SignificanceA high-quality genome assembly of Camellia sinensis var. sinensis facilitates genomic, transcriptomic, and metabolomic analyses of the quality traits that make tea one of the world’s most-consumed beverages. The specific gene family members critical for biosynthesis of key tea metabolites, monomeric galloylated catechins and theanine, are indicated and found to have evolved specifically for these functions in the tea plant lineage. Two whole-genome duplications, critical to gene family evolution for these two metabolites, are identified and dated, but are shown to account for less amplification than subsequent paralogous duplications. These studies lay the foundation for future research to understand and utilize the genes that determine tea quality and its diversity within tea germplasm.

About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n 5 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n 5 4x 5 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n 5 6x 5 42; AABBDD) 1,2 . Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker's flour 2 . Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.We selected Ae. tauschii accession AL8/78 for genome sequencing because it has been extensively characterized genetically (Supplementary Information). Using a whole genome shotgun strategy, we generated 398 Gb of high-quality reads from 45 libraries with insert sizes ranging from 200 bp to 20 kb (Supplementary Information). A hierarchical, iterative assembly of short reads employing the parallelized sequence assembler SOAPdenovo 3 achieved contigs with an N50 length (minimum length of contigs representing 50% of the assembly) of 4,512 bp (Table 1). Paired-end information combined with an additional 18.4 Gb of Roche/454 long-read sequences was used sequentially to generate 4.23-Gb scaffolds (83.4% were non-gapped contiguous sequences) with an N50 length of 57.6 kb (Supplementary Information). The assembly represented 97% of the 4.36-Gb genome as estimated by K-mer analysis (Supplementary Information). We also obtained 13,185 Ae. tauschii expressed sequence tag (EST) sequences using Sanger sequencing, of which 11,998 (91%) could be mapped to the scaffolds with more than 90% coverage (Supplementary Information).To aid in gene identification, we performed RNA-Seq (53.2 Gb for a 117-Mb transcriptome assembly) on 23 libraries representing eight tissues including pistil, root, seed, spike, stamen, stem, leaf and sheath (Supplementary Information). Using both evidence-based and de novo gene predictions, we identified 34,498 high-confidence protein-coding loci. FGENESH 4 and GeneID models were supported by a 60% overlap with either our ESTs and RNA-Seq reads, or with homologous proteins. More than 76% of the gene models had a significant match (E value # 10 25; alignment length $ 60%) in the ...

The growing world population and shrinkage of arable land demand yield improvement of rice, one of the most important staple crops. To elucidate the genetic basis of yield and uncover its associated loci in rice, we resequenced the core recombinant inbred lines of Liang-YouPei-Jiu, the widely cultivated super hybrid rice, and constructed a high-resolution linkage map. We detected 43 yield-associated quantitative trait loci, of which 20 are unique. Based on the high-density physical map, the genome sequences of paternal variety 93-11 and maternal cultivar PA64s of Liang-You-Pei-Jiu were significantly improved. The large recombinant inbred line population combined with plentiful high-quality single nucleotide polymorphisms and insertions/deletions between parental genomes allowed us to fine-map two quantitative trait loci, qSN8 and qSPB1, and to identify days to heading8 and lax panicle1 as candidate genes, respectively. The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yieldassociated loci in rice.Oryza sativa | QTL dissection | genome sequence update R ice is one of the most important staple crops in the world and serves as a model for monocots (1). Currently, rice breeding faces the challenge of overcoming the yield plateau. All important agronomic traits would ultimately need to consider their impacts on the yield, which is linked to various growth and developmental components, such as tiller number, seed number and set, and grain weight, to name a few. A number of quantitative trait loci (QTLs) have been reported to control these components, including those revealed by map-based cloning studies, such as IPA1/WFP for tiller and spikelet numbers (2, 3); days to heading8 (DTH8)/Ghd8 and Ghd7 for heading date, plant height, and spikelet number (4, 5); Gn1 for spikelet number (6); GIF1 for seed set (7); and grain size3 (GS3) and GW5 for grain size and weight (8, 9). Although a series of QTLs for yield components have been cloned, elucidation of the genetic mechanisms underlying the inheritance of superior yield in super hybrid rice still has a long way to go.Hybrid rice has a notable contribution to yield improvement. Various commercialized hybrids are derived by crossing different varieties within or between two subspecies, Oryza sativa ssp. indica and ssp. japonica (10, 11). As a pioneer super hybrid rice, Liang-You-Pei-Jiu (LYP9) realized the target of 10.5 tons/ha in 2000 (12). LYP9 was developed by a cross of the paternal 93-11, an indica variety widely grown in China (13), and the maternal PA64s cultivar with a mixed genetic background of indica and javanica. To date, it has been widely cultivated for commercial production in China. Such a feature was thought to make LYP9 recombinant inbred lines (RILs) ideal materials for exploring molecular mechanisms underlying rice yield.Here, we constructed a high-density linkage map by resequencing the parents of LYP9 and 132 c...

BackgroundLegumes are the second-most important crop family in agriculture for its economic and nutritional values. Disease resistance (R-) genes play an important role in responding to pathogen infections in plants. To further increase the yield of legume crops, we need a comprehensive understanding of the evolution of R-genes in the legume family.ResultsIn this study, we developed a robust pipeline and identified a total of 4,217 R-genes in the genomes of seven sequenced legume species. A dramatic diversity of R-genes with structural variances indicated a rapid birth-and-death rate during the R-gene evolution in legumes. The number of R-genes transiently expanded and then quickly contracted after whole-genome duplications, which meant that R-genes were sensitive to subsequent diploidization. R proteins with the Coiled-coil (CC) domain are more conserved than others in legumes. Meanwhile, other types of legume R proteins with only one or two typical domains were subjected to higher rates of loss during evolution. Although R-genes evolved quickly in legumes, they tended to undergo purifying selection instead of positive selection during evolution. In addition, domestication events in some legume species preferentially selected for the genes directly involved in the plant-pathogen interaction pathway while suppressing those R-genes with low occurrence rates.ConclusionsOur results provide insights into the dynamic evolution of R-genes in the legume family, which will be valuable for facilitating genetic improvements in the disease resistance of legume cultivars.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2736-9) contains supplementary material, which is available to authorized users.

BackgroundPlant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time.ResultsAnalysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases.ConclusionsOur analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0463-z) contains supplementary material, which is available to authorized users.

Biotic stresses do damage to the growth and development of plants, and yield losses for some crops. Confronted with microbial infections, plants have evolved multiple defense mechanisms, which play important roles in the never-ending molecular arms race of plant–pathogen interactions. The complicated defense systems include pathogen-associated molecular patterns (PAMP) triggered immunity (PTI), effector triggered immunity (ETI), and the exosome-mediated cross-kingdom RNA interference (CKRI) system. Furthermore, plants have evolved a classical regulation system mediated by miRNAs to regulate these defense genes. Most of the genes/small RNAs or their regulators that involve in the defense pathways can have very rapid evolutionary rates in the longitudinal and horizontal co-evolution with pathogens. According to these internal defense mechanisms, some strategies such as molecular switch for the disease resistance genes, host-induced gene silencing (HIGS), and the new generation of RNA-based fungicides, have been developed to control multiple plant diseases. These broadly applicable new strategies by transgene or spraying ds/sRNA may lead to reduced application of pesticides and improved crop yield.

Tea is a globally consumed non-alcohol beverage with great economic importance. However, lack of the reference genome has largely hampered the utilization of precious tea plant genetic resources towards breeding. To address this issue, we previously generated a high-quality reference genome of tea plant using Illumina and PacBio sequencing technology, which produced a total of 2,124 Gb short and 125 Gb long read data, respectively. A hybrid strategy was employed to assemble the tea genome that has been publicly released. We here described the data framework used to generate, annotate and validate the genome assembly. Besides, we re-predicted the protein-coding genes and annotated their putative functions using more comprehensive omics datasets with improved training models. We reassessed the assembly and annotation quality using the latest version of BUSCO. These data can be utilized to develop new methodologies/tools for better assembly of complex genomes, aid in finding of novel genes, variations and evolutionary clues associated with tea quality, thus help to breed new varieties with high yield and better quality in the future.

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