13215
2013
eng
567-572
5
45
article
1
2016-04-14
--
--
The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits
Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, X. maculatus, offers a unique model to better understand the molecular biology of such traits. We report here the sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps identified an unexpected evolutionary stability of chromosomes in fish, in contrast to in mammals. Genes associated with viviparity show signatures of positive selection, identifying new putative functional domains and rare cases of parallel evolution. We also find that genes implicated in cognition show an unexpectedly high rate of duplicate gene retention after the teleost genome duplication event, suggesting a hypothesis for the evolution of the behavioral complexity in fish, which exceeds that found in amphibians and reptiles.
Nature Genetics
10.1038/ng.2604
urn:nbn:de:bvb:20-opus-132152
Nature Genetics 2013 45, 5, 567-572. doi:10.1038/ng.2604
Manfred Schartl
Ronald B. Walter
Yingjia Shen
Tzintzuni Garcia
Julian Catchen
Angel Amores
Ingo Braasch
Domitille Chalopin
Jean-Nicolas Volff
Klaus-Peter Lesch
Angelo Bisazza
Pat Minx
LaDeana Hillier
Richard K. Wilson
Susan Fürstenberg
Jeffrey Boore
Steve Searle
John H. Postlethwait
Wesley C. Warren
eng
uncontrolled
genomics
eng
uncontrolled
genomic analysis
eng
uncontrolled
evolutionary biology
Humanphysiologie
open_access
Institut für Humangenetik
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/13215/158_Schartl_Nature_Genetics.pdf
11600
2014
eng
e100250
6
9
article
1
2015-07-16
--
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Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion
Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression.
PLOS ONE
10.1371/journal.pone.0100250
1932-6203
24945156
urn:nbn:de:bvb:20-opus-116000
PLoS ONE 9(6): e100250. doi:10.1371/journal.pone.0100250
Tzintzuni I. Garcia
Isa Matos
Yingjia Shen
Vagmita Pabuwal
Maria Manuela Coelho
Yuko Wakamatsu
Manfred Schartl
Ronald B. Walter
eng
uncontrolled
RNA-SEQ data
eng
uncontrolled
copy-number alteration
eng
uncontrolled
squalius alburnoides
eng
uncontrolled
gene expression
eng
uncontrolled
medaka
eng
uncontrolled
variant detection
eng
uncontrolled
transplantation
eng
uncontrolled
genome
eng
uncontrolled
generation
eng
uncontrolled
evolution
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/11600/070_Garcia_PLOS_ONE.pdf
14471
2015
eng
e0143057
12
10
article
1
2017-02-21
--
--
Whole body melanoma transcriptome response in medaka
The incidence of malignant melanoma continues to increase each year with poor prognosis for survival in many relapse cases. To reverse this trend, whole body response measures are needed to discover collaborative paths to primary and secondary malignancy. Several species of fish provide excellent melanoma models because fish and human melanocytes both appear in the epidermis, and fish and human pigment cell tumors share conserved gene expression signatures. For the first time, we have examined the whole body transcriptome response to invasive melanoma as a prelude to using transcriptome profiling to screen for drugs in a medaka (Oryzias latipes) model. We generated RNA-seq data from whole body RNA isolates for controls and melanoma fish. After testing for differential expression, 396 genes had significantly different expression (adjusted p-value <0.02) in the whole body transcriptome between melanoma and control fish; 379 of these genes were matched to human orthologs with 233 having annotated human gene symbols and 14 matched genes that contain putative deleterious variants in human melanoma at varying levels of recurrence. A detailed canonical pathway evaluation for significant enrichment showed the top scoring pathway to be antigen presentation but also included the expected melanocyte development and pigmentation signaling pathway. Results revealed a profound down-regulation of genes involved in the immune response, especially the innate immune system. We hypothesize that the developing melanoma actively suppresses the immune system responses of the body in reacting to the invasive malignancy, and that this mal-adaptive response contributes to disease progression, a result that suggests our whole-body transcriptomic approach merits further use. In these findings, we also observed novel genes not yet identified in human melanoma expression studies and uncovered known and new candidate drug targets for further testing in this malignant melanoma medaka model.
PLoS ONE
10.1371/journal.pone.0143057
urn:nbn:de:bvb:20-opus-144714
PLoS ONE 10(12): e0143057 (2015). DOI: 10.1371/journal.pone.0143057
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Manfred Schartl
Yingjia Shen
Katja Maurus
Ron Walter
Chad Tomlinson
Richard K. Wilson
John Postlethwait
Wesley C. Warren
eng
uncontrolled
metastatic melanoma
eng
uncontrolled
expression
eng
uncontrolled
fish
eng
uncontrolled
cancer
eng
uncontrolled
stage III
eng
uncontrolled
melanogenesis
eng
uncontrolled
genome cells
eng
uncontrolled
gene
eng
uncontrolled
contributes
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14471/082_Schartl_PLoS_ONE.pdf
16458
2016
eng
37
17
article
1
2018-07-16
--
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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