1. Updates and Future Direction
Good Morning. I’d like to thank the conference committee for the opportunity to update the community on new data and functionality in CottonGen and outline our plans for future development.
Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Jodi L. Humann, Deah McGaughey, Heidi Hough, B. Todd Campbell, Richard G. Percy, Don C. Jones, and Dorrie Main
WCRC-6/ICGI 2016 Research Conference Brazil, May, 2016

2. CottonGen Overview
CottonGen is the community database for genomics, genetics and breeding (GGB) data – it integrates curated data and tools to help facilitate basic, translational and applied research in cotton
Hosts the ICGI website within it and serves as a communication portal for cotton GGB science
It is funded by a partnership between the cotton industry, university and federal support (NRSP10)
Just a quick reminder about CottonGen – then read the slide essentially

3. Presentation Outline New web design New data New functionality
Future work
I am going to start by providing a quick overview of the new website design, followed by a summary of the major data and functionality, with a focus on what is new followed by some examples of the tools and then finish of with future activities so you know what is coming.

4. In the last six months we have redesigned CottonGen to make it easier for you to access all the data and tools it houses. From the top navigation bar, which should be available on every page, you can easily access all the data and tools and information housed in CottonGen 4

5. Species Data Search Tools ICGI General
Here we see all the current links available from the dropdown menu by category, which we have grouped according to species, data, search, tools and ICGI and more general information. Under the general category you will find links on usage of CottonGen and how to reference us (please do reference us if you use CottonGen in your research). You will also see what we are working on and what has been completed. 5

6. From the home page we have also added a Tools by category quick start menu and a major species quick start section so you can start the explore the database from here 6

7. For example if you click on the major species images here it will take you to individual species pages 7

8. From the individual species pages you can see links to all the specific data and tools available for that species of interest – in this case barbadense. These include links to genome browsers, synteny browsers, comparative map viewers, pathways and blast tools 8

9. Major Data Sets Summary – newly added
6 versions of 4 cotton genome sequences and annotations (A2, D5, AD1, AD2) – includes CottonGen functional annotation (KEGG, GO, DOMAINs, BLAST match description)
USDA NCGC images, phenotypic and genotypic data
52 Genetic maps - CottonSNP63K 3-79 x TM-1, F2 (2015) and CottonSNP63K Phytogen 72 x Stoneville 474, F2 (2015)
Cotton63KSNP array
In terms of major data sets we have the following, with the ones indicated in red just recently added to cottongen – read them out

10. Major Tools – newly added or updated
GBrowse - annotated 6 versions of 4 genome sequences
D5 (BGI and JGI), A2 (BGI), AD1 (NBI and BGI), and AD2 (NBI)
gene models, mapped transcripts, mapped markers, putative gene function assignment, KEGG, Interpro domains, GO
GBrowse_Syn - raimondii vs arboreum synteny
CottonCyc - raimondii (D5) and hirsutum (AD1)
Search genes, transcripts, markers, germplasm, traits, sequences, QTLs, and publications
Major functionality includes the following with those in red being either new or updated – read them out

11. GBrowse_Syn: D5-JGI.v2 and A2-BGI.v2
80.7% of A2 is collinear with D5 and 88.2 % of the D5 genome is collinear with the A2 genome
Just looking at a few of these new features, here is Gbrowse_Syn
CottonGen has now Gbrowse_Syn where you can browse conserved syntenic regions between genomes.
Currently we have done the analysis between G. arboreum (A2) genome BGI assembly v2.0 and G. raimondii (D5) genome JGI assembly v2.0.
The analysis was done using i-ADHoRe v3.0 and OrthoMCL program
80.7% of the A2 is collinear to D5 genome and 88.2 % of the D5 genome is collinear to A2 genome.
This image shows that a region of chromosome 5 of G. raimondii is conserved with regions in chromosomes 5 and 12 of G. arboreum.

12. CottonCyc and JBrowse
Browse and search the Cotton Genes Metabolic Pathways Database
View and search genome sequence, genes, mapped markers, etc. using GBrowse and JBrowse
In this slide you can see CottonCyc and Jbrowse where you can – read out the text

13. Search Traits
The search traits feature allows you to search for all the trait evaluation data stored in CottonGen

14. Retrieve Sequences
Retrieve fasta formatted files of any sequences in CottonGen using the Sequence Retrieval tool. For data associated with the genome sequences it includes ability to retrieve sequence for a specified number of bases upstream and downstream of sequence
From the retrieve sequence tool you can – read out the text on the right

15. Future Work
Create reference transcriptomes for major Cotton species using published RNASeq data and EST data from NCBI – functionally characterized, searchable and mapped to genomes
Development of Breeding Information Management System (BIMS)
Add synteny analysis and pathways for other cotton genomes
Add more phenotypic and genotypic data from multiple projects
Add Cotton Variety Test data and make them searchable
Future work includes – read out text

16. WCRC-6/ICGI 2016 Research Conference Brazil, May, 2016
Thanks and Questions?
WCRC-6/ICGI 2016 Research Conference Brazil, May, 2016

17. CottonGen Usage Mar 31, 2012 to Dec 31, 2015 Quarterly 22,607 visitors
47,574  visits
282,721 pages
155 countries
Quarterly
2000 visitors
4800  visits
23,000 pages
90 countries