Apple day
Apple Day is a celebration of everything related to apples. A celebration of their huge variety, cultural impact, and economical importance. Apples are entwined with human history for at least the past 3000 years. Today in the UK, there are more than 7000 different cultivated varieties (cultivars) of apples, from cooking, to dessert, to cider apples. Each individual apple represents an individual apple tree, frozen in time. There are some cultivars of apple eaten today which are direct copies of an original tree which may have existed over 1000 years ago.
We aim to study the DNA of apples more closely to understand what diversity there is at the genetic level, and why this might be important. As part of the Darwin Tree of Life (DToL) project, we have sequenced the whole genome of over 50 apple individuals, representing many cultivars of apples. We also include wild crab apples. Remarkably, using the newest sequencing data types, and with the expertise of the people working on the DToL project, we are able to assemble our five reference genomes into entire chromosomes. Using this data, we hope to uncover new biology!
This repository
Useful information about the data used in this project can be seen in the /data directory. This contains information about which cultivars and species were sequenced, and metadata associated with each one scraped from the national fruit collection website.
Most (if not all) the methods I have used to generate data and any analyses so far can be found in the /src directory. This includes everything from web scraping, to making HTML docs, fetching data, and other things like variant calling. There is a detailed run-through of the methods used in the README.md file in the /src/analysis directory.
Hello to any collaborators; if you wish to discuss/contribute please either email me (mb39 [at] sanger.ac.uk) or raise an issue in this repository!
Outreach
We have done several outreach projects so far. A growing list:
- Hinxton Hall: Hidden Heritage and Home Grown Veg.
- In collaboration with the Royal Botanical Gardens Edinburgh, we talked about Apple Day with the public, showcasing the many Scottish varieties of apple present in the gardens, discussing the origins of apples, and highlighting the research we are doing here at DToL. There is also an adapted post on the DToL website.
- RHS Wisley half term Apple Day outreach. An informal public forum for chatting to the public in the atrium of the newly built RHS Hilltop.
- Curiosity Club organised by Wellcome Connecting Science.
A special thanks to Jack Monaghan for organising these activities.
People
None of this would have been possible without the immense time and effort from a great many people. I am especially grateful to Michelle Hart who took the time to write a Standard Operating Procedure specifically for collecting apples and who shared it with all the partners.
The partner institutions are:
- Royal Botanical Garden Edinburgh
- Royal Botanical Gardens Kew
- Cambridge University Botanic Garden
- East Malling Research
- RHS Wisley
- Wellcome Sanger Research Institute
- The National Trust
There are many people to thank, I list them below:
- Mark Blaxter
- Kerstin Howe
- Marcela Uliano-Silva
- Matthieu Muffato
- Amanda Karlstrom
- Lee Outhwaite
- Kalman Konyves
- Markus Ruhsam
- Peter Hollingsworth
- Sam Brockington
- Jack Monaghan
- Caroline Howard
- Shane McCarthy
- Alan Tracey
- Max Coleman
- Alex Twyford
- Tom Hooijenga
- Nancy Holyroyd
- Ian Still
- Maja Todorovic
- Ilia Leitch
- Jennifer Johns
- Michelle Hart
- David Bell