18878
2016
eng
1151-1154
11
35
article
1
2019-10-15
--
--
Considerations for a European animal welfare standard to evaluate adverse phenotypes in teleost fish
No abstract available.
The EMBO Journal
10.15252/embj.201694448
urn:nbn:de:bvb:20-opus-188783
The EMBO Journal (2016) 35:11, 1151-1154. https://doi.org/10.15252/embj.201694448
false
true
CC BY-NC-ND: Creative-Commons-Lizenz: Namensnennung, Nicht kommerziell, Keine Bearbeitungen 4.0 International
Bettina Bert
Justyna Chmielewska
Sven Bergmann
Maximilian Busch
Wolfgang Driever
Karin Finger-Baier
Johanna Hößler
Almut Köhler
Nora Leich
Thomas Misgeld
Torsten Nöldner
Annegret Reiher
Manfred Schartl
Anja Seebach-Sproedt
Thomas Thumberger
Gilbert Schönfelder
Barbara Grune
eng
uncontrolled
Danio-rerio
eng
uncontrolled
Zebrafish
eng
uncontrolled
Pain
Physiologie und verwandte Themen
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/18878/Bert_TheEmboJournal_2016.pdf
16495
2016
eng
7207-7220
20
6
article
1
2018-07-19
--
--
Evolution of the elaborate male intromittent organ of Xiphophorus fishes
Internally fertilizing animals show a remarkable diversity in male genital morphology that is associated with sexual selection, and these traits are thought to be evolving particularly rapidly. Male fish in some internally fertilizing species have “gonopodia,” highly modified anal fins that are putatively important for sexual selection. However, our understanding of the evolution of genital diversity remains incomplete. Contrary to the prediction that male genital traits evolve more rapidly than other traits, here we show that gonopodial traits and other nongonopodial traits exhibit similar evolutionary rates of trait change and also follow similar evolutionary models in an iconic genus of poeciliid fish (Xiphophorus spp.). Furthermore, we find that both mating and nonmating natural selection mechanisms are unlikely to be driving the diverse Xiphophorus gonopodial morphology. Putative holdfast features of the male genital organ do not appear to be influenced by water flow, a candidate selective force in aquatic habitats. Additionally, interspecific divergence in gonopodial morphology is not significantly higher between sympatric species, than between allopatric species, suggesting that male genitals have not undergone reproductive character displacement. Slower rates of evolution in gonopodial traits compared with a subset of putatively sexually selected nongenital traits suggest that different selection mechanisms may be acting on the different trait types. Further investigations of this elaborate trait are imperative to determine whether it is ultimately an important driver of speciation.
Ecology and Evolution
10.1002/ece3.2396
urn:nbn:de:bvb:20-opus-164956
Ecology and Evolution 2016; 6(20):7207-7220
false
true
Julia C. Jones
Carmelo Fruciano
Anja Keller
Manfred Schartl
Axel Meyer
eng
uncontrolled
Male intromittent organ
eng
uncontrolled
reproductive character displacement
eng
uncontrolled
sexual selection
eng
uncontrolled
species diversification
eng
uncontrolled
Xiphophorus fish
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/16495/037_Jones_ECOLOGY AND EVOLUTION.pdf
14602
2016
eng
357
17
article
1
2017-03-22
--
--
Germ cell and tumor associated piRNAs in the medaka and \(Xiphophorus\) melanoma models
Background
A growing number of studies report an abnormal expression of Piwi-interacting RNAs (piRNAs) and the piRNA processing enzyme Piwi in many cancers. Whether this finding is an epiphenomenon of the chaotic molecular biology of the fast dividing, neoplastically transformed cells or is functionally relevant to tumorigenesisis is difficult to discern at present. To better understand the role of piRNAs in cancer development small laboratory fish models can make a valuable contribution. However, little is known about piRNAs in somatic and neoplastic tissues of fish.
Results
To identify piRNA clusters that might be involved in melanoma pathogenesis, we use several transgenic lines of medaka, and platyfish/swordtail hybrids, which develop various types of melanoma. In these tumors Piwi, is expressed at different levels, depending on tumor type. To quantify piRNA levels, whole piRNA populations of testes and melanomas of different histotypes were sequenced. Because no reference piRNA cluster set for medaka or Xiphophorus was yet available we developed a software pipeline to detect piRNA clusters in our samples and clusters were selected that were enriched in one or more samples. We found several loci to be overexpressed or down-regulated in different melanoma subtypes as compared to hyperpigmented skin. Furthermore, cluster analysis revealed a clear distinction between testes, low-grade and high-grade malignant melanoma in medaka.
Conclusions
Our data imply that dysregulation of piRNA expression may be associated with development of melanoma. Our results also reinforce the importance of fish as a suitable model system to study the role of piRNAs in tumorigenesis.
BMC Genomics
10.1186/s12864-016-2697-z
urn:nbn:de:bvb:20-opus-146028
BMC Genomics (2016) 17:357 DOI 10.1186/s12864-016-2697-z
Susanne Kneitz
Rasmi R. Mishra
Domitille Chalopin
John Postlethwait
Wesley C. Warren
Ronald B. Walther
Manfred Schartl
eng
uncontrolled
small RNA-sequencing
eng
uncontrolled
melanoma
eng
uncontrolled
piRNA
eng
uncontrolled
fish model
Menschliche Anatomie, Zytologie, Histologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2016
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14602/026_Kneitz_art_10.1186_s12864-016-2697-z.pdf
14784
2016
eng
34281
6
article
1
2017-05-05
--
--
Retinoic acid and meiosis induction in adult versus embryonic gonads of medaka
In vertebrates, one of the first recognizable sex differences in embryos is the onset of meiosis, known to be regulated by retinoic acid (RA) in mammals. We investigated in medaka a possible meiotic function of RA during the embryonic sex determination (SD) period and in mature gonads. We found RA mediated transcriptional activation in germ cells of both sexes much earlier than the SD stage, however, no such activity during the critical stages of SD. In adults, expression of the RA metabolizing enzymes indicates sexually dimorphic RA levels. In testis, RA acts directly in Sertoli, Leydig and pre-meiotic germ cells. In ovaries, RA transcriptional activity is highest in meiotic oocytes. Our results show that RA plays an important role in meiosis induction and gametogenesis in adult medaka but contrary to common expectations, not for initiating the first meiosis in female germ cells at the SD stage.
Scientific Reports
10.1038/srep34281
urn:nbn:de:bvb:20-opus-147843
Scientific Reports 6, 34281; doi: 10.1038/srep34281 (2016)
Mateus C. Adolfi
Amaury Herpin
Martina Regensburger
Jacopo Sacquegno
Joshua S. Waxman
Manfred Schartl
eng
uncontrolled
developmental biology
eng
uncontrolled
molecular biology
Genetik und Evolution
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2016
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14784/Adolfi_srep34281.pdf
16775
2016
eng
21571
6
article
1
2018-08-30
--
--
The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land
Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.
Scientific Reports
10.1038/srep21571
urn:nbn:de:bvb:20-opus-167753
Scientific Reports 6:21571 (2016). DOI: 10.1038/srep21571
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Maria Assunta Biscotti
Marco Gerdol
Adriana Canapa
Mariko Forconi
Ettore Olmo
Alberto Pallavicini
Marco Barucca
Manfred Schartl
eng
uncontrolled
lungfish
eng
uncontrolled
transcriptome
eng
uncontrolled
genome
eng
uncontrolled
sarcopterygian fish
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/16775/Biscotti_Scientific_Reports.pdf
14698
2016
eng
1600-1613
15
8
article
1
2017-04-07
--
--
Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates
The receptor tyrosine kinase (RTK) gene family, involved primarily in cell growth and differentiation, comprises proteins with a common enzymatic tyrosine kinase intracellular domain adjacent to a transmembrane region. The amino-terminal portion of RTKs is extracellular and made of different domains, the combination of which characterizes each of the 20 RTK subfamilies among mammals. We analyzed a total of 7,376 RTK sequences among 143 vertebrate species to provide here the first comprehensive census of the jawed vertebrate repertoire. We ascertained the 58 genes previously described in the human and mouse genomes and established their phylogenetic relationships. We also identified five additional RTKs amounting to a total of 63 genes in jawed vertebrates. We found that the vertebrate RTK gene family has been shaped by the two successive rounds of whole genome duplications (WGD) called 1R and 2R (1R/2R) that occurred at the base of the vertebrates. In addition, the Vegfr and Ephrin receptor subfamilies were expanded by single gene duplications. In teleost fish, 23 additional RTK genes have been retained after another expansion through the fish-specific third round (3R) of WGD. Several lineage-specific gene losses were observed. For instance, birds have lost three RTKs, and different genes are missing in several fish sublineages. The RTK gene family presents an unusual high gene retention rate from the vertebrate WGDs (58.75% after 1R/2R, 64.4% after 3R), resulting in an expansion that might be correlated with the evolution of complexity of vertebrate cellular communication and intracellular signaling.
Genome Biology Evolution
10.1093/gbe/evw103
urn:nbn:de:bvb:20-opus-146988
Genome Biology Evolution 8(5):1600–1613. doi:10.1093/gbe/evw103
Frédéric G. Brunet
Jean-Nicolas Volff
Manfred Schartl
eng
uncontrolled
receptor tyrosine kinase
eng
uncontrolled
vertebrates
eng
uncontrolled
deuterostomes
eng
uncontrolled
whole genome duplications
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2016
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14698/093_Brunet_evw103.pdf
16458
2016
eng
37
17
article
1
2018-07-16
--
--
X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species
Background
Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species.
Results
We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus.
Conclusions
Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.
BMC Genomics
10.1186/s12864-015-2361-z
urn:nbn:de:bvb:20-opus-164582
BMC Genomics (2016) 17:37
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Yingjia Shen
Domitille Chalopin
Tzintzuni Garcia
Mikki Boswell
William Boswell
Sergey A. Shiryev
Richa Agarwala
Jean-Nicolas Volff
John H. Postlethwait
Manfred Schartl
Patrick Minx
Wesley C. Warren
Ronald B. Walter
eng
uncontrolled
Xiphophorus
eng
uncontrolled
X. hellerii
eng
uncontrolled
Annotation
eng
uncontrolled
Single nucleotide change
eng
uncontrolled
Genome comparison
eng
uncontrolled
X. couchianus
eng
uncontrolled
Genome assembly
eng
uncontrolled
NGS
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/16458/017_Shen_BMC-GENOMICS.pdf