TY  - JOUR
A1  - Schartl, Manfred
A1  - Walter, Ronald B.
A1  - Shen, Yingjia
A1  - Garcia, Tzintzuni
A1  - Catchen, Julian
A1  - Amores, Angel
A1  - Braasch, Ingo
A1  - Chalopin, Domitille
A1  - Volff, Jean-Nicolas
A1  - Lesch, Klaus-Peter
A1  - Bisazza, Angelo
A1  - Minx, Pat
A1  - Hillier, LaDeana
A1  - Wilson, Richard K.
A1  - Fürstenberg, Susan
A1  - Boore, Jeffrey
A1  - Searle, Steve
A1  - Postlethwait, John H.
A1  - Warren, Wesley C.
T1  - The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits
JF  - Nature Genetics
N2  - 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.
KW  - genomics
KW  - genomic analysis
KW  - evolutionary biology
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-132152
VL  - 45
IS  - 5
ER  - 
TY  - JOUR
A1  - Shen, Yingjia
A1  - Chalopin, Domitille
A1  - Garcia, Tzintzuni
A1  - Boswell, Mikki
A1  - Boswell, William
A1  - Shiryev, Sergey A.
A1  - Agarwala, Richa
A1  - Volff, Jean-Nicolas
A1  - Postlethwait, John H.
A1  - Schartl, Manfred
A1  - Minx, Patrick
A1  - Warren, Wesley C.
A1  - Walter, Ronald B.
T1  - X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species
JF  - BMC Genomics
N2  - 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.
KW  - Xiphophorus
KW  - X. hellerii
KW  - Annotation
KW  - Single nucleotide change
KW  - Genome comparison
KW  - X. couchianus
KW  - Genome assembly
KW  - NGS
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-164582
VL  - 17
ER  -