16. January 2014, 16:15
Ernst-Abbe-Platz 2, seminar room 3423

A methodological review of genomic strategies to detect genetic diversity in plants

Thomas Schmutzer
(IPK Gatersleben; Department of Bioinformatics and Information Technology)

High-throughput  sequencing (HTS) methods provide reliable and at the same time cost efficient DNA sequencing. With the continues drop of costs genome project nowadays address more and more the broad diversity of multiple individuals or even whole populations.

Biodiversity in crops plants is challenging especially because of their large genome sizes and complexity, caused by an immense repeat content with up to 80 – 90% in barley or rye. The study is reviewing modern methods for diversity detection in plant genomes. Therefore the spectrum of species integrated in this study is broadly chosen. Captured species range from small genomes like the carnivorous plant species Genlisea nigrocaulis (86 Mb) to the crop plant rye with an almost 100-fold larger genome (7.9 Gb), including further genomes of  agricultural important crops like maize (2.3 Gb) and barley (5.1 Gb). The methodology review introduces various approaches of sequencing strategies like transcriptome sequencing (RNAseq), whole genome shotgun (WGS) sequencing or targeted sequencing like Sequence Capture (CapSeq), and is evaluating their applicability in large genome projects. Algorithms applied to these extensively produced HTS data are of crucial importance to construct reliable assemblies or read alignments, and in consequence detect meaningful genetic variation. The review of standard tools for the detection of diversity will introduce and evaluate various methods illustrating the impact of accuracy in all project phases.