Fruit has evolved myriad forms that facilitate seed dispersal in varied environmental and ecological contexts. Because fleshy fruits become attractive and nutritious to seed-dispersing animals, the ...transition from unripe to ripe fruit represents a dramatic shift in survival strategy-from protecting unripe fruit against damaging animals to making it appealing to those same animals once ripened. For optimal fitness, ripening therefore must be tightly controlled and coordinated with seed development. Fruits, like many vegetative tissues of plants that contribute to human diets, are also subject to decay, which is enhanced as a consequence of the ripening transition. As such, ripening control has enormous relevance for both plant biology and food security. Here, we review the complex interactions of hormones and transcription factors during fleshy-fruit ripening, with an emphasis on the recent discovery that epigenome dynamics are a critical and early regulator of the cascade of molecular events that ultimately contribute to fruit maturation and ripening.
The greenhouse whitefly, Trialeurodes vaporariorum Westwood, is an agricultural pest of global importance. Here we report a 787‐Mb high‐quality draft genome sequence of T. vaporariorum assembled from ...PacBio long reads and Hi‐C chromatin interaction maps, which has scaffold and contig N50 lengths of 70 Mb and 500 kb, respectively, and contains 18,275 protein‐coding genes. About 98.8% of the assembled contigs were placed onto the 11 T. vaporariorum chromosomes. Comparative genomic analysis reveals significantly expanded gene families such as aspartyl proteases in T. vaporariorum compared to Bemisia tabaci Mediterranean (MED) and Middle East‐Asia Minor 1 (MEAM1). Furthermore, the cytochrome CYP6 subfamily shows significant expansion in T. vaporariorum and several genes in this subfamily display developmental stage‐specific expression patterns. The high‐quality T. vaporariorum genome provides a valuable resource for research in a broad range of areas such as fundamental molecular ecology, insect–plant/insect–microorganism or virus interactions and pest resistance management.
Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and ...characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding.
The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence ...supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago （Mya）, respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima ×C. moschata interspecific F1 hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops.
Abstract
Solanum pimpinellifolium
(SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in ...modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.
Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 ...cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome. Population genomic analyses provide insights into spinach genetic diversity and population differentiation. Genome-wide association studies of 20 agronomical traits identify numerous significantly associated regions and candidate genes for these traits. Domestication sweeps in the spinach genome are identified, some of which are associated with important traits (e.g., leaf phenotype, bolting and flowering), demonstrating the role of artificial selection in shaping spinach phenotypic evolution. This study provides not only insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding.
Key message
We identified QTLs associated with gummy stem blight resistance in an interspecific F
2:3
Citrullus
population and developed marker assays for selection of the loci in watermelon.
Gummy ...stem blight (GSB), caused by three
Stagonosporopsis
spp., is a devastating fungal disease of watermelon (
Citrullus lanatus
) and other cucurbits that can lead to severe yield losses. Currently, no commercial cultivars with genetic resistance to GSB in the field have been reported. Utilizing GSB-resistant cultivars would reduce yield losses, decrease the high cost of disease control, and diminish hazards resulting from frequent fungicide application. The objective of this study was to identify quantitative trait loci (QTLs) associated with GSB resistance in an F
2:3
interspecific
Citrullus
mapping population (
N
= 178), derived from a cross between Crimson Sweet (
C. lanatus
) and GSB-resistant PI 482276 (
C. amarus
). The population was phenotyped by inoculating seedlings with
Stagonosporopsis citrulli
12178A in the greenhouse in two separate experiments, each with three replications. We identified three QTLs (
ClGSB3.1
,
ClGSB5.1
and
ClGSB7.1
) associated with GSB resistance, explaining between 6.4 and 21.1% of the phenotypic variation. The genes underlying
ClGSB5.1
includes an NBS-LRR gene (
ClCG05G019540
) previously identified as a candidate gene for GSB resistance in watermelon
.
Locus
ClGSB7.1
accounted for the highest phenotypic variation and harbors twenty-two candidate genes associated with disease resistance. Among them is
ClCG07G013230
, encoding an Avr9/Cf-9 rapidly elicited disease resistance protein, which contains a non-synonymous point mutation in the DUF761 domain that was significantly associated with GSB resistance. High throughput markers were developed for selection of
ClGSB5.1
and
ClGSB7.1.
Our findings will facilitate the use of molecular markers for efficient introgression of the resistance loci and development of GSB-resistant watermelon cultivars.
Expressed Sequence Tags (ESTs) have played significant roles in gene discovery and gene functional analysis, especially for non-model organisms. For organisms with no full genome sequences available, ...ESTs are normally assembled into longer consensus sequences for further downstream analysis. However current de novo EST assembly programs often generate large number of assembly errors that will negatively affect the downstream analysis. In order to generate more accurate consensus sequences from ESTs, tools are needed to reduce or eliminate errors from de novo assemblies.
We present iAssembler, a pipeline that can assemble large-scale ESTs into consensus sequences with significantly higher accuracy than current existing assemblers. iAssembler employs MIRA and CAP3 assemblers to generate initial assemblies, followed by identifying and correcting two common types of transcriptome assembly errors: 1) ESTs from different transcripts (mainly alternatively spliced transcripts or paralogs) are incorrectly assembled into same contigs; and 2) ESTs from same transcripts fail to be assembled together. iAssembler can be used to assemble ESTs generated using the traditional Sanger method and/or the Roche-454 massive parallel pyrosequencing technology.
We compared performances of iAssembler and several other de novo EST assembly programs using both Roche-454 and Sanger EST datasets. It demonstrated that iAssembler generated significantly more accurate consensus sequences than other assembly programs.
The dependable functioning of switchgear is essential to maintain the stability of power supply systems. Partial discharge (PD) is a critical phenomenon affecting the insulation of switchgear, ...potentially leading to equipment failure and accidents. PDs are generally grouped into metal particle discharge, suspended discharge, and creeping discharge. Different types of PDs are closely related to the severity of a PD. Partial discharge pattern recognition (PDPR) plays a vital role in the early detection of insulation defects. In this regard, a Back Propagation Neural Network (BPNN) for PDPR in switchgear is proposed in this paper. To eliminate the sensitivity to initial values of BPNN parameters and to enhance the generalized ability of the proposed BPRN, an improved Mantis Search Algorithm (MSA) is proposed to optimize the BPNN. The improved MSA employs some boundary handling strategies and adaptive parameters to enhance the algorithm's efficiency in optimizing the network parameters of BPNN. Principal Component Analysis (PCA) is introduced to reduce the dimensionality of the feature space to achieve significant time saving in comparable recognition accuracy. The initially extracted 14 feature values are reduced to 7, reducing the BPNN parameter count from 183 with 14 features to 113 with 7 features. Finally, numerical results are presented and compared with Decision Tree (DT), k-Nearest Neighbor classifiers (KNN), and Support Vector Machine (SVM). The proposed method in this paper exhibits the highest recognition accuracy in metal particle discharge and suspended discharge.
Cutin and suberin are hydrophobic lipid biopolyester components of the cell walls of specialized plant tissue and cell-types, where they facilitate adaptation to terrestrial habitats. Many steps in ...their biosynthetic pathways have been characterized, but the basis of their spatial deposition and precursor trafficking is not well understood. Members of the GDSL lipase/esterase family catalyze cutin polymerization, and candidate proteins have been proposed to mediate interactions between cutin or suberin and other wall components. Comparative genomic studies of charophyte algae and early diverging land plants, combined with knowledge of the biosynthesis, trafficking and assembly mechanisms, suggests an origin for the capacity to secrete waxes, as well as aliphatic and phenolic compounds before the first colonization of true terrestrial habitats.
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