TY  - GEN
A1  - Beermann, Jan
A1  - Westbury, Michael V.
A1  - Hofreiter, Michael
A1  - Hilgers, Leon
A1  - Deister, Fabian
A1  - Neumann, Hermann
A1  - Raupach, Michael J.
T1  - Cryptic species in a well-known habitat
BT  - applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida)
T2  - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
N2  - Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1059 
KW  - multiple sequence alignment
KW  - Oxidase Subunit-I
KW  - mitochondrial genome
KW  - control region
KW  - Ribosomal-RNA
KW  - asellota crustacea
KW  - gammarus crustacea
KW  - deep-sea
KW  - DNA
KW  - evolution
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-460792
SN  - 1866-8372
IS  - 1059
ER  - 
TY  - GEN
A1  - Grau, José Horacio
A1  - Hackl, Thomas
A1  - Koepfli, Klaus-Peter
A1  - Hofreiter, Michael
T1  - Improving draft genome contiguity with reference-derived in silico mate-pair libraries
T2  - GigaScience
N2  - Background

Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available.

Findings

In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico.

Conclusions

We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 477 
KW  - genome assembly
KW  - mate-pairs
KW  - in silico
KW  - scaffolding
KW  - shotgun sequencing
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-419225
ER  -