Quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) is a highly nutritious crop that is adapted to thrive in a wide range of agroecosystems. It was presumably first domesticated more than 7,000 years ago by pre-Columbian cultures and was known as the 'mother grain' of the Incan Empire 1 . Quinoa has adapted to the high plains of the Andean Altiplano (> 3,500 m above sea level), where it has developed tolerance to several abiotic stresses [2][3][4] . Quinoa has gained international attention because of the nutritional value of its seeds, which are gluten-free, have a low glycaemic index 5 , and contain an excellent balance of essential amino acids, fibre, lipids, carbohydrates, vitamins, and minerals 6 . Quinoa has the potential to provide a highly nutritious food source that can be grown on marginal lands not currently suitable for other major crops. This potential was recognized when the United Nations declared 2013 as the International Year of Quinoa, this being one of only three times a plant has received such a designation.Despite its agronomic potential, quinoa is still an underutilized crop 7 , with relatively few active breeding programs 8 . Breeding efforts to improve the crop for important agronomic traits are needed to expand quinoa production worldwide. To accelerate the improvement of quinoa, we present here the allotetraploid quinoa genome. We demonstrate the utility of the genome sequence by identifying a gene that probably regulates the presence of seed triterpenoid saponin content. Moreover, we sequenced the genomes of additional diploid and tetraploid Chenopodium species to characterize genetic diversity within the primary germplasm pool for quinoa and to understand sub-genome evolution in quinoa. Together, these resources provide the foundation for accelerating the genetic improvement of the crop, with the objective of enhancing global food security for a growing world population. Sequencing, assembly and annotationWe sequenced and assembled the genome of the coastal Chilean quinoa accession PI 614886 (BioSample accession code SAMN04338310) using single-molecule real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) and optical and chromosome-contact maps from BioNano Genomics 9 and Dovetail Genomics 10 . The assembly contains 3,486 scaffolds, with a scaffold N50 of 3.84 Mb and 90% of the assembled genome contained in 439 scaffolds (Table 1). The total assembly size of 1.39 gigabases (Gb) is similar to the reported size estimates of the quinoa genome (1.45-1.50 Gb (refs 11,12)). To combine scaffolds into pseudomolecules, an existing linkage map from quinoa 13 was integrated with two new linkage maps. The resulting map (Extended Data Fig. 1) of 6,403 unique markers spans a total length of 2,034 centimorgans (cM) and consists of 18 linkage groups (Supplementary Table 7), corresponding to the haploid chromosome number of quinoa. Pseudomolecules (hereafter referred to as chromosomes, which are numbered according to a previously published single-nucleotide polymorphism (SNP) linkage ...

SUMMARYSmall RNAs that interact with Argonaute (AGO) proteins play central roles in RNA-mediated silencing. MEI-OSIS ARRESTED AT LEPTOTENE1 (MEL1), a rice AGO, has specific functions in the development of pre-meiotic germ cells and the progression of meiosis. Here, we show that MEL1, which is located mostly in the cytoplasm of germ cells, associates preferentially with 21-nucleotide phased small interfering RNAs (phasiRNAs) that bear a 5 0 -terminal cytosine. Most phasiRNAs are derived from 1171 intergenic clusters distributed on all rice chromosomes. From these clusters, over 700 large intergenic, non-coding RNAs (lincRNAs) that contain the consensus sequence complementary to miR2118 are transcribed specifically in inflorescences, and cleaved within the miR2118 site. Cleaved lincRNAs are processed via DICER-LIKE4 (DCL4) protein, resulting in production of phasiRNAs. This study provides the evidence that the miR2118-dependent and the DCL4-dependent pathways are both required for biogenesis of 21-nt phasiRNAs associated with germlinespecific MEL1 AGO in rice, and over 700 lincRNAs are key factors for induction of this biogenesis during reproductive-specific stages.

A wide range of resources on gene expression profiling enhance various strategies in plant molecular biology particularly in characterization of gene function. We have updated our gene expression profile database, RiceXPro (http://ricexpro.dna.affrc.go.jp/), to provide more comprehensive information on the transcriptome of rice encompassing the entire growth cycle and various experimental conditions. The gene expression profiles are currently grouped into three categories, namely, ‘field/development’ with 572 data corresponding to 12 data sets, ‘plant hormone’ with 143 data corresponding to 13 data sets and ‘cell- and tissue-type’ comprising of 38 microarray data. In addition to the interface for retrieving expression information of a gene/genes in each data set, we have incorporated an interface for a global approach in searching an overall view of the gene expression profiles from multiple data sets within each category. Furthermore, we have also added a BLAST search function that enables users to explore expression profile of a gene/genes with similarity to a query sequence. Therefore, the updated version of RiceXPro can be used more efficiently to survey the gene expression signature of rice in sufficient depth and may also provide clues on gene function of other cereal crops.

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.