Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically ...representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding.
Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and ...domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an "ancient" isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.Apple is one of the most important fruit crops. Here, the authors perform deep genome resequencing of 117 diverse accessions and reveal comprehensive models of apple origin, speciation, domestication, and fruit size evolution as well as candidate genes associated with important agronomic traits.
Spinach is an important leafy vegetable enriched with multiple necessary nutrients. Here we report the draft genome sequence of spinach (Spinacia oleracea, 2n=12), which contains 25,495 ...protein-coding genes. The spinach genome is highly repetitive with 74.4% of its content in the form of transposable elements. No recent whole genome duplication events are observed in spinach. Genome syntenic analysis between spinach and sugar beet suggests substantial inter- and intra-chromosome rearrangements during the Caryophyllales genome evolution. Transcriptome sequencing of 120 cultivated and wild spinach accessions reveals more than 420 K variants. Our data suggests that S. turkestanica is likely the direct progenitor of cultivated spinach and spinach domestication has a weak bottleneck. We identify 93 domestication sweeps in the spinach genome, some of which are associated with important agronomic traits including bolting, flowering and leaf numbers. This study offers insights into spinach evolution and domestication and provides resources for spinach research and improvement.
Due to the advantage of negative selection algorithm (NSA) in classification domain, this paper proposes an intrusion detection model named as wireless sensor networks (WSN-NSA) based on an improved ...V-detector algorithm for WSN. To overcome the problem of resource constraints of storage space, computing capacity and energy in WSN, the main strategy of the WSN-NSA is to establish a three level detection mechanism by taking the advantage of the cooperation of the base station, detection nodes, and ordinary nodes considering their different capabilities, and to modify the V-detector algorithm by modifying the detector generation rule and optimizing the detectors, and to use the principal component analysis to reduce the detection features. Two kinds of detectors sets which are memory detector set and mature detector set are used to detect the intrusion. The simulation results show that the proposed model outperforms the intrusion detection systems using the V-detector in the reduction of data storage space and computation, the increased detection rate, and the quick response to the secondary attack.
China—the largest developing country in the world—is experiencing both rapid economic maturation and large-scale urbanization. These situations have led to waste disposal problems, and the need to ...identify alternative energy sources. Waste-to-energy (WTE) conversion processes, a source of renewable energy, are expected to play an increasingly important role in China’s sustainable management of municipal solid waste (MSW). The purpose of this research is to investigate the key problems and opportunities associated with WTE, to provide recommendations for the government. This paper begins by describing China’s current MSW management situation and analyzing its waste disposal problems. The major challenges associated with China’s WTE incineration are then discussed from economic, environmental and social points of view. These include the high costs associated with constructing necessary facilities, the susceptibility of facilities to corrosion, the lower heating value of China’s MSW, air pollutant emissions and especially public opposition to WTE incineration. Since discarded waste can be used to produce energy for electricity and heat—thus reducing its volume and the production of greenhouse gas (GHG) emissions—with government policies and financial incentives, the use of WTE incineration as a renewable energy source and part of a sustainable waste management strategy will be of increasing importance in the future. The paper concludes by summarizing the management, economic and social benefits that could be derived from developing the country’s domestic capacity for producing the needed incineration equipment, improving source separation capabilities, standardizing regulatory and legal responsibilities and undertaking more effective public consultation processes.
Tomato (Solanum lycopersicum) is an established model for studying fruit biology; however, most studies of tomato fruit growth and ripening are based on homogenized pericarp, and do not consider the ...internal tissues, or the expression signatures of individual cell and tissue types. We present a spatiotemporally resolved transcriptome analysis of tomato fruit ontogeny, using laser microdissection (LM) or hand dissection coupled with RNA-Seq analysis. Regulatory and structural gene networks, including families of transcription factors and hormone synthesis and signaling pathways, are defined across tissue and developmental spectra. The ripening program is revealed as comprising gradients of gene expression, initiating in internal tissues then radiating outward, and basipetally along a latitudinal axis. We also identify spatial variations in the patterns of epigenetic control superimposed on ripening gradients. Functional studies elucidate previously masked regulatory phenomena and relationships, including those associated with fruit quality traits, such as texture, color, aroma, and metabolite profiles.
Transmission is a crucial part of a viral life cycle and transmission mode can have an important impact on virus biology. It was demonstrated that transmission mode can influence the virulence and ...evolution of a virus; however, few empirical data are available to describe the direct underlying changes in virus population structure dynamics within the host. Potato virus Y (PVY) is an RNA virus and one of the most damaging pathogens of potato. It comprises several genetically variable strains that are transmitted between plants via different transmission modes. To investigate how transmission modes affect the within-plant viral population structure, we have used a deep sequencing approach to examine the changes in the genetic structure of populations (in leaves and tubers) of three PVY strains after successive passages by horizontal (aphid and mechanical) and vertical (via tubers) transmission modes. Nucleotide diversities of viral populations were significantly influenced by transmission modes; lineages transmitted by aphids were the least diverse, whereas lineages transmitted by tubers were the most diverse. Differences in nucleotide diversities of viral populations between leaves and tubers were transmission mode-dependent, with higher diversities in tubers than in leaves for aphid and mechanically transmitted lineages. Furthermore, aphid and tuber transmissions were shown to impose stronger genetic bottlenecks than mechanical transmission. To better understand the structure of virus populations within the host, transmission mode, movement of the virus within the host, and the number of replication cycles after transmission event need to be considered. Collectively, our results suggest a significant impact of virus transmission modes on the within-plant diversity of virus populations and provide quantitative fundamental data for understanding how transmission can shape virus diversity in the natural ecosystems, where different transmission modes are expected to affect virus population structure and consequently its evolution.
Fruit softening is a key component of the irreversible ripening program, contributing to the palatability necessary for frugivore-mediated seed dispersal. The underlying textural changes are complex ...and result from cell wall remodeling and changes in both cell adhesion and turgor. While a number of transcription factors (TFs) that regulate ripening have been identified, these affect most canonical ripening-related physiological processes. Here, we show that a tomato fruit ripening-specific
(
) TF,
, up-regulates a suite of cell wall-associated genes during late maturation and ripening of locule and pericarp tissues.
repression in transgenic fruit impedes softening, while overexpression throughout the plant under the direction of the 35s promoter confers precocious induction of cell wall gene expression and premature softening. Transcript and protein levels of the wall-loosening protein EXPANSIN1 (
) are strongly suppressed in
RNA interference lines, while
is induced in
-overexpressing transgenic leaves and fruit. In contrast to the role of ethylene and previously characterized ripening TFs, which are comprehensive facilitators of ripening phenomena including softening,
participates in a regulatory subcircuit predominant to cell wall dynamics and softening.
Summary
Carotenoids are critically important to plants and humans. The ORANGE (OR) gene is a key regulator for carotenoid accumulation, but its physiological roles in crops remain elusive. In this ...study, we generated transgenic tomato ectopically overexpressing the Arabidopsis wild‐type OR (AtORWT) and a ‘golden SNP’‐containing OR (AtORHis). We found that AtORHis initiated chromoplast formation in very young fruit and stimulated carotenoid accumulation at all fruit developmental stages, uncoupled from other ripening activities. The elevated levels of carotenoids in the AtOR lines were distributed in the same subplastidial fractions as in wild‐type tomato, indicating an adaptive response of plastids to sequester the increased carotenoids. Microscopic analysis revealed that the plastid sizes were increased in both AtORWT and AtORHis lines at early fruit developmental stages. Moreover, AtOR overexpression promoted early flowering, fruit set and seed production. Ethylene production and the expression of ripening‐associated genes were also significantly increased in the AtOR transgenic fruit at ripening stages. RNA‐Seq transcriptomic profiling highlighted the primary effects of OR overexpression on the genes in the processes related to RNA, protein and signalling in tomato fruit. Taken together, these results expand our understanding of OR in mediating carotenoid accumulation in plants and suggest additional roles of OR in affecting plastid size as well as flower and fruit development, thus making OR a target gene not only for nutritional biofortification of agricultural products but also for alteration of horticultural traits.
It is well-known that drought has considerable effects on plant traits from leaf to ecosystem scales; however, little is known about the relative contributions of various traits within or between ...tree species in determining the plant's sensitivity or the tolerance to drought under field conditions. We conducted a field throughfall exclusion experiment to simulate short-term drought (∼67% throughfall exclusion during the dry season from October to March) and prolonged drought (∼67% throughfall exclusion prolonging the dry season from October to May) and to understand the effects of drought on two dominant tree species (
and
) in subtropical forests of southern China. The morphological, physiological, and nutritional responses of the two species to the two types of drought were determined. There were significantly different morphological (leaf max length, max width, leaf mass per area), physiological (leaf proline) and nutritional (P, S, N, K, Ca, Mg) responses by
and
to prolonged drought. Comparison between the drought treatments for each species indicated that the trees responded species-specifically to the short-term and prolonged drought, with
exhibiting larger plasticity and higher adaption than
responded more sensitively to prolonged drought in terms of morphology, proline content, and nutritional traits and to short-term drought with regard to soluble sugars content. The differential species-specific responses to drought will allow us to estimate the changes in dominant trees in subtropical forests of China that have experienced a decade's worth of annual seasonal drought.
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