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The genome of the cucumber, Cucumis sativus L.
TLDR
This study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo, and identifies 686 gene clusters related to phloem function.
The tomato genome sequence provides insights into fleshy fruit evolution
TLDR
A high-quality genome sequence of domesticated tomato is presented, a draft sequence of its closest wild relative, Solanum pimpinellifolium, is compared, and the two tomato genomes are compared to each other and to the potato genome.
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
TLDR
The data show that the epigenome is not static during development and may have been selected to ensure the fidelity of developmental processes such as ripening, and Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenomes.
Genomic analyses provide insights into the history of tomato breeding
TLDR
A comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions provides evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor.
Draft genome of the kiwifruit Actinidia chinensis
TLDR
As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage.
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions
TLDR
A high-quality draft genome sequence of the east Asia watermelon cultivar 97103 containing 23,440 predicted protein-coding genes is reported, which 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.
Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum
TLDR
Based on the recently released tomato whole-genome sequences, 81 SlWRKY genes were identified that were classified into three main groups, with the second group further divided into five subgroups and the tomato WRKYs from each group were shown to share similar motif compositions.
A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity
TLDR
The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding and finds a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value.
The Transcriptome of the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus in Trichoplusia ni Cells
TLDR
This study reports the first comprehensive analysis of AcMNPV transcription over the course of infection in Trichoplusia ni cells, by a combination of strand-specific RNA sequencing (RNA-Seq) and deep sequencing of 5′ capped transcription start sites and 3′ polyadenylation sites, and identifies four clusters of genes associated with distinctive patterns of mRNA accumulation.
Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor (nor, rin) and Ethylene Receptor (Nr) Mutants Reveals Novel
TLDR
This study presents systems analysis of nor, rin, and Nr at the transcriptomic, proteomic, and metabolomic levels during development and ripening, and observed very strong correlation between ripening-associated transcripts and specific metabolite groups, underlining the importance of these metabolic pathways during fruit ripening.
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