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
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