Plastid genome assembly from low coverage WGSS data

This post describes the steps I took to assemble plastid genomes from low-coverage WGSS data. An overview of the approach can be found here.

Essentially, the method involves first mapping of quality-filtered reads to a reference plastid genome, and only selecting plastome-like reads from this mapping step for subsequent de-novo assembly. For the assembly step, I used the VELVET assembler, which performs well for small genomes and is quite fast.

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DNA ploidy and genome size estimation using flow cytometry (Dan B.)

Flow cytometry (FCM) is – in principle – a relatively simple technique that allows one to measure properties of cells or organelles as they are intercepted (individually) by a high-intensity light source. In plant biology, it is often used to analyze extracts of intact nuclei, with the aim of determining DNA content and (indirectly) ploidy levels (this is the application I will focus on here). A good reference (including troubleshooting tips) can be found here.

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