The 63rd Annual Meeting of JSPP
The 18th Database Workshop
March 24, 2022

Yoshihiro Kawahara1, Tomoko Hirozane-Kishikawa1,
Xiaohui Wang1, Ryo Hirata2(1Advanced Analysis Center, NARO (NAAC), 2IMSBIO Co., Ltd.)

NARO

Literature-based curation ofgene annotation, genomic variations,and transcriptomics informationin RAP-DB

Rice Annotation Project Database (RAP-DB)
Over the past 15 years, through several updates, RAP-DB has
continued to provide rice genome annotation.

https://rapdb.dna.affrc.go.jp
1History of RAP-DB
Over the past 15 years, through several updates, RAP-DB has
continued to provide rice genome annotation.
- 2005: International Rice Genome Sequencing Project, Nature
The map-based sequence of the rice genome- 2006: Ohyanagi, H., et al., Nucleic Acids Res.
The rice annotation project database (RAP-DB): hub for Oryza sativa
ssp. japonica genome information- 2008: Rice Annotation Project, Nucleic Acids Res.
The Rice Annotation Project Database (RAP-DB): 2008 update- 2013: Kawahara, Y., et al., Rice
Improvement of the Oryza sativa Nipponbare reference genome using
next generation sequence and optical map data

- 2013: Sakai, H., et al., Plant & Cell Physiol.
Rice Annotation Project Database (RAP-DB): An integrative andinteractive database for rice genomics

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Monthly accesses
approximately 300,000 pageviews and >20,000 visits per month3

Users by country
The most accesses are from China, and that from Japan is second.
This trend has started from mid-2017.

Shown only countries with an average monthly pageviews > 5004

Members of RAP-DB team
LeaderYoshihiro Kawahara (NAAC)
Curators
Tomoko Hirozane-Kishikawa (NAAC)
Xiaohui Wang (NAAC)
Programmer
Ryo Hirata (IMSBIO Co., Ltd.)
AdviserTakeshi Itoh (National Taiwan University)
Collaboraters• Shoko Kawamoto, Yutaka Sato (Oryzabase@NIG)• Pankaj Jaiswal, Sushma Naithani (Gramene)
This work is supported by• Grant-in-Aid for Publication of Scientific Research Results (Databases, 2017-2021)• MAFF Project (DIT2001, 2018-2022)

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RAP-DB was updated on March 11

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Take-home messages
RAP-DB …
- is the only primary database for rice that continues toupdate gene annotation data by manual curation.
- provides gene expression profiles under >500 experimentalconditions. Currently, TENOR, RiceXPro and RiceFREND arepartially integrated into RAP-DB.
- provides genome-wide variations among >600 rice varieties
through TASUKE+.
- provides the list of 365 agronomically important rice genes
and 762 known functional alleles/mutations on the genes.
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Take-home messages
RAP-DB …
- is the only primary database for rice that continues toupdate gene
Functionalannotation data
annotation
by manual curation.
- provides gene expression profiles under >500 experimentalconditions. Currently, TENOR, RiceXPro and RiceFREND arepartially integrated
into RAP-DB.
Geneexpression- provides genome-wide variations among >600 rice varieties
through TASUKE+.

Variations (alleles & mutations)- provides the list of 365 agronomically important rice genes
and 762 known functional alleles/mutations on the genes.
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Take-home messages
RAP-DB …
- is the only primary database for rice that continues toupdate gene annotation data by manual curation.
- provides gene expression profiles under >500 experimentalconditions. Currently, TENOR, RiceXPro and RiceFREND arepartially integrated into RAP-DB.
- provides genome-wide variations among >600 rice varieties
through TASUKE+.
- provides the list of 365 agronomically important rice genes
and 762 known functional alleles/mutations on the genes.
9The number of literatures on “rice genes”
continues to grow
Emergence of NGS(Illumina)

Spread of theNGS technology“Nipponbare” genome
sequencing completed

The literatures on “rice genes” were searched by Pubmed using “rice” and “gene” as keywords

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Literature-based curation ofgene function and structures
Collect literatures describing
rice genes and its function

Extract structural and functional
information on rice genes througha careful review of the literature.

Curators

Gene annotation in RAP-DB is updated twicea year.
So far, >4,000 genes have been manuallycurated (May 2009–March 2022).

Edit rice gene annotation
through in-house curation system.11

The number of literatures on “rice gene”
by journal
PCP (8th)*shown only journals
with >100 literatures

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Take-home messages
RAP-DB …
- is the only primary database for rice that continues toupdate gene annotation data by manual curation.
- provides gene expression profiles under >500 experimentalconditions. Currently, TENOR, RiceXPro and RiceFREND arepartially integrated into RAP-DB.
- provides genome-wide variations among >600 rice varieties
through TASUKE+.
- provides the list of 365 agronomically important rice genes
and 762 known functional alleles/mutations on the genes.
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Rice gene expression databases
Those expression data has been integrated into RAP-DB.
TENOR

RNA-Seq data under 140 environmental
stresses and plant hormone treatedconditions.

RiceXPro

Microarray data of tissues/organs encompassing theentire growth of the rice plant under natural field
conditions, etc.

RiceFREND

A platform for retrieving coexpressed gene networks
in riceKawahara Y. et al. 2016 Plant Cell Physiol.

Sato Y. et al. 2013 Nucleic Acids Res.

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Update of TENOR
Published RNA-Seq data of 565 experiments was collected andmeta-data was curated.
The expression profiles and read alignments are provided in RAP-DB.
Analyzed conditions by Plant Experimental
Conditions Ontology (PECO)

Analyzed tissues by Trait Ontology (TO)15

Demo:
Viewing gene annotation in RAP-DB• Search by Gene ID, symbol, name, etc.
• locus/transcript annotation page (beta version)

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Search by Gene ID, symbol, name, etc.

17You can get the list of genes
between chromosomal positions or markers

18New locus/transcript annotation pages
have been opened

19Locus annotation page (beta version)
Description, symbol, name and structures

RiceXPro (Microarray data)

Sequence and structure
RiceFREND (Coexpression network)20Transcript annotation page (beta version)
Description, symbol, name, GO, InterPro, etc.

Genome-wide variation data
Known functional alleles & mutations

TENOR (RNA-Seq data)

TASUKE+21

JBrowse• RAP-DB, MSU, RefSeq, IsoSeq transcripts structures• Alignment of RNA-Seq readsetc.

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Take-home messages
RAP-DB …
- is the only primary database for rice that continues toupdate gene annotation data by manual curation.
- provides gene expression profiles under >500 experimental
conditions. Currently, TENOR, RiceXPro and RiceFREND arepartially integrated into RAP-DB.
- provides genome-wide variations among >600 rice varieties
through TASUKE+.
- provides the list of 365 agronomically important rice genes
and 762 known functional alleles/mutations on the genes.
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Towards population-level genomics
Most resequencing data is used only once.
It could be used more effectively.
Xu et al. 2011 Nature Biotech.

Zhao et al. 2018 Nature Genetics

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Tanaka et al. 2020 Nature Biotech.

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Wang et al. 2018 Nature119

3,010

Number of varieties sequenced in the paper

24Collection & curation of resequence data

685 varieties from 44 literatures

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Standardized analysis pipeline
Our analysis pipeline for SNP & InDel detection is publicly available

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Genome-wide variation
among 685 rice varieties on TASUKE+TASUKE+ is a web-based genome browser that visualizes variation
and read depth data of genome resequencing data analysis
https://tasuke.dna.affrc.go.jp/

27Genome-wide variation
among 685 rice varieties on TASUKE+
Variations within the Hd16 locus. Koshihikari and some TEJ varieties
have a nonsynonymous mutations (Ala331Thr).

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Curation of known alleles and mutations

an alanine amino acid in Nipponbarechanged to a threonine amino acid inKoshihikari.
…
One non-synonymous substitution in
Hd16 resulted in decreased photoperiod
sensitivity in rice.

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Known functional alleles & mutations
We’re collecting known functional alleles from literatures

Related traits

Types of variations

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Demo:Viewing genome-wide variation on TASUKE+
and known functional alleles/mutations in RAP-DB31

Agronomically important genes
365 agronomically important rice genes are listed.

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TASUKE+, known functional alleles &mutations in the “Diversity” section

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TASUKE+GS3 locus related to grain size

Temperate
japonica

Tropicaljaponica

SNPs & InDels against
the “Nipponbare” genome

Aroma
Aus
Indica34

TASUKE+
Sorted by the pattern of variations at the GS3 locus

Stop gained("High" impact)c.165C>Ap.Cys55*35

Known functional alleles & mutations
We’re collecting known functional alleles from literatures

Takano-Kai et al. 2009

Stop gained("High" impact)c.165C>Ap.Cys55*

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Take-home messages
RAP-DB …
- is the only primary database for rice that continues toupdate gene annotation data by manual curation.
- provides gene expression profiles under >500 experimentalconditions. Currently, TENOR, RiceXPro and RiceFREND arepartially integrated into RAP-DB.
- provides genome-wide variations among >600 rice varieties
through TASUKE+.
- provides the list of 365 agronomically important rice genes
and 762 known functional alleles/mutations on the genes.
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Information about RAP-DB and rice genes• Literature information about rice genes• Maintenance and update information ofRAP-DB@rapdbjp (#RAPDB)
rapdb@ml.affrc.go.jp

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