User Annotation track description:

* User Annotation

User's own track for adding annotation instantly. Red item stands for public one, while blue item stands for private one.

Oryza sativa L. ssp. japonica tracks description:

* Affymetrix GeneChip Rice Genome Array

Probes from the Affymetrix array mapped to the MSU Japonica Pseudomolecules (Release 6.1) using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Those probes that are uniquely aligned to the rice pseudomolecules are shown in green. Those that have aligned to more than one location are displayed in red.

* Agilent Rice Oligo Microarray

Probes from the Agilent array mapped to the MSU Japonica Pseudomolecules (Release 6.1) using BLASTN at 100% identity over 100% of their length. Those probes that are uniquely aligned to the rice pseudomolecules are shown in green. Those that have aligned to more than one location are displayed in red.

* Anther development

Rice gene expression throughout the reproductive process from GEO Series GSE14304. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Fujita M et al. (2010) Rice expression atlas in reproductive development. Plant Cell Physiol. 51:2060-81.

* Anther development (Agilent data)

Rice gene expression throughout the reproductive process from GEO Series GSE14304. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 95%.
Color key:
color key
Reference:
Fujita M et al. (2010) Rice expression atlas in reproductive development. Plant Cell Physiol. 51:2060-81.

* Arabidopsis PlantGDB PUTs

Arabidopsis thaliana PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 65% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Avena sativa PlantGDB PUTs

Avena sativa PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Best Arabidopsis Hit

Best match of a MSU Japonica protein (Release 6.1) to the Arabidopsis thaliana proteome (TAIR Release 9) using BLASTP with e-value 1e-10. Red if mutual best hit, green otherwise.

* Best indica HIT

Best match of a MSU Japonica protein (Release 6.1) to the Indica proteome using BLASTP with e-value 1e-10. Red if mutual best hit, green otherwise.

* Best Sorghum Hit

Best match of a MSU Japonica protein (Release 6.1) to the Sorghum bicolor proteome (JGI version Sbi1_4) using BLASTP with e-value 1e-10. Red if mutual best hit, green otherwise.

* BLASTP Hits

Top 3 BLASTP hits for each model searched against the Uniprot UniRef100 protein database using BLASTP with a cutoff e-value of 1e-5. Red for '+' and blue for '-' orientation.

* Brachypodium distachyon mRNA

Brochypodium distachyon mRNA (Realease 1.0) location were mapped to the MSU Japonica Pseudomolecules (Release 6.1) according to Oryza sativa, Sorghum bicolor, Brachypodium distachyon multiple alignment. Red for '+' and blue for '-' orientation. The pink and light blue stand for 3'UTR, while the dark red and dark blue stand for 5'UTR.

* Brachypodium distachyon PlantGDB PUTs

Brachypodium distachyon PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* CSRDB smRNAs

Small RNAs from the Cereal Small RNAs Database have been mapped onto the the MSU Japonica Pseudomolecules (Release 6.1) using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Red for '+' and blue for '-' orientation.

* Early embryogenesis

Rice gene expression throughout the reproductive process from GEO Series GSE14304. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Fujita M et al. (2010) Rice expression atlas in reproductive development. Plant Cell Physiol. 51:2060-81.

* Epigenetics modification (shoots of four-leaf stage seedlings of japonica)

The DNAmethyl_McrBC-Seq_Nipponbare, H3K4me3_ChIP-Seq_Nipponbare, H3K9ac_ChIP-Seq_Nipponbare and H3K27me3_ChIP-Seq_Nipponbare sequences are mapped to the genome using MAQ, then use MACS to call the peaks. The results are drawn according to the value of the score. (DNAmethl: DNA methylation. H3K4me3: Histone 3 lysine 4 tri-methylation. H3K9ac: Histone 3 lysine 9 acetylation. H3K27me3: Histone 3 lysine 27 tri-methylation)
Reference:
He G et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 22:17-33.
Color key:
color key

* Festuca arundinacea PlantGDB PUTs

Festuca arundinacea PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* GeneMarkHMM Predictions

Gene model derived from GeneMark.hmm-ES algorithm based on the MSU Japonica Pseudomolecules (Release 6.1). Red for '+' and blue for '-' orientation.

* GlimmerHMM Predictions

Gene model derived from GlimmerHMM algorithm (rice matrix) using MSU Japonica Pseudomolecules (Release 6.1). Red for '+' and blue for '-' orientation.

* Gramene QTL

[Gramene annotation] Rice QTL data come from Gramene release 32.

* Hordeum vulgare PlantGDB PUTs

Hordeum vulgare PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* IRGSP V5 Pseudomolecules Alignment

IRGSP pseudomolecules (Build 5.0) aligned to the MSU Japonica Pseudomolecules (Release 6.1) using NUCMER.

* japonica EST

Japonica EST sequence from GenBank are mapped to MSU Japonica Pseudomolecules (Release 6.1) using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* japonica-indica ColinearGene

ColinearGene of MSU Japonica Pseudomolecules (Release 6.1) against Indica Pseudomolecules, which is refer to dynamic programming for colinearity analysis of genomes.

* japonica-japonica ColinearGene

ColinearGene of MSU Japonica Pseudomolecules (Release 6.1) against itself, which is refer to dynamic programming for colinearity analysis of genomes.

* japonica mRNA

Japonica mRNA sequence from GenBank are mapped to MSU Japonica Pseudomolecules (Release 6.1) using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* japonica Transcription Factor

Japonica Transcription Factor from PlantTFDB. Red for '+' and blue for '-' orientation.

* Long Noncoding RNA

Predicted Japonica long noncoding RNAs based on the EST sequences downloaded from PlantGDB database and published plant microRNAs retrieved from miRBase database.

* Maize Genetic Markers

Maize genetic markers in the IBM2 2008 Neighbors high-resolution genetic map from MaizeGDB were aligned to the MSU Japonica Pseudomolecules (Release 6.1) by BLASTN with e-value of 1e-10, criteria of 70% sequence identity over 70% length or hit length >=150 bp. Only the best hit is displayed. Red for '+' and blue for '-' orientation.

* Maize PlantGDB PUTs

Zea mays PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* miRBase Oryza miRNAs

[miRBase annotation] Release 15 of the miRBase database at the Sanger Centre. Mapping to the MSU Japonica Pseudomolecules (Release 6.1) obtained from the osa GFF from miRBase. Red for '+' and blue for '-' orientation.

* MPSS Tags

MPSS Tags aligned to the MSU Japonica Pseudomolecules (Release 6.1) using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Tags that are unique in the genome are shown in green. Tags with multiple copies are shown in red.

* MSU Osa1 Pseudomolecules vs BGI Pseudomolecules

Indica pseudomolecules downloaded from BGI and aligned to the MSU Japonica Pseudomolecules (Release 6.1) using NUCMER.

* MSU Osa1 Pseudomolecules vs BGI Pseudomolecules SNPs

Indica pseudomolecules downloaded from BGI aligned to the MSU Japonica Pseudomolecules (Release 6.1) using the NUCMER SNP pipeline.

* MSU Osa1 Rice Gene Models

[MSU annotation] MSU japonica pseudomolecules and genome annotation (Release 6.1). Red for '+' and blue for '-' orientation. The pink and light blue stand for 3'UTR, while the dark red and dark blue stand for 5'UTR.

* MSU Osa1 Rice Loci

[MSU annotation] MSU Japonica genes annotated by the Rice Genome Annotation Project. Green: known or putative function; Yellow: Expressed protein; Blue: Conserved Hypothetical Protein; Red: Hypothetical protein; Black: Transposable Element Related

* Noncoding RNAs

Unique Oryza snoRNAs and snRNAs were downloaded from NONCODE (Liu et al., 2005). The sequences were mapped to the MSU Japonica Pseudomolecules (Release 6.1) using BLASTN with evalue 1e-10. Red for '+' and blue for '-' orientation.
Reference:
Liu, Changning, Bai, Baoyan, Skogerbo, Geir, Cai, Lun, Deng, Wei, Zhang, Yong, Bu, Dongbo, Zhao, Yi, Chen, Runsheng. (2005) NONCODE: an integrated knowledge database of non-coding RNAs. Nucl. Acids Res. 33:D112-115

* NSF 20k Rice Oligo Microarray

Probes from the NSF Rice 20k Oligo array mapped to the MSU Japonica Pseudomolecules (Release 6.1) using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Those probes that are uniquely aligned to the rice pseudomolecules are shown in green. Those that have aligned to more than one location are displayed in red.

* NSF 45k Rice Oligo Microarray

Probes from the NSF Rice 45k Oligo array mapped to the MSU Japonica Pseudomolecules (Release 6.1) using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Those probes that are uniquely aligned to the rice pseudomolecules are shown in green. Those that have aligned to more than one location are displayed in red.

* Organellar Insertions

The rice chloroplast genome and the rice mitochondrial genome were aligned to the MSU Japonica Pseudomolecules (Release 6.1) using NUCMER (min cluster size 300bp, %identity > 90%). Organelle Type: Mitochondrion - red, Chloroplast - green.

* Orthologous Groups

Genes from MSU Japonica Pseudomolecules (release 6.1), Arabidopsis (release 9), poplar (release 1.1), grapevine (release 1), sorghum (release 1.4) were used for identification of orthologous groups using OrthoMCL with default parameters (Li et al., 2003). Blue, green, yellow, pink, and red glyphs indicate that the rice gene has homolog to one, two, three, four and five other species, respectively. The number of homologous genes from each species is shown.

* Oryza BAC End Alignments

BAC end sequences were aligned to the MSU Japonica Pseudomolecules (Release 6.1) using GMAP. The sequences used here are from BAC libraries that have been made for O. australiensis, O. alta, O. brachyantha, O. coarctata, O. granulata, O. glaberimma, O. minuta, O. officinalis, O. ridleyi, O. nivara, O. rufipogon, O.punctata. Those sequences were obtained from the OMap Project. Sequences from BAC ends from an O. sativa (Indica cultivar-group) variety Kasalath library were also aligned to the pseudomolecules. The Kasalath sequences were obtained from the Rice Genome Research Program. Red for '+' and blue for '-' orientation.

* Oryza Repeats

The MSU Japonica Pseudomolecules (Release 6.1) were searched against the Rice Repeat Database v3.2.8 with RepeatMasker. Matches with a score above 225 were collapsed. Red for '+' and blue for '-' orientation.

* Oryza_sativa-Sorghum_bicolor-Brachypodium_distachyon MAF

The multiple alignment of MSU Japonica Pseudomolecules (Release 6.1), sorghum (JGI version Sbi1_4) and brachypodium distachyon (Release 1.0) without gap. Red for '+' and blue for '-' orientation.

* Oryza_sativa-Sorghum_bicolor-Brachypodium_distachyon MAF with GAP

The multiple alignment of MSU Japonica Pseudomolecules (Release 6.1), sorghum (JGI version Sbi1_4) and brachypodium distachyon (Release 1.0) with gap. Red for '+' and blue for '-' orientation.

* Oryza SwissProt

The Oryza protein sequences from SwissProt were aligned to the MSU Japonica Pseudomolecules (Release 6.1) using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* Pack MULES MSU

Pack-MULEs are Mutator-like elements containing genes or gene fragments and were identified by the Jiang lab (MSU) and have been aligned to the MSU Japonica Pseudomolecules (Release 6.1) using BLASTN with evalue 1e-10. Red for '+' and blue for '-' orientation.
Reference:
Hanada K., Vallejo V., Nobuta K.,R. Slotkin R.K., Lisch D., Meyers, B.C., Shiu, S.H., and Jiang N. (2009) The functional role of Pack-MULEs in rice inferred from purifying selection and expression profile. The Plant Cell. 21:25-38

* Panicum virgatum PlantGDB PUTs

Panicum virgatum PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* PhastCons

The PhastCons value for Oryza_sativa-Sorghum_bicolor-Brachypodium_distachyon multiple alignment using PhastCons with subst-mod HKY85, sorghum and brachypodium distachyon with step 1.

* Pollination Fertilization

Rice gene expression throughout the reproductive process from GEO Series GSE14304. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Fujita M et al. (2010) Rice expression atlas in reproductive development. Plant Cell Physiol. 51:2060-81.

* RAP Loci

RAP-DB loci mapped to the MSU Japonica Pseudomolecules (Release 6.1) using GMAP with a minimum threshold of 95% identity over 95% of the length of the locus. Red for '+' and blue for '-' orientation.

* RGP All Annotatied Results

Annotatied results by Rice Genome Research Group are mapped to MSU Japonica Pseudomolecules (Release 6.1) using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* RGP Predicted Geneset

Predicted GeneSet by Rice Genome Research Group are mapped to MSU Japonica Pseudomolecules (Release 6.1) using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* Rice FL cDNA

Full-length cDNAs for rice from KOME. Aligned to the MSU Japonica Pseudomolecules (Release 6.1) using GMAP (Wu and Watanabe, 2005). The displayed matches have 95% identity over at least 90% of the length of the cDNA. Red for '+' and blue for '-' orientation.

* Rice PlantGDB PUTs

Rice PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP program with a minimum identity of 95% over 90% of the length of the PUT. Red for '+' and blue for '-' orientation.

* Rice SSR Markers Gramene

[Gramene annotation] Known SSR Markers in Oryza sativa as determined by Gramene Release 31.

* Rice SSR Markers putative

Putative Rice SSRs in the MSU Japonica Pseudomolecules (Release 6.1) identified by the Simple Sequence Repeat Identification Tool.
Reference:
Temnykh et al. (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research. 11:1441-1452.

* RNA-seq (shoots of four-leaf stage seedlings of japonica)

The mRNA-Seq_Nipponbare sequences are mapped to the genome using tophat, then use Cufflinks to assemble the transcripts.
Reference:
He G et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 22:17-33.
Color key:
color key

* Saccharum officinarum PlantGDB PUTs

Saccharum officinarum PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* SAGE Tags

SAGE Tags aligned to the MSU Japonica Pseudomolecules (Release 6.1) using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Tags that are unique in the genome are shown in green. Tags with multiple copies are shown in red.
Reference:
Gowda,M., Jantasuriyarat, C., Dean, R.A., and Wang, G.L. (2004) Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol. 134:890-897.

* Secale cereale PlantGDB PUTs

Secale cereale PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* small RNAs (shoots of four-leaf stage seedlings of japonica)

The smRNA-Seq_Nipponbare sequences are firstly filtered by fastx_clipper and then mapped to the genome using MAQ.
Reference:
He G et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 22:17-33.

* Sorghum bicolor Gene Models

Transcripts from the predicted Sorghum bicolor transcriptome (JGI version Sbi1_4) were aligned to the MSU Japonica Pseudomolecules (Release 6.1). Sequences were aligned to the rice genome using the GMAP program with a minimum identity of 70% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Sorghum bicolor mRNA

Sorghum bicolor mRNA (JGI version Sbi1_4) location were mapped to the MSU Japonica Pseudomolecules (Release 6.1) according to Oryza sativa, Sorghum bicolor, Brachypodium distachyon multiple alignment. Red for '+' and blue for '-' orientation. The pink and light blue stand for 3'UTR, while the dark red and dark blue stand for 5'UTR.

* Sorghum bicolor PlantGDB PUTs

Sorghum bicolor PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 70% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Sorghum propinquum PlantGDB PUTs

Sorghum propinquum PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* tRNA Predictions

tRNA in the MSU Japonica Pseudomolecules (Release 6.1) identified using the tRNAScan-SE algorithm (Lowe and Eddy, 1997). Red for '+' and blue for '-' orientation.

* Triticum aestivum PlantGDB PUTs

Triticum aestivum PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Triticum monococcum PlantGDB PUTs

Triticum monococcum PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Triticum turgidum subsp durum PlantGDB PUTs

Triticum turgidum subsp. durum PUTs (putative unique transcript assemblies) from the PlantGDB database were aligned to the MSU Japonica Pseudomolecules (Release 6.1). The transcript assemblies were aligned to the Japonica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Uniprot Plants

Plant protein sequences from Uniprot database are mapped to MSU Japonica Pseudomolecules (Release 6.1) using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* Vegetative tissues

Rice gene expression throughout the reproductive process from GEO Series GSE14304. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Fujita M et al. (2010) Rice expression atlas in reproductive development. Plant Cell Physiol. 51:2060-81.

* VISTA Plot: Arabidopsis

[VISTA annotation] The conservation curve for japonica and A. thaliana (TAIR9) alignment from VISTA comparative genomics resource.

* VISTA Plot: Brachypodium distachyon

[VISTA annotation] The conservation curve for japonica and B. distachyon alignment from VISTA comparative genomics resource.

* VISTA Plot: Cucumis sativus

[VISTA annotation] The conservation curve for japonica and C. sativus alignment from VISTA comparative genomics resource.

* VISTA Plot: Maize

[VISTA annotation] The conservation curve for japonica and Maize v4 alignment from VISTA comparative genomics resource.

* VISTA Plot: Mimulus guttatus

[VISTA annotation] The conservation curve for japonica and M. guttatus alignment from VISTA comparative genomics resource.

* VISTA Plot: Poplar

[VISTA annotation] The conservation curve for japonica and Poplar v2.0 alignment from VISTA comparative genomics resource.

* VISTA Plot: Sorghum

[VISTA annotation] The conservation curve for japonica and Sorghum v1.0 alignment from VISTA comparative genomics resource.

* VISTA Plot: Soybean

[VISTA annotation] The conservation curve for japonica and Soybean alignment from VISTA comparative genomics resource.

* VISTA Plot: Wine grape

[VISTA annotation] The conservation curve for japonica and Wine grape alignment from VISTA comparative genomics resource.

* Wheat Mapped Markers

Wheat EST markers associated with the wheat Bin map from GrainGenes were aligned to the MSU Japonica Pseudomolecules (Release 6.1) by BLASTN with a cutoff of 70% sequence identity and 70% length match or a continuous match of >=150 bp. Red for '+' and blue for '-' orientation.
Reference:
Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, et al. (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics. 168:701-712.

Oryza sativa L. ssp. indica tracks description:

* Affymetrix GeneChip Rice Genome Array

Probes from the Affymetrix array mapped to the Indica pseudomolecules using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Those probes that are uniquely aligned to the rice pseudomolecules are shown in green. Those that have aligned to more than one location are displayed in red.

* Agilent Rice Oligo Microarray

Probes from the Agilent array mapped to the Indica pseudomolecules using BLASTN at 100% identity over 100% of their length. Those probes that are uniquely aligned to the rice pseudomolecules are shown in green. Those that have aligned to more than one location are displayed in red.

* Arabidopsis PlantGDB PUTs

Arabidopsis thaliana PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the gmap alignment program with a minimum identity of 65% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Avena sativa PlantGDB PUTs

Avena sativa PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Best Arabidopsis Hit

Best match of a Indica protein to the Arabidopsis thaliana proteome (TAIR Release 9) using BLASTP with e-value 1e-10. Red if mutual best hit, green otherwise.

* Best japonica HIT

Best match of a Indica protein to the MSU Japonica proteome (Release 6.1) using BLASTP with e-value 1e-10. Red if mutual best hit, green otherwise.

* Best Sorghum Hit

Best match of a Indica protein to the Sorghum bicolor proteome (JGI version Sbi1_4) using BLASTP with e-value 1e-10. Red if mutual best hit, green otherwise.

* BGF

[BGI annotation] Prediction genes of the Indica genome by BGF. Red for '+' and blue for '-' orientation.

* BGI Pseudomolecules vs MSU Osa1 Pseudomolecules

MSU Japonica Pseudomolecules (Release 6.1) aligned to the Indica pseudomolecules using NUCMER.

* BGI Pseudomolecules vs MSU Osa1 Pseudomolecules SNPs

MSU Japonica Pseudomolecules (Release 6.1) aligned to the Indica pseudomolecules using the NUCMER SNP pipeline.

* BGI Repeat

[BGI annotation] Repeat in the Indica Pseudomolecules. Red for '+' and blue for '-' orientation.

* BLASTP Hits

Top 3 BLASTP hits for each model searched against the Uniprot UniRef100 protein database using BLASTP with a cutoff e-value of 1e-5. Red for '+' and blue for '-' orientation.

* Brachypodium distachyon PlantGDB PUTs

Brachypodium distachyon PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Callus Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* CSRDB smRNAs

Small RNAs from the Cereal Small RNAs Database have been mapped onto the Indica pseudomolecules using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Red for '+' and blue for '-' orientation.

* Endosperm Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* Epigenetics modification (shoots of four-leaf stage seedlings of indica)

The DNAmethyl_McrBC-Seq_93-11, H3K4me3_ChIP-Seq_93-11, H3K9ac_ChIP-Seq_93-11 and H3K27me3_ChIP-Seq_93-11 sequences are mapped to the genome using MAQ, then use MACS to call the peaks. The results are drawn according to the value of the score. (DNAmethl: DNA methylation. H3K4me3: Histone 3 lysine 4 tri-methylation. H3K9ac: Histone 3 lysine 9 acetylation. H3K27me3: Histone 3 lysine 27 tri-methylation)
Reference:
He G et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 22:17-33.
Color key:
color key

* Festuca arundinacea PlantGDB PUTs

Festuca arundinacea PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* FgeneSH

[BGI annotation] Prediction genes of the Indica genome by FgeneSH. Red for '+' and blue for '-' orientation.

* GeneMarkHMM Predictions

Gene model derived from GeneMark.hmm-ES algorithm based on the Indica pseudomolecules. Red for '+' and blue for '-' orientation.

* Germinating seed Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* GLEAN

[BGI annotation] Prediction genes of the Indica genome by GLEAN. Red for '+' and blue for '-' orientation.

* GlimmerHMM Predictions

Gene model derived from GlimmerHMM algorithm (rice matrix) using Indica Pseudomolecules. Red for '+' and blue for '-' orientation.

* Hordeum vulgare PlantGDB PUTs

Hordeum vulgare PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* indica EST

Indica EST sequence from GenBank are mapped to the Indica pseudomolecules using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* indica-indica ColinearGene

ColinearGene of Indica against itself, which is refer to dynamic programming for colinearity analysis of genomes.

* indica-japonica ColinearGene

ColinearGene of Indica against the MSU Japonica Pseudomolecules (Release 6.1), which is refer to dynamic programming for colinearity analysis of genomes.

* indica mRNA

Indica mRNA sequence from GenBank are mapped to the Indica pseudomolecules using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* indica Transcription Factor

Indica Transcription Factor from PlantTFDB. Red for '+' and blue for '-' orientation.

* IRGSP V5 Pseudomolecules Alignment

IRGSP pseudomolecules (Build 5.0) aligned to the Indica pseudomolecules using NUCMER.

* Leaf Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* Long Noncoding RNA

Predicted Indica long noncoding RNAs based on the EST sequences downloaded from PlantGDB database and published plant microRNAs retrieved from miRBase database.

* Maize Genetic Markers

Maize genetic markers in the IBM2 2008 Neighbors high-resolution genetic map from MaizeGDB were aligned to the Indica Pseudomolecules by BLASTN with e-value of 1e-10, criteria of 70% sequence identity over 70% length or hit length >=150 bp. Only the best hit is displayed. Red for '+' and blue for '-' orientation.

* Maize PlantGDB PUTs

Zea mays PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* miRBase Oryza miRNAs

Release 15 of the miRBase database at the Sanger Centre. Mapping to the Indica pseudomolecules using BLAT with identity 0.96, coverage 0.9 and score 30. Yellow stands for mature RNA and red for loop.

* miRNA

[BGI annotation] miRNA in the Indica Pseudomolecules. Red for '+' and blue for '-' orientation.

* MPSS Tags

MPSS Tags aligned to the Indica pseudomolecules using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Tags that are unique in the genome are shown in green. Tags with multiple copies are shown in red.

* Noncoding RNAs

Unique Oryza snoRNAs and snRNAs were downloaded from NONCODE (Liu et al., 2005). The sequences were mapped to the Indica pseudomolecules using BLASTN with evalue 1e-10. Red for '+' and blue for '-' orientation.
Reference:
Liu, Changning, Bai, Baoyan, Skogerbo, Geir, Cai, Lun, Deng, Wei, Zhang, Yong, Bu, Dongbo, Zhao, Yi, Chen, Runsheng. (2005) NONCODE: an integrated knowledge database of non-coding RNAs. Nucl. Acids Res. 33:D112-115

* NSF 20k Rice Oligo Microarray

Probes from the NSF Rice 20k Oligo array mapped to the Indica pseudomolecules using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Those probes that are uniquely aligned to the rice pseudomolecules are shown in green. Those that have aligned to more than one location are displayed in red.

* NSF 45k Rice Oligo Microarray

Probes from the NSF Rice 45k Oligo array mapped to the Indica pseudomolecules using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Those probes that are uniquely aligned to the rice pseudomolecules are shown in green. Those that have aligned to more than one location are displayed in red.

* Organellar Insertions

The rice chloroplast genome and the rice mitochondrial genome were aligned to the Indica pseudomolecules using NUCMER (min cluster size 300bp, %identity > 90%). Organelle Type: Mitochondrion - red, Chloroplast - green.

* Orthologous Groups

Genes from Indica Pseudomolecules, Arabidopsis (release 9), poplar (release 1.1), grapevine (release 1), sorghum (release 1.4) were used for identification of orthologous groups using OrthoMCL with default parameters. Blue, green, yellow, pink, and red glyphs indicate that the rice gene has homolog to one, two, three, four and five other species, respectively. The number of homologous genes from each species is shown.

* Oryza BAC End Alignments

BAC end sequences were aligned to the Indica pseudomolecules using GMAP. The sequences used here are from BAC libraries that have been made for O. australiensis, O. alta, O. brachyantha, O. coarctata, O. granulata, O. glaberimma, O. minuta, O. officinalis, O. ridleyi, O. nivara, O. rufipogon, O.punctata. Those sequences were obtained from the OMap Project. Sequences from BAC ends from an O. sativa (Indica cultivar-group) variety Kasalath library were also aligned to the pseudomolecules. The Kasalath sequences were obtained from the Rice Genome Research Program. Red for '+' and blue for '-' orientation.

* Oryza Repeats

The Indica pseudomolecules were searched against the Rice Repeat Database v3.2.8 with RepeatMasker. Matches with a score above 225 were collapsed.

* Oryza SwissProt

The Oryza protein sequences from SwissProt were aligned to the Indica pseudomolecules (Release 6.1) using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* Pack MULES MSU

Pack-MULEs are Mutator-like elements containing genes or gene fragments and were identified by the Jiang lab (MSU) and have been aligned to the Indica pseudomolecules using BLASTN with evalue 1e-10. Red for '+' and blue for '-' orientation.
Reference:
Hanada K., Vallejo V., Nobuta K.,R. Slotkin R.K., Lisch D., Meyers, B.C., Shiu, S.H., and Jiang N. (2009) The functional role of Pack-MULEs in rice inferred from purifying selection and expression profile. The Plant Cell. 21:25-38

* Palea/lemma Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* Panicle Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* Panicum virgatum PlantGDB PUTs

Panicum virgatum PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Plumule Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* Radicle Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* RAP Loci

RAP-DB loci mapped to the Indica pseudomolecules using GMAP with a minimum threshold of 95% identity over 95% of the length of the locus. Red for '+' and blue for '-' orientation.

* RGP All Annotatied Results

Annotatied results by Rice Genome Research Group are mapped to Indica pseudomolecules using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* RGP Predicted Geneset

Predicted GeneSet by Rice Genome Research Group are mapped to Indica pseudomolecules using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* Rice FL cDNA

Full-length cDNAs for rice from KOME. Aligned to the Indica pseudomolecules using GMAP. The displayed matches have 95% identity over at least 90% of the length of the cDNA. Red for '+' and blue for '-' orientation.

* Rice PlantGDB PUTs

Rice PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP program with a minimum identity of 95% over 90% of the length of the PUT. Red for '+' and blue for '-' orientation.

* Rice SSR Markers Gramene

[Gramene annotation] Known SSR Markers in Oryza sativa Indica Group as determined by Gramene 31.

* Rice SSR Markers putative

Putative Rice SSRs in Indica identified by the Simple Sequence Repeat Identification Tool.
Reference:
Temnykh et al. (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research. 11:1441-1452.

* RNA-seq (shoots of four-leaf stage seedlings of indica)

The mRNA-Seq_93-11 sequences are mapped to the genome using tophat, then use Cufflinks to assemble the transcripts.
Reference:
He G et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 22:17-33.
Color key:
color key

* Root Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* rRNA

[BGI annotation] rRNA in the Indica Pseudomolecules. Red for '+' and blue for '-' orientation.

* Saccharum officinarum PlantGDB PUTs

Saccharum officinarum PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* SAGE Tags

SAGE Tags aligned to the Indica pseudomolecules using BOAT (Zhao SQ et al. 2009) at 100% identity over 100% of their length. Tags that are unique in the genome are shown in green. Tags with multiple copies are shown in red.

* Secale cereale PlantGDB PUTs

Secale cereale PUTs from the PlantGDB database were aligned to the Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Seedling Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* Sheath Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* Shoot Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* small RNAs (shoots of four-leaf stage seedlings of indica)

The smRNA-Seq_93-11 sequences are firstly filtered by fastx_clipper and then mapped to the genome using MAQ.
Reference:
He G et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 22:17-33.

* snRNA

[BGI annotation] snRNA in the Indica Pseudomolecules. Red for '+' and blue for '-' orientation.

* Sorghum bicolor Gene Models

Transcripts from the predicted Sorghum bicolor transcriptome (JGI version Sbi1_4) were aligned to the Indica pseudomolecules. Sequences were aligned to the rice genome using the GMAP program with a minimum identity of 70% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Sorghum bicolor PlantGDB PUTs

Sorghum propinquum PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Sorghum propinquum PlantGDB PUTs

Sorghum propinquum PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Spikelet Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* sRNA

[BGI annotation] sRNA in the Indica Pseudomolecules. Red for '+' and blue for '-' orientation.

* Stamen Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* Stem Minghui 63

Dissecting the developmental transcriptomes of rice from GEO Series GSE19024. The sequence are mapped to genome using BLAT with min identity 95% and min coverage 50%.
Color key:
color key
Reference:
Wang L et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61:752-66.

* tRNA

[BGI annotation] tRNA in the Indica Pseudomolecules identified using the tRNAScan-SE algorithm. Red for '+' and blue for '-' orientation.

* Triticum aestivum PlantGDB PUTs

Triticum aestivum PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Triticum monococcum PlantGDB PUTs

Triticum monococcum PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Triticum turgidum subsp durum PlantGDB PUTs

Triticum turgidum subsp. durum PUTs from the PlantGDB database were aligned to Indica pseudomolecules. The transcript assemblies were aligned to the Indica genome using the GMAP alignment program with a minimum identity of 80% over 70% of the length of the transcript assembly. Red for '+' and blue for '-' orientation.

* Uniprot Plants

Plant protein sequences from Uniprot database are mapped to the Indica pseudomolecules using BLAT with identity 0.96, coverage 0.9 and score 30. Red for '+' and blue for '-' orientation.

* Wheat Mapped Markers

Wheat EST markers associated with the wheat Bin map from GrainGenes were aligned to Indica Pseudomolecules by BLASTN with a cutoff of 70% sequence identity and 70% length match or a continuous match of >=150 bp. Red for '+' and blue for '-' orientation.
Reference:
Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, et al. (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics. 168:701-712.