Science

Latest science blog posts from the Royal Botanic Garden Edinburgh

Aug 282015
 
Wartime Rhododendron

  In the Autumn of 1914, George Forrest was travelling in China. His letters written at the time mention the difficulties he was facing in getting permission to cross the river into the Mekong-Salwin divide. He also describes the difficult weather conditions. In August he wrote: ‘The whole country is under water, the hills and […]

Aug 142015
 
Capturing Genes from Herbaria. VIII. Amplification

Both the Tru-Seq and NEB libraries were amplified pre-hybrid capture – another step at which modifications were made, according to how much DNA there was in each library. Bioanalyser traces for the pre-amplification Tru-Seq libraries are shown below: The number of PCR amplification cycles used for both Tru-Seq and NEB for each library are given […]

Aug 142015
 

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 quantity of 100 ng. We also used NEB‘s NEBNext Ultra library preparation kit for Illumina (E7370S), which has been optimized for as little as 5 ng of […]

Aug 122015
 
Amorphophallus titanum – Preserving it for posterity

The flowering of our Amorphophallus titanum (titan arum) was a tremendous event with c 19,000 people visiting the Glasshouses to see the plant growing from a small bud to a massive 2.6 metre inflorescence.  As the flower began to fade and flop we took the opportunity to collect important parts of the plant and preserve […]

Aug 102015
 
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 experiences with Inga, where herbarium DNA required very little, if any, fragmentation. However, this is only part of the library preparation; we optimized other parts of the […]

Aug 042015
 
British Algae online

Here at the RBGE we have just finished digitising our collection of British Rhodophyta (Red Algae), a total of 7850 specimens. Our collection dates from present day right back to 1777 with the Menzies Herbarium. Red algae get their colour from pigments such as Phycoerythrin and Phycocyanin that block or mask other pigments such as […]

Jul 312015
 
Capturing Genes from Herbaria. V. Fragmenting the DNA

The mantra for many years for next generation sequencing has been, like “garbage in, garbage out”, that the optimal starting point is high quality, high molecular weight DNA. For many of my favourite plants, getting this DNA, and not the actual sequencing, is the hardest part of the project. It’s a bit upsetting, then, when […]

Jul 302015
 
Capturing Genes from Herbaria. IV. DNA

In March this year, having already chosen and obtained the plant material that we were going to use for our NBAF project on using a hybrid bait protocol to recover DNA sequences from herbarium material, Michelle Hollingsworth and I started on the DNA extractions. Although there were only seven accessions of Inga umbellifera, multiple DNA […]

Jul 302015
 
Capturing Genes from Herbaria. III. The Samples.

Having chosen Inga umbellifera as the study organism for our NBAF-funded project to test the use of hybrid baits for recovery of DNA sequences from herbarium material, we had to pick a set of herbarium specimens from which to extract DNA. The funding we had received would allow us to make and sequence about 30 […]

Jul 292015
 
Capturing Genes from Herbaria. II. Inga.

About 300 species of Inga (Leguminosae: Mimosoideae: Ingeae) grow in lowland and montane rain forest throughout the humid tropical zone, from Mexico to Uruguay. Most species diversity is in the Andean foothills of Peru, Ecuador, Colombia and southern Central America, where it occupies a variety of habitats up to 3000m. The genus was monographed in […]