Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.Cultivated rice (Oryza sativa L.), which is grown worldwide and is one of the most important cereals for human nutrition, is considered to have been domesticated from wild rice (Oryza rufipogon) thousands of years ago 1-4 . The differences between O. sativa and O. rufipogon are reflected in a wide range of morphological and physiological traits [5][6][7][8][9] . Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated. The puzzles about rice domestication include: (1) where the geographic origin of cultivated rice was, (2) which types of O. rufipogon served as its direct wild progenitor, and (3) whether the two subspecies of cultivated rice, indica and japonica, are derived from a single or multiple domestications.A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 . However, the well-characterized domestication genes in rice were found to be fixed in both subspecies with the same alleles, thus supporting a single domestication origin [6][7][8][9]16 . Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 . Meanwhile, population genetics analyses of genome-wide data of cultivated and wild rice have tended to suggest that indica and japonica genomes generally appear to be of independent origin 1...

l e t t e r sBamboo represents the only major lineage of grasses that is native to forests and is one of the most important nontimber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between droughtresponsive and flowering genes.Bamboo is one of the most important non-timber forest products in the world. About 2.5 billion people depend economically on bamboo, and international trade in bamboo amounts to over 2.5 billion US dollars per year 1 . Bamboo has a rather striking life history, characterized by a prolonged vegetative phase lasting decades before flowering, thereby inhibiting genetic improvement. Recent genomic studies in bamboo have included genome-wide full-length cDNA sequencing 2 , chloroplast genome sequencing 3 , identification of syntenic genes between bamboo and other grasses 4 and phylogenetic analysis of Bambusoideae subspecies 5 . Fifty-nine simple sequence repeat markers from rice and sugarcane were used in the genetic diversity analyses of 23 bamboo species 6 , and 2 species-specific sequence-characterized amplified region markers were developed in the identification of different bamboo species 7 .Here, we report the draft genome of moso bamboo, a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area. Comparative genome-wide analyses of bamboo to other grass species, including rice, maize and sorghum, yielded new genetic insights into the rapid and marked phenotypic and ecological divergence of bamboo and closely related grasses.The moso bamboo genome contains 24 pairs of chromosomes 8 (2n = 48) and is characteristic of a diploid (Supplementary Fig. 1a). We conducted a flow cytometry analysis and estimated that it had a genome size of 2.075 Gb (2C = 4.24 pg; Supplementary Fig. 1b), which was very close to that estimated in a previous report 9 .Because it is difficult to generate an inbred line of moso bamboo, owing to its infrequent sexual reproduction and the long periods of time between flowering intervals, we selected five plants from a single individual rhizome of the moso bamboo ecotype (P. heterocycla var. pubescens) and performed whole-genome shotgun sequencing. We generated 295 Gb of raw sequence data (approximately 147-fold coverage), including Illumina short reads and 10,327 pairs of BAC end ...