Resources Available for Fragaria Research through the Genome Database for Rosaceae Dorrie Main, Sook Jung, Chun-Huai Cheng, Stephen Ficklin, Taein Lee, Jodi Humann, Jing Yu, Ping Zheng, Cameron Peace, Kate Evans, Ksenjia Gasic, Mercy Olmstead, Lisa Wasko DeVetter, Michael Kahn, Jim McFerson, Albert Abbott, Nahla Bassil* 8th International Strawberry Symposium August 13-17, 2016 Quebec, Canada Thank you for the opportunity to present the available fragaria resources in GDR at this symposium.

Introduction GDR was initiated in 2003 to curate, house and integrate emerging Rosaceae genomics, genetics and breeding data provide access to data mining tools facilitate comparative genomics within the family Funded through 2019 (USDA SCRI, NRSP10, NSF) Fragaria genomic and genetic data in GDR is provided by the community and collected from publications. Nahla this is just a slide introducing GDR to the audience (many won’t be familiar with it) You can essentially just read this slide point by point.

Last week a newly designed GDR was released Last week a newly designed GDR was released. The new design addresses many of the suggestions made by the community through a user survey and should make it more obvious for scientists to access the information they are looking for. In the next few slides I will give a brief overview of data and functionality relevant for Fragaria scientists (advance slide). So the first thing you can see is that we now have a major genera quick start and highlighted here is the genus fragaria. If you click on this it will take you to the same all fragaria species page available through the species dropdown menu on the top navigation bar <advance to next slide> New GDR Design

In the Species pages we also show major species for which there is data available, for fragaria <advance slide> this is vesca <advance slide> and x ananassa. If we select one of these it takes us to the species overview page <advance slide>

Species Overview Page - vesca So the species overview page is divided into 3 main sections <advance slide> the fist is the central panel which gives you a quick summary about the species, including genome size and numbers for major data types. So in this case we can see there are 96,910 markers in the databases for vesca and 3 genome assembles but no phenotypic or genotypic data available. On the side panels <advance slide> we have a section for data and here it only lists those data categories for which there is data available <advance slide> and the bottom left pane shows what tools are available for that species.For vesca this includes genome browsers, synteny browsers, fragaria pathway database, Kegg browser etc <advance slide>

Species Overview Page – ananassa So the species overview page is divided into 3 main sections <advance slide> the fist is the central panel which gives you a quick summary about the species, including genome size and numbers for major data types. So in this case we can see there are 96,910 markers in the databases for vesca and 3 genome assembles but no phenotypic or genotypic data available. On the side panels <advance slide> we have a section for data and here it only lists those data categories for which there is data available <advance slide> and the bottom left pane shows what tools are available for that species.For vesca this includes genome browsers, synteny browsers, fragaria pathway database, Kegg browser etc <advance slide>

Under the data dropdown in the navigation bar are various categories providing information on data available, how to submit data and a new feature we added <advance slide> was a link to all the NCBI RNASeq and DNA data sets <advance slide>

Please note we only list those SRA datasets that have are associated with a publication. For the RNASeq data we are in the process of creating Reference Transcriptomes for all the major genera and major species in GDR. Look at the Rubus RefSeq v1.0 in GDR to see what that delivers. It includes mapping to the reference genomes and annotation of the reference transcripts, which are fully searchable in the gene and transcript search page <advance slide> Links to published NCBI SRA For the RNASeq data we are creating Reference Transcriptomes for all the major genera and major species in GDR (see Rubus)

Here is a list of the current search pages available on GDR Here is a list of the current search pages available on GDR. Many of the search pages have been modified and short audio visual and text tutorials are available for each of them on each search page. <advance slide> Lets look at an example of the Gene and transcripts search feature. Many of the search features on GDR have been modified and short audio visual and text tutorials are available for each search page and the site overview.

Here you choose Fragaria genus, NCBI Rosaceae gene and mRNA sequences dataset, which is a dataset with the genes and mRNAs parsed out from all NCBI nucleotide sequence database, and type GBSS as a gene name. You can download the data in Excel table or download the sequences in Fasta file. To view the detail of the gene in a gene page, you can click the gene name. All Fragaria NCBI genes and mRNAs are aligned against the F. vesca v1.1 genome when they had enough homology. You can view the genomic region where the NCBI sequences are aligned. If you want to see the details of the F. vesca genes in that region, click this link. <advance slide>

In this gene details page, find out all the associated genome location, functional annotation, sequence, alignments, analyses etc for that gene. From the gene details page, find out all the associated genome location, functional annotation, sequence, alignments, analyses etc for that gene.

New synteny analysis between apple, peach, strawberry and pear In the Tools dropdown section you can see all the tools available on GDR. Please note that in the two blast servers you have access to ALL the sequence datasets in GDR that you can blast your sequences too. New synteny analysis between apple, peach, strawberry and pear

Choose the synteny analysis depending on what version of the genome assembly you are working with – v2.0 or v1.1 Choose the synteny analysis depending on what version of genome assembly you are working with – v2.0 or v1.1

peach strawberry apple strawberry pear This shows a syntenic region from the latest analysis. This genomic segment has conserved synteny among all four genomes. The upper part shows syntenic regions of strawberry and peach and the lower part shows those of strawberry, apple and pear. pear

The Breeders Toolbox provides access to current RosBREED 1 data for strawberry. New comprehensive Breeding Information Management System being developed in GDR In the Tools dropdown section you will also see the breeders toolbox. The Breeders Toolbox provides access to current RosBREED data for strawberry <advance slide>

Browse or search available phenotype, genotype or haplotype data Here you can Browse or search available phenotype, genotype or haplotype data <advance slide> Browse or search available phenotype, genotype or haplotype data

And finally ….. Explore GDR to find all the data and functionality available for Fragaria research – contact us about using FieldBook App for phenotype data collection Join our GDR mailing list to find out what is new, receive newsletters events etc. Let us know if you have any problems, request new or improved functionality Attend our 2 hr training workshop at PAG where most presentations will be by users of GDR If you use GDR please site us (Jung et al., 2014) As always thanks for your continued support of GDR  17

Acknowledgements USDA SCRI, USDA NRSP10, NSF Plant Genome Program, USDA-ARS, SAAEDS, Washington Tree Fruit Research Commission, Cotton Incorporated, USA Dry Pea and Lentil Commission, Northern Pulse Growers, Mars Inc. Mainlab bioinformatics team and various projects CoPIs/PIs Rosaceae, Citrus, Blueberry, Legume, Cacao, Cotton and Bioinformatics Communities US Land Grant University researchers and extension agents 18