Update and description of the blueberry genome. Describes annotation process of using gage and pathview to identify key pathways detected in the genome.
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Update on the assembly and annotation of the blueberry genome
1. www.P2EP.org
THE CURRENT STATUS OF THE
BLUEBERRY GENOME
Robert Reid
rreid2@uncc.edu
Department of Bioinformatics & Genomics
University of North Carolina Charlotte
BLUEPRINTS FOR BLUEBERRY
5. www.P2EP.org
MARKER ALIGNMENT TO
SCAFFOLDS
Linkage Map # of markers # of scaffolds Size (bp)
*Tetraploid - Draper 689 358 121,530,818
*Tetraploid - Jewel 576 328 112,427,224
Interspecific hybrid 322 190 74,069,152
Diploid 318 153 56,781319
Cranberry 138 40 15,934975
696 scaffolds were assigned to at least one linkage group, the total size was 214
Mb
*earlier version of map markers than what was published
11. www.P2EP.org
2 AVAILABLE ONLINE ANNOTATION
RESOURCES
https://www.vaccinium.org
Anne Lorraine http://bioviz.org/igb/index.html
Dorrie Maine - WSU
12. www.P2EP.org
FUTURE STEPS FOR GENOMICS
• Improving the genome
• Massimo Iorizzo
• Hamid Ashrafi
• Jeannie Rowland
• Improve contiguity
• Resolve repeat regions
• Fill in the gaps
• Improving the linkage maps
• Higher density map
• More anchoring points
• Optical map
• To improve scaffold / contig ordering
13. ACKNOWLEDGEMENTS
• Allan Brown –CGIAR
• Ying-Chen Lin –NC State
• Mary Ann Lila –NC State
• Ra’ad Gharaibeh -UNCC
• Rachel Walstead -UNCC
• Gregario Lingchanco-UNCC
• Cory R Brouwer -UNCC
• Jeannie Rowland –USDA-ARS
• Dorrie Maine - WSU
• Garron Wright – DHMRI
• Mark Burk – DHMRI
• James Olmstead – U of Florida
• And many more
Editor's Notes
P2EP started approximately 3 years ago and is a collaboration between universities and industry studying the nutritional qualities of blueberries, broccoli, oats, strawberries, pineapple and bananas. The program has a major educational component as well and last summer we had 40 grad, undergrad and even a couple high school students actively participating in nutritional research.
The blueberry genomic project in NC State has been actively carried out for several years. Here I want to when and what we have done on this project.
Before 2011, we've already have some Illimina short sequences, which were only 36~76 basepairs, we also have long sequences from 454-pyroseuqences.
I came to the United States and joined this project in 2012. During these three years, so far, we did one more sequencing using Illumina, and created several version of assembly with different assembler software.
Before this April, Newbler assembly was the primary assembly we used for this project. But after we got the BAC-end sequence from BAC libraries, we were able to re-assemble the scaffolds, putting some small pieces together which was really difficult when you only have fragmented scaffolds. Then, now we have a more SSPACE assembly that contained much larger scaffolds than previous one.
For all the species that have been studied well in anthocyanin biosynthesis, grapevine (Vitis vinifera) is suggested to be the closest related species, which just published early this year, so here we used grape protein sequences as reference to search in blueberry genome.
The first step was to search grape's protein sequences in KEGG pathway (Kyoto Encyclopedia of Genes and Genomes), then blast against blueberry scaffold data, which is stored in genome database for vaccinium website. From the blast results, we can know which scaffold contained putative genes, and start/stop point of the genes, also got the blueberry protein sequences.
