Profiles

Jörg Bachmann

Jörg Bachmann

Doktorand

Visa sidan på svenska
Works at Department of Ecology, Environment and Plant Sciences
Telephone 08-16 37 52
Email jorg.bachmann@su.se
Visiting address Svante Arrhenius väg 20 A
Room N505
Postal address Institutionen för ekologi miljö och botanik 106 91 Stockholm

About me

I am a PhD student in the Evolutionary Ecology pogram focusing my work on Evolutionary Genomics. My thesis is part of the project “Evolutionary consequences of dominance at a locus under long-term balancing selection”. 

My thesis is supervised by Tanja Slotte (Associate Senior Lecturer) and my work is split between Scilifelab Stockholm and the Department of Ecology, Environment and Plant Sciences (DEEP) at Stockholm University.

Other

I act as the chairman of the PhD council at DEEP. You can contact me or vice-chariman Peter Bruce directly on PhD related issues or bring up anything during our regular PhD meetings. Follow me on twitter, for topics related to Evolutionary Genomics.

Research

Self-incompatibility (SI) describes a genetic mechanism that promotes outbreeding between hermaphrodites by rejection of “self-pollen” on pistils. 

In Brassicaceae, genes coding for recognition between pollen and pistil are found tightly linked at a genomic region (S-locus). My project focuses on mating system evolution in the genus Capsella, where I am investigating the genetic basis of S-locus dominance and its consequences at the sequence and phenotypic level, as well as parallel losses of SI

Publications

A selection from Stockholm University publication database
  • 2018. Jörg A. Bachmann (et al.). G3 8 (4), 1327-1333

    Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7x10(-5). A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach.

Show all publications by Jörg Bachmann at Stockholm University

Last updated: December 11, 2018

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