Center for Molecular Biodiversity Research

Tsukuba, Japan

Center for Molecular Biodiversity Research

Tsukuba, Japan
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Yoshikawa N.,Center for Molecular Biodiversity Research | Nagata N.,Collection Center
Current Herpetology | Year: 2017

We developed 18 novel microsatellite markers for Onychodactylus japonicus using Illumina Miseq System, and tried cross-amplifications in three congeners. The number of alleles and expected heterozygosity at each locus in O. japonicus were 3-15 (mean=6.83) and 0.45-0.89 (mean=0.73), respectively. Cross-amplifications in congeners succeeded in 9-13 of 18 loci, and eight loci were consistently amplified across all four species. The markers described here will be useful not only for investigating phylogeography and fine-scale genetic structure, but also for estimating genetic diversity of endangered species or populations for conservation management. © 2017 by The Herpetological Society of Japan.

Koevoets T.,University of Groningen | Niehuis O.,Center for Molecular Biodiversity Research | Van De Zande L.,University of Groningen | Beukeboom L.W.,University of Groningen
Heredity | Year: 2012

The occurrence of hybrid incompatibilities forms an important stage during the evolution of reproductive isolation. In early stages of speciation, males and females often respond differently to hybridization. Haldane's rule states that the heterogametic sex suffers more from hybridization than the homogametic sex. Although haplodiploid reproduction (haploid males, diploid females) does not involve sex chromosomes, sex-specific incompatibilities are predicted to be prevalent in haplodiploid species. Here, we evaluate the effect of sex/ploidy level on hybrid incompatibilities and locate genomic regions that cause increased mortality rates in hybrid males of the haplodiploid wasps Nasonia vitripennis and Nasonia longicornis. Our data show that diploid F 1 hybrid females suffer less from hybridization than haploid F 2 hybrid males. The latter not only suffer from an increased mortality rate, but also from behavioural and spermatogenic sterility. Genetic mapping in recombinant F 2 male hybrids revealed that the observed hybrid mortality is most likely due to a disruption of cytonuclear interactions. As these sex-specific hybrid incompatibilities follow predictions based on Haldane's rule, our data accentuate the need to broaden the view of Haldane's rule to include species with haplodiploid sex determination, consistent with Haldane's original definition. © 2012 Macmillan Publishers Limited All rights reserved.

De Vries J.,Heinrich Heine University Düsseldorf | Habicht J.,Heinrich Heine University Düsseldorf | Woehle C.,Heinrich Heine University Düsseldorf | Huang C.,Heinrich Heine University Düsseldorf | And 5 more authors.
Genome Biology and Evolution | Year: 2013

Plastids sequestered by sacoglossan sea slugs have long been a puzzle. Some sacoglossans feed on siphonaceous algae and can retain the plastids in the cytosol of their digestive gland cells. There, the stolen plastids (kleptoplasts) can remain photosynthetically active in some cases for months. Kleptoplast longevity itself challenges current paradigms concerning photosystem turnover, because kleptoplast photosystems remain active in the absence of nuclear algal genes. In higher plants, nuclear genes are essential for plastid maintenance, in particular, for the constant repair of the D1 protein of photosystem II. Lateral gene transfer was long suspected to underpin slug kleptoplast longevity, but recent transcriptomic and genomic analyses show that no algal nuclear genes are expressed from the slug nucleus. Kleptoplast genomes themselves, however, appear expressed in the sequestered state. Here we present sequence data for the chloroplast genome of Acetabularia acetabulum, the food source of the sacoglossan Elysia timida, which can maintain Acetabularia kleptoplasts in an active state for months. The data reveal what might be the key to sacoglossan kleptoplast longevity: plastids that remain photosynthetically active within slugs for periods of months share the property of encoding ftsH, a D1 quality control protease that is essential for photosystem II repair. In land plants, ftsH is always nuclear encoded, it was transferred to the nucleus from the plastid genome when Charophyta and Embryophyta split. A replenishable supply of ftsH could, in principle, rescue kleptoplasts from D1 photodamage, thereby influencing plastid longevity in sacoglossan slugs. © The Author(s) 2013.

PubMed | Center for Molecular Biodiversity Research, University of Geneva and University of Illinois at Urbana - Champaign
Type: | Journal: Genome biology and evolution | Year: 2017

Insects comprise the most diverse and successful animal group with over one million described species that are found in almost every terrestrial and limnic habitat, with many being used as important models in genetics, ecology, and evolutionary research. Genome sequencing projects have greatly expanded the sampling of species from many insect orders, but genomic resources for species of certain insect lineages have remained relatively limited to date. To address this paucity, we sequenced the genome of the banded demoiselle, Calopteryx splendens, a damselfly (Odonata: Zygoptera) belonging to Palaeoptera, the clade containing the first winged insects. The 1.6 Gbp C. splendens draft genome assembly is one of the largest insect genomes sequenced to date and encodes a predicted set of 22,523 protein-coding genes. Comparative genomic analyses with other sequenced insects identified a relatively small repertoire of C. splendens detoxification genes, which could explain its previously noted sensitivity to habitat pollution. Intriguingly, this repertoire includes a cytochrome P450 gene not previously described in any insect genome. The C. splendens immune gene repertoire appears relatively complete and features several genes encoding novel multi-domain peptidoglycan recognition proteins. Analysis of chemosensory genes revealed the presence of both gustatory and ionotropic receptors, as well as the insect odorant receptor coreceptor gene (OrCo) and at least four partner odorant receptors (ORs). This represents the oldest known instance of a complete OrCo/OR system in insects, and provides the molecular underpinning for odonate olfaction. The C. splendens genome improves the sampling of insect lineages that diverged before the radiation of Holometabola and offers new opportunities for molecular-level evolutionary, ecological, and behavioral studies.

PubMed | Center for Molecular Biodiversity Research, China National GeneBank, University of Bonn, Zoological Research Museum Alexander Koenig and China Agricultural University
Type: | Journal: Genome biology and evolution | Year: 2017

RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders. We inferred the phylogenetic origin of insect-specific RNAi pathway genes and also identified several hitherto unrecorded gene expansions using whole-body transcriptome data from the international 1KITE (1000 Insect Transcriptome Evolution) project as well as other resources such as i5K (5000 Insect Genome Project). Specifically, we traced the origin of the double stranded RNA binding protein R2D2 to the last common ancestor of winged insects (Pterygota), the loss of Sid-1/Tag-130 orthologs in Antliophora (fleas, flies and relatives, and scorpionflies in a broad sense), and confirm previous evidence for the splitting of the Argonaute proteins Aubergine and Piwi in Brachyceran flies (Diptera, Brachycera). Our study offers new reference points for future experimental research on RNAi-related pathway genes in insects.

PubMed | Hiroshima University, Center for Molecular Biodiversity Research and University of Tokyo
Type: | Journal: Parasitology international | Year: 2017

Praobdellid leech species have been known to infest vertebrate mucous-membrane; some of them have been assumed to be invertebrate bloodsuckers. Praobdellid individuals were found feeding on the Japanese freshwater crab, Geothelphusa dehaani, at Mt. Tsukuba, Ibaraki Prefecture, Japan. The leech had inserted its head into the intersegmental membrane between the crabs carapace and legs. Our findings represent a first invertebrate host record for praobdellid leeches. Additionally, molecular phylogenetic trees based on nuclear 18S and 28S rRNA, mitochondrial cytochrome c oxidase subunit I, and 12S rRNA sequences as well as the leech morphological characteristics showed that the present leech might belong to an unrecognized praobdellid lineage: a taxonomic revision of the Japanese praobdellid species is needed.

Christa G.,Center for Molecular Biodiversity Research | Christa G.,Heinrich Heine University Düsseldorf | De Vries J.,Heinrich Heine University Düsseldorf | Jahns P.,Heinrich Heine University Düsseldorf | Gould S.B.,Heinrich Heine University Düsseldorf
Communicative and Integrative Biology | Year: 2014

Sometimes the elementary experiment can lead to the most surprising result. This was recently the case when we had to learn that so-called ''photosynthetic slugs'' survive just fine in the dark and with chemically inhibited photosynthesis. Sacoglossan sea slugs feed on large siphonaceous, often single-celled algae by ingesting their cytosolic content including the organelles. A few species of the sacoglossan clade fascinate researcher from many disciplines, as they can survive starvation periods of many months through the plastids they sequestered, but not immediately digested - a process known as kleptoplasty. Ever since the term ''leaves that crawl'' was coined in the 1970s, the course was set in regard to how the subject was studied, but the topics of how slugs survive starvation and what for instance mediates kleptoplast longevity have often been conflated. It was generally assumed that slugs become photoautotrophic upon plastid sequestration, but most recent results challenge that view and the predominant role of the kleptoplasts in sacoglossan sea slugs. © 2014 Landes Bioscience.

Osigus H.-J.,Stiftung Tierarztliche Hochschule Hanover | Eitel M.,Stiftung Tierarztliche Hochschule Hanover | Eitel M.,University of Hong Kong | Bernt M.,University of Leipzig | And 3 more authors.
Molecular Phylogenetics and Evolution | Year: 2013

Unraveling the base of metazoan evolution is of crucial importance for rooting the metazoan Tree of Life. This subject has attracted substantial attention for more than a century and recently fueled a burst of modern phylogenetic studies. Conflicting scenarios from different studies and incongruent results from nuclear versus mitochondrial markers challenge current molecular phylogenetic approaches. Here we analyze the presently most comprehensive data sets of mitochondrial genomes from non-bilaterian animals to illuminate the phylogenetic relationships among early branching metazoan phyla. The results of our analyses illustrate the value of mitogenomics and support previously known topologies between animal phyla but also identify several problematic taxa, which are sensitive to long branch artifacts or missing data. © 2013 Elsevier Inc.

Yoshikawa N.,Center for Molecular Biodiversity Research
Current Herpetology | Year: 2016

Antipredator behavior of Cynops pyrrhogaster was observed in the field. A male, found in a temporal pool (11.7C), tightly coiled his body around the observer's finger (putative model of predator) when he was touched from lateral side. The body-coiling was formed both dextrally and sinistrally, depending on direction from which the newt's body was touched. Undulation of tail and noxious secretion accompanied the behavior. The coiling-Around behavior was aborted immediately when the newt lost physical contact with finger. Apart from this, pushing on the head with a finger caused Unken reflex, which is commonly known as defensive behavior of newts. It is suggested that C. pyrrhogaster varies their defensive behavior depending on the situation of encounter with the predator.

Hiruta S.F.,Center for Molecular Biodiversity Research | Kakui K.,Hokkaido University
Zootaxa | Year: 2016

We describe three new species of brackish-water ostracods representing two genera in the ostracod tribe Thalassocypridini from mangrove forests in the Ryukyu Islands, subtropical southwestern Japan, and provide their barcoding sequences for the mitochondrial cytochrome c oxidase subunit I (COI) gene. Mangalocypria ryukyuensis sp. nov. was found on Okinawa Island. We also found a Mangalocypria population on Ishigaki Island that was morphologically identical to M. ryukyuensis on Okinawa, but an individual differed by 4.7% in COI sequence (K2P distance) from an individual from Okinawa. This is the first record for Japan of a species in Mangalocypria. Paracypria longiseta sp. nov., obtained from Okinawa Island, is similar to Pontoparta hartmanni. Paracypria plumosa sp. nov. from Ishigaki Island is similar to Pa. adnata described from Yakushima Island, Japan. The COI genetic distance between individuals of Pa. longiseta and Pa. plumosa was roughly as large as that between either of these species and individuals in the Mangalocypria populations. Our study underscores that genera in Thalassocypridini may not represent natural groups, and that this tribe needs taxonomic revision. © 2016 Magnolia Press.

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