Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.Oryza sativa | reference genomes | BAC-by-BAC strategy | transcriptome R ice is one of the most important food crops in the world and provides more than 20% of the caloric intake for one-half of the world's population. Asian cultivated rice can be divided into two subspecies-that is, Oryza sativa subsp. indica and O. sativa subsp. japonica-which are highly distinctive in geographical distribution, reproductively isolated, and have been shown to have extensive differentiation in genome structure and gene content (1). Indica rice accounts for more than 70% of world rice production (2) and is genetically much more diverse than japonica rice (3). Genomic studies have established that indica rice can be further subdivided into two major varietal groups, indica I and indica II, which have been independently bred and widely cultivated in China and Southeast Asia, respectively (4). Hybrids between these groups usually show strong heterosis, which provided the basis for the great success of hybrid rice in several countries, including China and the United States. For example, Zhenshan 97 (ZS97, indica I) and Minghui 63 (MH63, indica II) are the parents of the elite hybrid Shanyou 63 (SY63) (SI Appendix, Fig. S1 A and B), which exhibits superiority for a large array of agronomic traits including yield, resistance to multiple diseases, wide adaptability, and good eating quality, and thus has been the most widely cultivated hybrid in China over the past three decades (SI Appendix, Fig. S1C).Because of the importance of hybrid rice in helping to ensure a stable and secure food supply for generations, a series of attempts have been...

Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. With these data, we successfully assembled two platinum standard reference genomes that have been publicly released. Here we provide the full sets of raw data used to generate these two reference genome assemblies. These data sets can be used to test new programs for better genome assembly and annotation, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general.

BackgroundThe coffee berry borer, Hypothenemus hampei, reproduces and feeds exclusively on the mature endosperm of the coffee seed, which has a cell wall composed mainly of a heterogeneous mixture of hemicellulose polysaccharides, including arabinoxylans. Xylanases are digestive enzymes responsible for the degradation of xylan based polymers, hydrolyzing them into smaller molecules that are easier to assimilate by insects. We report the cloning, expression and enzymatic characterization of a xylanase gene that was identified in the digestive tract of the coffee berry borer.MethodsThe complete DNA sequence encoding a H. hampei xylanase (HhXyl) was obtained using a genome walking technique in a cDNA library derived from the borer digestive tract. The XIP-I gene was amplified from wheat (Triticum aestivum variety Soisson). A Pichia pastoris expression system was used to express the recombinant form of these enzymes. The xylanase activity and XIP-I inhibitory activity was quantified by the 3,5-dinitrosalicylic (DNS). The biological effects of XIP-I on borer individuals were evaluated by providing an artificial diet enriched with the recombinant XIP-I protein to the insects.ResultsThe borer xylanase sequence contains a 951 bp open reading frame that is predicted to encode a 317-amino acid protein, with an estimated molecular weight of 34.92 kDa and a pI of 4.84. Bioinformatic analysis revealed that HhXyl exhibits high sequence homology with endo-β-D-xylanases of Streptomyces bingchenggensis from glycosyl hydrolase 10 (GH10). The recombinant xylanase showed maximal activity at pH 5.5 and 37°C. XIP-I expressed as a recombinant protein inhibited HhXyl activity in vitro and caused individual H. hampei mortality in bioassays when included as a supplement in artificial diets.ConclusionA xylanase from the digestive tract of the coffee berry borer was identified and functionally characterized. A xylanase inhibitor protein, XIP-I, from wheat was shown to be a potent inhibitor of this xylanase, suggesting that its deployment has potential as a strategy to control coffee berry borer colonization of coffee plants.

The root-knot nematode Meloidogyne spp. causes yield losses of up to 68% on tomato (Solanum lycopersicum L.) crops. Genetic resistance in the host plant makes the crop sustainable and it can breakdown when there is a high population density of the pathogen. The objective of this study was to determine the nematode population density that allow determining the resistance potential of tomato germplasm associated with the Mi-1 resistance gen. The Mi-1 gene was evaluated with the molecular marker SCAR Mi-23 and specific primers in the genotypes COLY007, IAC1687, LA0445, IAC1622 and two commercial controls (susceptible and resistant). The damage scale and the number of individuals recovered (eggs and juveniles) were assessed, with different population densities of the pathogen inoculated (0, 1000, 2000, 3000, 4000 and 5000 individuals plant -1 ), in a split plot design, with six replicates and a plant as the experimental unit. The genotype IAC1687 and the resistant commercial control presented the resistance allele of the Mi-1 gene and were classified as moderately resistant to a density of 1000 individuals plant -1 . Despite having the Mi-1 gene, the COLY007 genotype was classified as moderately susceptible and with densities greater than 1000 individuals plant -1 can break resistance in all genotypes evaluated. Additionally, it is necessary to correlate the genotypic and phenotypic responses to guarantee the success of the selection supported by molecular markers such as SCAR Mi-23 and identify promising genotypes that could be included in a long-term breeding and also used as rootstocks in an integrated management of root-knot nematode.