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All the plastid genes were manually curated on the Artemis genome browser38.
To validate and improve gene models, we manually curated inaccurately annotated genes: 335 genes were manually added, and 86 genes were reclassified as pseudogenes.
To generate a reference for evaluating methods for network construction, genes were manually partitioned into 102 phenotypic classes, predicting functions for uncharacterized genes across diverse cellular processes.
378 NBS-encoding genes were manually verified after initial searching, comprising ∼1% of the total gene set, similar to the proportion found in other cereal genomes (Supplementary Table 16).
Two genes were manually selected, each with two known isoforms and different intensities.
To understand the reason of this difference, each of incongruent genes were manually evaluated.
High quality amino acid translations of these genes were manually obtained using the MultiContig/Geneview features at the Ensembl database.
Genomic annotation information of the target genes were manually inspected through the Rice Genome Browser (URL: http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/).
A few of these missed genes were manually annotated on the contigs based on the alignment of the closest fungal homologs using GeneWise [36].
These genes were manually annotated.
These genes were manually selected and annotated.
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