2013

iPlant workshopMarcela Karey Monaco

2013

What is Gramene?

• An integrated plant reference genome resource

• Comparative genomics hub of data & tools for the analysis and visualization of plant genomes data informed by evolutionary histories

• Genome sequence, gene annotations, genetic & structural variants, metabolic & regulatory pathways

2013

Gramene offers…

• Genome sequence & gene annotations– 28 complete & 9 partial reference genome assemblies

2013

Gramene Release 39• 28 complete reference genomes•15 Monocots• 9 Eudicots• 4 Lower plants• 9 partial assemblies

Fully sequenced reference genomes in Gramene

2013

Gramene offers…

• Genome sequence & gene annotations– 28 complete & 9 partial reference genome assemblies– Variation data for 9 plant varieties

2013

Variation in Gramene Ensembl Browsers

Species Variants Source Studies

Oryza sativa ssp japonica 3,332,525160K SNPs x 20 accessions1311 SNPs x 395 accessionsNCBI dbSNP

McNally et al. (2009). PNAS 106:12273-12278Zhao et al. 2010. PLoS ONE. 5:e10780

Oryza sativa ssp indica 4,747,883 NCBI dbSNP

Zea mays 50,719,843HapMap1: NAM founder linesHapMap2: pre-domesticated & domesticated lines

Gore et al. 2009. Science 326:1115-1117. Chia et al. 2013. Genet 44:803-807.

Arabidopsis thaliana 14,234,197SV: 13,667

250K SNPs x 1179 accessions1001 genomes project: 411 resequenced accessions

Atwell et al. 2010. Nature. 465:627-631.

Brachypodium distachyon 327,988 2 accessions of Brachypodium sylvaticum

Fox et al. (2013) Applications in Plant Sciences 1(3):1200011. 2013

Vitis vinifera 457,404 Resequencing USDA germplasm collection Myles S, et al. 2010. PLoS ONE. 5:e8219.

Hordeum vulgare 12,994,003 Resequencing 4 accessions plus wild barely

The International Barley Genome Sequencing Consortium. 2012. Nature 491, 711–716

Oryza glaberrima 7,704,409 Resequenced 20 accessions African rice & wild progenitor Oryza Genome Evolution project

Sorghum bicolor SV: 64,507 Structural variants from Database of Genomic Variants archive (dGVA) Zheng et al. 2011. Genome Biol.. 12:R114.

2013

Gramene offers…

• Genome sequence & gene annotations– 28 complete & 9 partial reference genome assemblies– Variation data for 9 plant varieties

• Comparative analysis– Phylogenetic gene trees => Ortholog predictions– 56 whole genome alignments– 20 synteny maps

2013

Gramene offers…

• Genome sequence & gene annotations• Comparative analysis• New functionalities

– Highlight gene trees with InterPro & GO – Variant Effect Predictor service: user loads VCF– Upload private data and view in browser (BAM, VCF, GFF) – Assembly converter service

2013

Demo of www.gramene.org

2013

Gramene offers…

• Genome sequence & gene annotations• Comparative analysis• Tools & services

– Genome browser– GrameneMart– FTP site– Public MySQL

2013

GrameneMart

Use case: Find transcription factors having “stop_gained” alleles

• Custom queries for data mining• Gene-based & SNP-based queries• Map, markers, and QTL data

2013

FTP site & MySQL serverFTP site for bulk downloads:

ftp://ftp.gramene.org/pub/gramene/

> mysql -hgramenedb.gramene.org -pgramene

2013

Gramene offers…

• Genome sequence & gene annotations• Comparative analysis• Tools & services• Metabolic & regulatory pathways

– BioCyc platform– Plant Reactome

2013

BioCyc-formatted Pathway DBs

Developed by Developed by GrameneGramene

Developed by Developed by GrameneGramene

2013

Pathway Database Browse Options

Download to get a stand alone copy of the RiceCyc database

2013

Gibberellin Biosynthesis I (non C-3, non C-13 hydroxylation)

Manual Curation?Evidence / SupportManual Curation?

Evidence / Support

EnzymeEnzyme

Zoom up to chemical structures

Zoom up to chemical structures

Compound /

Metabolite

Compound /

Metabolite

2013

Object Comparison Organism Selection page

Comparison of a Metabolic Pathway Across Species

Click to visit pathway

Click to visit pathway

Click to visit the Gene/

gene product

Click to visit the Gene/

gene product

Click to visit the reactionClick to visit the reaction

2013

Pathways• BioCyc databases• Plant Reactome

– 129 rice pathways – Arabidopsis, maize, other plant models

2013

2013

Search for pathways, reactions, and genes

2013

Advanced Search

2013

Synergy between Gramene & iPlant

• Genetic variation data submission– VCF formatting of data for import into Ensembl Variation

repository

• Representation of the Pan-Genome– Large computational cost of genetic (k-mer) mapping

• BioCyc-formatted databases to be served from an iPlant virtual server

2013SAB 2013

AcknowledgementsDoreen Ware, PI (USDA ARS, CSHL)Yinping Jiao, Sunita Kumari, Zhenyuan Lu, Marcela K. Monaco, Andrew Olson, Shiran Pasternak, Joshua Stein, Jim Thomason, Sharon Wei, Ken Youens-Clark, Bo Wang, Liya Wang Pankaj Jaiswal, Co-PI (OSU) Vindhya Amarasinghe, Palitha Dharmawardhana, Sushma Naithani, Justin Preece

Paul Kersey / Helen Parkinson (EMBL-EBI)Dan Bolser, Arnaud Kerhornou, Dan Staines, Brandon Walts / Nuno Fonseca, Maria Keays, Robert Petrysyk, Eleanor Williams

Lincoln Stein (OICR) Robin Haw; Peter D’Eustachio (NYU); Guanming Wu; David Croft (EBI)

Crispin Taylor (ASPB)Patty Lockhart