Tag: hybrid capture

Polytrichum baits: cutting cleaned mosses

Following on from the rather unpredictable results we obtained from fragmenting duplicate aliquots of CTAB-extracted Polytrichum DNA in the Bioruptor, Isuru cleaned aliquots of IK31 and IK53 using…

Polytrichum baits: Cutting mosses

We started our lab work on the Polytrichum hybrid baits project on the 1st of October, by normalising some CTAB-extracted DNA with 0.1X TE to 55 µL of…

Generating a phylogeny of Polytrichum using hybrid baits

The current Next Gen Sequencing lab project at the Botanics involves looking at the phylogeny of Polytrichum section Polytrichum, using hybrid capture. The work will form part of…

Hybrid capture from degraded DNA: quality metrics for duplicate extractions

For one of the taxa in our study set, Begonia scottii (living collection no. 20170076), we made a few replicate DNA extractions using Qiagen DNeasy plant mini-kits, and…

Hybrid capture from degraded DNA: bead cleaning degraded Begonia DNAs

The set of DNA extractions from one of our test plants (#8, Begonia stictopoda RBGE accession 20170115) contained rather low concentrations of DNA. We decided against preparing NGS…

Hybrid capture from degraded DNA: test Begonia sample quality

Keen to see the effects of different specimen preservation techniques on DNA quantity and quality, we have assessed extractions of DNA from nine Begonia accessions x seven preservation…

Hybrid capture from degraded DNA: Squashing Begonia

In order to look at the effects of herbarium preservation methods on DNA quality, Hannah Wilson and Mark Hughes took a trip down to our research glasshouses, and…

Hybrid capture from degraded DNA: choosing Begonia

The megadiverse genus Begonia L. is one of the world’s largest plant genera, comprising over 1,800 species, an estimated 200 of which are endemic to New Guinea. A…

Hybrid capture from degraded DNA: stockpiling Begonia DNA for protocol testing

When working out new protocols, it’s very useful to have a big stash of DNA to test them on. Just now, in a collaborative project with Dr Michelle…

Capturing Genes from Herbaria. XI. Some metagenomics of a herbarium specimen

As part of our hybrid capture project, we sampled from an Inga umbellifera specimen that was collected about 180 years ago, by Andrew Mathews, in Peru in 1835….

Capturing Genes from Herbaria. VII. Comparisons.

As previously mentioned, we tested two different kits in our NBAF project. The first is the Illumina Tru-Seq Nano library preparation kit (FC-121-4001), which recommends a starting DNA…

Capturing Genes from Herbaria. VI. Size selection

A few days ago, I read a tweet from the Botany2015 meeting in Alberta that described DNA extracted from herbarium specimens as “pre-sheared”. This resonates with our own…