We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

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Key message Candidate genes were identified and the role of phytohormones such as JA-Me and ABA in the synthesis of S-RNase was emphasized in pear selfincompatibility. Abstract Self-incompatibility (SI) occurs widely in flowering plants as an intraspecific reproductive barrier. This phenomenon promotes variation within species, but for some species such as Pyrus, SI is a nuisance rather than a benefit in agricultural production. Although many studies have been conducted on SI in pears, its mechanism remains unclear. In this study, high-throughput Illumina RNA sequencing (RNA-seq) was used to identify SI-related genes in pear styles. Using transcriptome comparisons, differentially expressed genes of unpollinated (UP), crosspollinated (CP), and self-pollinated (SP) styles were identified after 48 h. A total of 1796 and 1890 genes were identified in DSC (UP vs. CP) and DSI (UP vs. SP), respectively. KEGG analysis revealed that genes involved in the ''plant hormone signal transduction pathway'' and ''plant-pathogen interaction pathway'' were significantly enriched in DSI (UP vs. SP) compared to those in DSC (UP vs. CP). The expression level of S-glycoprotein ribonuclease (S-RNase) was dramatically reduced in cross-pollinated (CP) styles. To better understand the relationship between the expression patterns of S-RNase and two major KEGG pathways, the concentrations of phytohormones were measured, and the expression pattern of S-RNase was analysed using qRT-PCR. Our results demonstrate that methyl jasmonate and abscisic acid may enhance the expression level of S-RNase, and pollination can affect the synthesis of methyl jasmonate and abscisic acid in pear styles. Overall, this study is a global transcriptome analysis of SI in pear. A relationship between self-rejection, plant hormones, and pathogen defence was shown in pear.Keywords Pear (Pyrus bretschneideri Rehd.) Á Selfincompatibility Á Transcriptome Á S-RNase Á Methyl jasmonate