TY  - JOUR
A1  - Schmidt, Thomas S. B.
A1  - Hayward, Matthew R.
A1  - Coelho, Luiis P.
A1  - Li, Simone S.
A1  - Costea, Paul I.
A1  - Voigt, Anita Y.
A1  - Wirbel, Jakob
A1  - Maistrenko, Oleksandr M.
A1  - Alves, Renato J. C.
A1  - Bergsten, Emma
A1  - de Beaufort, Carine
A1  - Sobhani, Iradj
A1  - Heintz-Buschart, Anna
A1  - Sunagawa, Shinichi
A1  - Zeller, Georg
A1  - Wilmes, Paul
A1  - Bork, Peer
T1  - Extensive transmission of microbes along the gastrointestinal tract
JF  - eLife
N2  - The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.
KW  - Colonization
KW  - Annotation
KW  - Dynamics
KW  - Accurate
KW  - Strains
KW  - Barrier
KW  - Health
KW  - Acids
KW  - Research Article
KW  - Computational and Systems Biology
KW  - Microbiology and Infectious Disease
KW  - microbiome
KW  - gastrointestinal tract
KW  - colorectal cancer
KW  - rheumatoid arthritis
KW  - metagenomics
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228954
VL  - 8
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  -