Comparative genome analysis data resource

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Comparative genome analysis data resource

• Or, Gramene, A Web-accessible database available
  at http//www.gramene.org

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Overview

• Background (Gary)
• Genomic sequence data (Aaron)
• Databases and ontologies (Paul)
• Web site overview (Zhiping)
• Real world query (Nolan)

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What is a comparative genome analysis data
resource?

• Our goal is to facilitate the study of
  cross-species homology relationships using
  information derived from public projects involved
  in genomic and EST sequencing, protein structure
  and function analysis, genetic and physical
  mapping, interpretation of biochemical pathways,
  gene and QTL localization and descriptions of
  phenotypic characters and mutations.

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Where does Gramene fit in?

• Lies somewhere between a resource like a Model
  Organism Database (MOD) and a resource like the
  National Center for Biotechnology Information
  (NCBI)
• Gramene
• MOD (specific) NCBI (general)
• NCBI
• a national resource for molecular biology
  information

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What is a MOD?

• Model Organisms
• Set of organisms studied in great detail
• Advantages for experimental research
• e.g. S. cerevisiae, D. melanogaster, D. rerio,
• Model Organism Databases
• Core data resource for a community
• Integrates data from many sources with expert
  domain knowledge, e.g. FlyBase http//flybase.bio.
  indiana.edu
• Gramene
• Is like a MOD for Rice
• And a comparative grass genomics resource

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Gramene scope

• Genomic data Phenotypic data

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Gramene scope

• Rice
• whole genome sequence
• Other crop grasses
• Maize
• Sorghum
• Millet
• Sugarcane
• Wheat
• Oats
• Barley

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Synteny in Gramene

• Synteny
• genes on the same chromosome
• Conserved synteny
• genes on same chromsome in one species also found
  together on same chromsome in another species
• Synteny among crop grasses
• Rice genomic sequence a window onto other genomes

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Gramene curation

• Curation is the use of expert domain knowledge to
  enter data into a database
• Much of the rice data is curated
• Maps
• Markers
• Proteins
• Phenotypes
• Literature
• Other data automated

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Importance of MODs()

• Researchers becoming dependent on for information
  needed to do research
• Gramene uses rice as framework to organize
  information for other grasses
• Provides comparative maps
• Maize has huge amount of classical genetic data
• Whole is greater than the sum of the parts

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Crown Eukaryote Genome Sequencing Projects
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Cereal Genome Sizes

• Sorghum 1000 Mb
• Maize 3000 Mb
• Barley 5000 Mb
• Wheat 16,000 Mb
• Rice 420 Mb

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Two rice genomes

• Beijing Genomics Institute (established 1999)
• Private nonprofit, sequence available on GenBank
• Oryza sativa indica
• 4 x coverage, 99.9 accuracy
• Shotgun sequencing of small insert clones
• RePS assembly (repeat-masked Phrap with
  scaffolding)
• Did not assemble across highly repetitive regions
• Syngenta
• Private, sequence available, but not on GenBank
• Oryza sativa japonica
• 6 x coverage, 99.8 accuracy, 10 of cost of
  IRGSP
• Shotgun sequencing of small insert clones,
  assembly anchored by genetic and physical maps
• Compared against International Rice Genome
  Sequencing Project sequence for quality control

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Japonica and Indica
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The Rice Genome

• 32,000 62,000 genes, depending on how you
  predict genes and count them
• 77 of predicted genes showed homology to another
  predicted gene within genome
• estimated 15,000 gene families
• Polyploidization event 40-50 mya
• 85 of Arabidopsis genes have homolog in rice
• 50 of predicted rice genes have Arabidopsis
  homolog (annotation problems?)
• 8000 Arabidopsis proteins (33) found in rice but
  no other sequenced genome plant specific
• 25 of genes involved in metabolism

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Predicted Functions
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Proportion of genome allocated to given functions
similar Rice - Arabidopsis
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Cereal GC content unusual among sequenced genomes
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Comparing the two subspecies
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Repetitive Elements
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Genes from other cereal genomes have homologs in
Rice
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Rice and Maize Synteny
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Ontology/Controlled vocabulary

• Ontology as a Collaboration tool
• Gene Ontology Gene Ontology Consortium
• Molecular function of a gene product
• Biological process
• Cellular component that identifies the
  localization of the protein in a cell
• Plant Ontology
• Anatomy
• Developmental stages
• Trait Ontology
• Traits

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Trait Ontology (TO) to describe
Mutants/phenotypes in rice
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Informatics Organization
Firewall
Phenotype
Map CUGI,FPC
Ontology GO,TO,PO
Grass Genes and Proteins
SWISSPROT_ACC SWISSPROT_ID Gene_Product_Descripti
on Q06967 1433_ORYSA 14-3-3-like protein S94
Q07215 1A11_ORYSA 1-aminocyclopropane-1-carboxyla
te synthase 1ACC1ACC synthase
1S-adenosyl-L-methionine methylthioadenosine-lyas
e 1 P17814 4CL1_ORYSA 4-coumarate--CoA ligase
14CL14-coumaroyl-CoA synthase 14CL4CL 1
Q42982 4CL2_ORYSA 4-coumarate--CoA ligase
24CL24-coumaroyl-CoA synthase 24CL 24CL.2
P37833 AATC_ORYSA Aspartate aminotransferase,
cytoplasmicTransaminase A
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Rice Protein Sequence

• gt1433_ORYSAQ06967
• MSPAEASREENVYMAKLAEQAERYEEMVEFMEKVAKTTDVGELTVEERNL
  LSVAYK
• ARRASWRIISSIEQKEESRGNEAYVASIKEYRSRIETELSKICDGILKLL
  DSHLVPSATA
• AESNVFYLKMKGDYHRYLAEFKSGAERKEAAENTLVAYKSAQDIALADLP
  TTHPIRLG
• LNLSVFYYEILNSPDRACNLAKQAFDDAIAELDTLGEESYKDSTLIMQLL
  RDNLTLWTS
• NAEDGGDEIKEAAKPEGEGH

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Gramene a tool for grass genomics(www.plantphysi
ol.org/cgi/doi/10.1104/pp.015248)

• A comparative genome mapping database for grasses
  and a community resource for rice.
• It combines cereal genomics, ESTs, genetic maps,
  map relations and publications.
• Comparative maps of rice, maize, sorghum, barley
  and oat.

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Map SearchComparativeMaps
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Map Search matrix
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Map Search Physical Maps
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Map Search Physical Maps
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Map Search Physical Maps
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Rice Genome Browser
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Orthology, paralogy and determining gene functions

• Nolan Kane

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Homologs, orthologs and paralogs

• Homologs - any genes related by common decent.
• Orthologs - genes in different species that
  evolved from a common ancestral gene by
  speciation.
• Paralogs - genes related by duplication within a
  genome.

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Orthologs Gene A in several species
Gene A
Gene A
Gene A
Gene A
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Paralogs genes A and B
Gene A
Gene A Gene B
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Paralogs and orthologs
Gene A
Gene A Gene B
Gene A Gene B
Gene A Gene B
Gene A Gene B
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Homologs orthologs or paralogs
www.ncbi.nlm.nih.gov/Education/
BLASTinfo/orthologs3.gif
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Anthocyanins
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An important gene Lc

• A41388 Lc regulatory protein -
  maizegi100897pirA41388100897

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Finding homologs BLAST
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Rice CDS search
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IRGSP search nearby genes
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Info on Ra through Gramene
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Mutant phenotypes
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Rice Ra

• Gene Name Rice R gene-a
• Gene Symbol Ra
• Phenotypic Description One rice R gene. An
  active homologue with extensive homology with
  other R genes. Located at a position on
  chromosome 4 previously shown to be in synteny
  with regions of maize chromosomes 2 and 10 that
  contain the B and R loci, respectively. Ra gene
  can activate the anthocyanin pathway.
• 53 other genes in R gene family in rice.

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Maize Lc and Rice Ra Orthologs?

• Reciprocal best hits
• Very similar function
• But not easy to tell because of similarity to
  other genes in the gene family

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Homologues in A. thaliana

• SCORE P ACCESSION GI PROTEIN
  DESCRIPTION
• 765 11 AAB72192 2335192 bHLH protein
• 761 11 AAG52418 12324939 putative
  transcription factor
• 608 11 Q9FT81 27151708 TRANSPARENT TESTA 8
  protein
• Transcription factors, 2 of which are involved in
  regulating anthocyanin biosynthesis in ATH

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Conclusions

• Gene function can be established through homology
  to known genes.
• Orthology can be determined by reciprocal BLAST
  hits
• Related genes can be found in EST and other
  databases for numerous species
• Conserved synteny may aid in confirming orthology
  and in building new maps