenetic relationship of Phascolosoma sp. are investigated due to protein-coding genes of mitochondrial genome. Due to the lack of recorded data, P. esculenta has been observed is the closest species to Phascolosoma sp. and they are belonging to the monophyletic group. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of Rhopilema esculentum collected from Jiaozhou Bay, China, was determined by next-generation sequencing. The mitogenome is a circular molecule 15,855 bp in length, including 13 protein-coding genes (Cox 1, Cox2, Atp 8, Atp 6, Cox 3, ND2, ND5, ND 6, ND3, ND4L, ND1,ND4, Cytb), 5 tRNAs (tRNA-Trp, tRNA-Met, tRNA-Leu, tRNA-Ser, tRNA-Gln), 2 rRNA genes (small subunit RNA and large subunit RNA) and 1 putative control region. The phylogenetic tree in the related species showed that R. esculentum is close to Nemopilema nomurai. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence of a funnel-web weaving spider, Agelena silvatica (Agelenidae), was obtained using long PCR and conventional PCR methods. The circular genome is 14,776 bp in length. It contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. The A + T content (74.46%) of the all base composition is higher than G + C content (25.54%). Bayesian and maximum likelihood phylogenetic analyses demonstrate that Agelena silvatica is the sister clade of the water spider, Argyroneta aquatica. [ABSTRACT FROM AUTHOR]

Ixodes persulcatus is a species of hard tick which is a predominant tick species that spreads a wide array of serious human and animal pathogens. Here, we first assemble the complete mitogenome of I. persulcatus of China. The total length of the mitogenome was 14,539 bp included 36 genes and with a mitogenome structure similar to other ticks. Phylogenetic tree was constructed based on the complete mitogenome of I. persulcatus and closely related 19 species ticks to assess their phylogenic relationship and evolution. We also analyze the differences between the mitogenomes of I. persulcatus of Japan and China. The complete mitogenome data would be useful for further study of I. persulcatus. [ABSTRACT FROM AUTHOR]

Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders. [ABSTRACT FROM AUTHOR]

Sea urchins of the genus Tripneustes are among the most abundant and ecologically important pan-tropical marine invertebrates. Recognized as potent ecosystem engineers due to their intense grazing of macroalgae and sea grass and highly valued for their gonads, wild populations of Tripneustes are commercially exploited for fisheries and aquaculture. Recently, a new species, Tripneustes kermadecensis (Bronstein et al. 2017), was described from the southern Pacific Ocean, off the Kermadec Islands, near the tropical/sub-tropical transition zone. Here, we explore the range of Tripneustes and, in particular, T. kermadecensis by morphological and genetic tools to determine whether it also occurs in Australia. We report, for the first time, the presence of a second Tripneustes species, T. kermadecensis, from Australia. We show that T. kermadecensis is in fact highly abundant throughout most of sub-tropical eastern Australia, where it occurs in association with coral and temperate reefs and has been recognized for decades as the 'lamington sea urchin'. As commercial exploitation and stock-release programs of Tripneustes are rapidly expanding, and as global warming causes tropicalization of eastern Australia, driving the southern expansion of its congener T. gratilla, we call for re-evaluation of the conservation vulnerability of T. kermadecensis along the Australian continent and action by the aquaculture industry to genetically confirm the species identity of stocks in their facilities. [ABSTRACT FROM AUTHOR]

Echinoderms form an abundant and ecologically important group of marine animals, and they are found in nearly every marine environment, from shallow tropical waters to deep polar benthos and even in the pelagic zone. They exhibit a wide diversity of reproductive strategies that range from broadcasting millions of gametes, with no parental care, to internal brooding of a few embryos for several weeks. While many echinoderm species have become model systems for studies of community ecology, evolutionary genetics, and development biology, very little is known about the distribution of mating and reproductive success in natural populations. In this study, we examined patterns of genetic maternity and paternity in the six-rayed sea star Leptasterias sp., an important predator of many intertidal communities and a species that exhibits maternal care of embryos. We used next-generation sequencing to rapidly develop informative microsatellite markers for this species, and used these markers to genotype 439 juveniles across 15 broods collected from the intertidal in Fogarty Creek, Oregon, USA. Our data show an unambiguous pattern of multiple paternity in all but one clutch examined, with some broods showing some of the highest levels of polyandry reported for a marine invertebrate. Moreover, we detected two cases of mixed maternity in which a female sea star carried another mother's offspring mixed with her own. Alloparental care by females is rare, and since female Leptasterias do not eat during the 40-60 days brooding period, this expensive behavior may provide a useful system for examining the evolutionary costs and benefits of parental care in dynamic intertidal environments. [ABSTRACT FROM AUTHOR]