The genome of the mesopolyploid crop species Brassica rapaThe Brassica rapa Genome Sequencing Project Consortium 1 Abstract:The Brassicaceae family which includes Arabidopsis thaliana, is a natural priority for reaching beyond botanical models to more deeply sample angiosperm genomic and functional diversity. Here we report the draft genome sequence and its annoation of Brassica rapa, one of the two ancestral species of oilseed rape. We modeled 41,174 protein-coding genes in the B. rapa genome. B. rapa has experienced only the second genome triplication reported to date, with its close relationship to A. thaliana providing a useful outgroup for investigating many consequences of triplication for its structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one copy containing a greater proportion of genes expected to have been present in its ancestor (70%) than the remaining two (46% and 36%). Both a generally rapid evolutionary rate, and specific copy number amplifications of particular gene families, may contribute to the remarkable propensity of Brassica species for the development of new morphological variants. The B. rapa genome provides a new resource for comparative and evolutionary analysis of the Brassicaceae genomes and also a platform for genetic improvement of Brassica oil and vegetable crops.2

Cotton is one of the most economically important crop plants worldwide. Its fiber, commonly known as cotton lint, is the principal natural source for the textile industry. Approximately 33 million ha (5% of the world's arable land) is used for cotton planting 1 , with an annual global market value of textile mills of approximately $630.6 billion in 2011 (MarketPublishers; see URLs). Apart from its economic value, cotton is also an excellent model system for studying polyploidization, cell elongation and cell wall biosynthesis 2-5 .The Gossypium genus contains 5 tetraploid (AD 1 to AD 5 , 2n = 4×) and over 45 diploid (2n = 2×) species (where n is the number of chromosomes in the gamete of an individual), which are believed to have originated from a common ancestor approximately 5-10 million years ago 6 . Eight diploid subgenomes, designated as A to G and K, have been found across North America, Africa, Asia and Australia. The haploid genome size of diploid cottons (2n = 2× = 26) varies from about 880 Mb (G. raimondii Ulbrich) in the D genome to 2,500 Mb in the K genome 7,8 . Diploid cotton species share a common chromosome number (n = 13), and high levels of synteny or colinearity are observed among them 9-12 . The tetraploid cotton species (2n = 4× = 52), such as G. hirsutum L. and Gossypium barbadense L., are thought to have formed by an allopolyploidization event that occurred approximately 1-2 million years ago, which involved a D-genome species as the pollen-providing parent and an A-genome species as the maternal parent 13,14 . To gain insights into the cultivated polyploid genomes-how they have evolved and how their subgenomes interact-it is first necessary to have a basic knowledge of the structure of the component genomes. Therefore, we have created a draft sequence of the putative D-genome parent, G. raimondii, using DNA samples prepared from Cotton Microsatellite Database (CMD) 10 (refs. 15,16), a genetic standard originated from a single seed (accession D 5 -3) in 2004 and brought to near homozygosity by six successive generations of self-fertilization. We believe that sequencing of the G. raimondii genome will not only provide a major source of candidate genes important for the genetic improvement of cotton quality and productivity, but it may also serve as a reference for the assembly of the tetraploid G. hirsutum genome. RESULTS Sequencing and assemblyA whole-genome shotgun strategy was used to sequence and assemble the G. raimondii genome. A total of 78.7 Gb of next-generation Illumina paired-end 50-bp, 100-bp and 150-bp reads was generated by sequencing genome shotgun libraries of different fragment lengths (170 bp, 250 bp, 500 bp, 800 bp, 2 kb, 5 kb, 10 kb, 20 kb and 40 kb) that covered 103.6-fold of the 775.2-Mb assembled G. raimondii genome (Supplementary Table 1). The resulting assembly appeared to cover a very large proportion of the euchromatin of the G. raimondii genome. The unassembled genomic regions are likely to contain heterochromatic satellites, large repetitive sequences or ribosoma...

The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 1943 coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these,~28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other~5.4-21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C39H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2x = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism

SUMMARYFlax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94· raw, approximately 69· filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N 50 = 694 kb, including contigs with N 50 = 20.1 kb. The contig assembly contained 302 Mb of nonredundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43 384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K s ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on wholegenome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.