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  - 
TY  - JOUR
A1  - Lu, Yuan
A1  - Boswell, Mikki
A1  - Boswell, William
A1  - Kneitz, Susanne
A1  - Klotz, Barbara
A1  - Savage, Markita
A1  - Salinas, Raquel
A1  - Marks, Rebacca
A1  - Regneri, Janine
A1  - Postlethwait, John
A1  - Warren, Wesley C.
A1  - Schartl, Manfred
A1  - Walter, Ronald
T1  - Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model
JF  - PLoS Genetics
N2  - Understanding the genetic mechanisms underlying segregation of phenotypic variation through successive generations is important for understanding physiological changes and disease risk. Tracing the etiology of variation in gene expression enables identification of genetic interactions, and may uncover molecular mechanisms leading to the phenotypic expression of a trait, especially when utilizing model organisms that have well-defined genetic lineages. There are a plethora of studies that describe relationships between gene expression and genotype, however, the idea that global variations in gene expression are also controlled by genotype remains novel. Despite the identification of loci that control gene expression variation, the global understanding of how genome constitution affects trait variability is unknown. To study this question, we utilized Xiphophorus fish of different, but tractable genetic backgrounds (inbred, F1 interspecies hybrids, and backcross hybrid progeny), and measured each individual’s gene expression concurrent with the degrees of inter-individual expression variation. We found, (a) F1 interspecies hybrids exhibited less variability than inbred animals, indicting gene expression variation is not affected by the fraction of heterozygous loci within an individual genome, and (b), that mixing genotypes in backcross populations led to higher levels of gene expression variability, supporting the idea that expression variability is caused by heterogeneity of genotypes of cis or trans loci. In conclusion, heterogeneity of genotype, introduced by inheritance of different alleles, accounts for the largest effects on global phenotypical variability.
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-237318
VL  - 14
ER  -