TY - JOUR A1 - Meyer, Axel A1 - Schloissnig, Siegfried A1 - Franchini, Paolo A1 - Du, Kang A1 - Woltering, Joost M. A1 - Irisarri, Iker A1 - Wong, Wai Yee A1 - Nowoshilow, Sergej A1 - Kneitz, Susanne A1 - Kawaguchi, Akane A1 - Fabrizius, Andrej A1 - Xiong, Peiwen A1 - Dechaud, Corentin A1 - Spaink, Herman P. A1 - Volff, Jean-Nicolas A1 - Simakov, Oleg A1 - Burmester, Thorsten A1 - Tanaka, Elly M. A1 - Schartl, Manfred T1 - Giant lungfish genome elucidates the conquest of land by vertebrates JF - Nature N2 - Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, ‘conquered’ the land and ultimately gave rise to all land vertebrates, including humans1,2,3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-370750 VL - 590 ER - TY - JOUR A1 - Lu, Yuan A1 - Bierbach, David A1 - Ormanns, Jenny A1 - Warren, Wesley C. A1 - Walter, Ronald B. A1 - Schartl, Manfred T1 - Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly JF - Genome Research N2 - The Amazon molly is a unique clonal fish species that originated from an interspecies hybrid between Poecilia species P. mexicana and P. latipinna. It reproduces by gynogenesis, which eliminates paternal genomic contribution to offspring. An earlier study showed that Amazon molly shows biallelic expression for a large portion of the genome, leading to two main questions: (1) Are the allelic expression patterns from the initial hybridization event stabilized or changed during establishment of the asexual species and its further evolution? (2) Is allelic expression biased toward one parental allele a stochastic or adaptive process? To answer these questions, the allelic expression of P. formosa siblings was assessed to investigate intra- and inter-cohort allelic expression variability. For comparison, interspecies hybrids between P. mexicana and P. latipinna were produced in the laboratory to represent the P. formosa ancestor. We have identified inter-cohort and intra-cohort variation in parental allelic expression. The existence of inter-cohort divergence suggests functional P. formosa allelic expression patterns do not simply reflect the atavistic situation of the first interspecies hybrid but potentially result from long-term selection of transcriptional fitness. In addition, clonal fish show a transcriptional trend representing minimal intra-clonal variability in allelic expression patterns compared to the corresponding hybrids. The intra-clonal similarity in gene expression translates to sophisticated genetic functional regulation at the individuum level. These findings suggest the parental alleles inherited by P. formosa form tightly regulated genetic networks that lead to a stable transcriptomic landscape within clonal individuals. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-369578 VL - 31 ER - TY - JOUR A1 - Li, Ming A1 - Zhang, Rui A1 - Fan, Guangyi A1 - Xu, Wenteng A1 - Zhou, Qian A1 - Wang, Lei A1 - Li, Wensheng A1 - Pang, Zunfang A1 - Yu, Mengjun A1 - Liu, Qun A1 - Liu, Xin A1 - Schartl, Manfred A1 - Chen, Songlin T1 - Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus JF - Molecular Biology and Evolution N2 - Sex chromosomes are a peculiar constituent of the genome because the evolutionary forces that fix the primary sex-determining gene cause genic degeneration and accumulation of junk DNA in the heterogametic partner. One of the most spectacular phenomena in sex chromosome evolution is the occurrence of neo-Y chromosomes, which lead to X1X2Y sex-determining systems. Such neo-sex chromosomes are critical for understanding the processes of sex chromosome evolution because they rejuvenate their total gene content. We assembled the male and female genomes at the chromosome level of the spotted knifejaw (Oplegnathus punctatus), which has a cytogenetically recognized neo-Y chromosome. The full assembly and annotation of all three sex chromosomes allowed us to reconstruct their evolutionary history. Contrary to other neo-Y chromosomes, the fusion to X2 is quite ancient, estimated at 48 Ma. Despite its old age and being even older in the X1 homologous region which carries a huge inversion that occurred as early as 55–48 Ma, genetic degeneration of the neo-Y appears to be only moderate. Transcriptomic analysis showed that sex chromosomes harbor 87 genes, which may serve important functions in the testis. The accumulation of such male-beneficial genes, a large inversion on the X1 homologous region and fusion to X2 appear to be the main drivers of neo-Y evolution in the spotted knifejaw. The availability of high-quality assemblies of the neo-Y and both X chromosomes make this fish an ideal model for a better understanding of the variability of sex determination mechanisms and of sex chromosome evolution. KW - neo-Y KW - evolution; KW - spotted knifejaw KW - genome Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-364215 VL - 38 ER - TY - JOUR A1 - Kuhl, Heiner A1 - Guiguen, Yann A1 - Höhne, Christin A1 - Kreuz, Eva A1 - Du, Kang A1 - Klopp, Christophe A1 - Lopez-Roques,, Céline A1 - Yebra-Pimentel, Elena Santidrian A1 - Ciorpac, Mitica A1 - Gessner, Jörn A1 - Holostenco, Daniela A1 - Kleiner, Wibke A1 - Kohlmann, Klaus A1 - Lamatsch, Dunja K. A1 - Prokopov, Dmitry A1 - Bestin, Anastasia A1 - Bonpunt, Emmanuel A1 - Debeuf, Bastien A1 - Haffray, Pierrick A1 - Morvezen, Romain A1 - Patrice, Pierre A1 - Suciu, Radu A1 - Dirks, Ron A1 - Wuertz, Sven A1 - Kloas, Werner A1 - Schartl, Manfred A1 - Stöck, Matthias T1 - A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes JF - Philosophical Transactions of the Royal Society B N2 - Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’. KW - acipenseridae KW - sturgeon KW - sex chromosomes KW - female-specific KW - polyploidy KW - evolution Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-363050 VL - 376 ER - TY - JOUR A1 - Adolfi, Mateus C. A1 - Du, Kang A1 - Kneitz, Susanne A1 - Cabau, Cédric A1 - Zahm, Margot A1 - Klopp, Christophe A1 - Feron, Romain A1 - Paixão, Rômulo V. A1 - Varela, Eduardo S. A1 - de Almeida, Fernanda L. A1 - de Oliveira, Marcos A. A1 - Nóbrega, Rafael H. A1 - Lopez-Roques, Céline A1 - Iampietro, Carole A1 - Lluch, Jérôme A1 - Kloas, Werner A1 - Wuertz, Sven A1 - Schaefer, Fabian A1 - Stöck, Matthias A1 - Guiguen, Yann A1 - Schartl, Manfred T1 - A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas) JF - Scientific Reports N2 - Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGF beta signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes. KW - evolutionary genetics KW - genetic markers KW - genome Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-265672 VL - 11 IS - 1 ER - TY - JOUR A1 - Helmprobst, Frederik A1 - Kneitz, Susanne A1 - Klotz, Barbara A1 - Naville, Magali A1 - Dechaud, Corentin A1 - Volff, Jean-Nicolas A1 - Schartl, Manfred T1 - Differential expression of transposable elements in the medaka melanoma model JF - PLoS One N2 - Malignant melanoma incidence is rising worldwide. Its treatment in an advanced state is difficult, and the prognosis of this severe disease is still very poor. One major source of these difficulties is the high rate of metastasis and increased genomic instability leading to a high mutation rate and the development of resistance against therapeutic approaches. Here we investigate as one source of genomic instability the contribution of activation of transposable elements (TEs) within the tumor. We used the well-established medaka melanoma model and RNA-sequencing to investigate the differential expression of TEs in wildtype and transgenic fish carrying melanoma. We constructed a medaka-specific TE sequence library and identified TE sequences that were specifically upregulated in tumors. Validation by qRT- PCR confirmed a specific upregulation of a LINE and an LTR element in malignant melanomas of transgenic fish. KW - melanoma KW - genomics KW - transposable elements KW - cancer genomics KW - malignant tumors KW - gene prediction KW - human genomics KW - retrotransposons Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-260615 VL - 16 IS - 10 ER - TY - JOUR A1 - Hojsgaard, Diego A1 - Schartl, Manfred T1 - Skipping sex: A nonrecombinant genomic assemblage of complementary reproductive modules JF - BioEssays N2 - The unusual occurrence and developmental diversity of asexual eukaryotes remain a puzzle. De novo formation of a functioning asexual genome requires a unique assembly of sets of genes or gene states to disrupt cellular mechanisms of meiosis and gametogenesis, and to affect discrete components of sexuality and produce clonal or hemiclonal offspring. We highlight two usually overlooked but essential conditions to understand the molecular nature of clonal organisms, that is, a nonrecombinant genomic assemblage retaining modifiers of the sexual program, and a complementation between altered reproductive components. These subtle conditions are the basis for physiologically viable and genetically balanced transitions between generations. Genomic and developmental evidence from asexual animals and plants indicates the lack of complementation of molecular changes in the sexual reproductive program is likely the main cause of asexuals' rarity, and can provide an explanatory frame for the developmental diversity and lability of developmental patterns in some asexuals as well as for the discordant time to extinction estimations. KW - amphimixis KW - apomixis KW - automixis KW - gynogenesis KW - hybridogenesis KW - parthenogenesis Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-225818 VL - 43 IS - 1 ER - TY - JOUR A1 - Adolfi, Mateus C. A1 - Herpin, Amaury A1 - Martinez-Bengochea, Anabel A1 - Kneitz, Susanne A1 - Regensburger, Martina A1 - Grunwald, David J. A1 - Schartl, Manfred T1 - Crosstalk Between Retinoic Acid and Sex-Related Genes Controls Germ Cell Fate and Gametogenesis in Medaka JF - Frontiers in Cell and Developmental Biology N2 - Sex determination (SD) is a highly diverse and complex mechanism. In vertebrates, one of the first morphological differences between the sexes is the timing of initiation of the first meiosis, where its initiation occurs first in female and later in male. Thus, SD is intimately related to the responsiveness of the germ cells to undergo meiosis in a sex-specific manner. In some vertebrates, it has been reported that the timing for meiosis entry would be under control of retinoic acid (RA), through activation of Stra8. In this study, we used a fish model species for sex determination and lacking the stra8 gene, the Japanese medaka (Oryzias latipes), to investigate the connection between RA and the sex determination pathway. Exogenous RA treatments act as a stress factor inhibiting germ cell differentiation probably by activation of dmrt1a and amh. Disruption of the RA degrading enzyme gene cyp26a1 induced precocious meiosis and oogenesis in embryos/hatchlings of female and even some males. Transcriptome analyzes of cyp26a1–/–adult gonads revealed upregulation of genes related to germ cell differentiation and meiosis, in both ovaries and testes. Our findings show that germ cells respond to RA in a stra8 independent model species. The responsiveness to RA is conferred by sex-related genes, restricting its action to the sex differentiation period in both sexes. KW - sex determination KW - retinoic acid KW - meiosis KW - gametogenesis KW - medaka Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-222669 SN - 2296-634X VL - 8 ER -