Organelle-derived nuclear DNAs, nuclear plastid DNAs (NUPTs), and nuclear mitochondrial DNAs (NUMTs) have been identified in plants. Most, if not all, genes residing in NUPTs/NUMTs (NUPGs/NUMGs) are known to be inactivated and pseudogenized. However, the role of epigenetic control in silencing NUPGs/NUMGs and the dynamic evolution of NUPTs/NUMTs with respect to organismal phylogeny remain barely explored. Based on the available nuclear and organellar genomic resources of wheat (genus Triticum) and goat grass (genus Aegilops) within Triticum/Aegilops complex species, we investigated the evolutionary fates of NUPTs/NUMTs in terms of their epigenetic silencing and their dynamic occurrence rates in the nuclear diploid genomes and allopolyploid subgenomes. NUPTs and NUMTs possessed similar genomic atlas, including (i) predominantly located in intergenic regions and preferential integration to gene regulation regions and (ii) generating sequence variations in the nuclear genome. Unlike nuclear indigenous genes, the alien NUPGs/NUMGs were associated with repressive epigenetic signals, namely high levels of DNA methylation and low levels of active histone modifications. Phylogenomic analyses suggested that the species-specific and gradual accumulation of NUPTs/NUMTs accompanied the speciation processes. Moreover, based on further pan-genomic analyses, we found significant subgenomic asymmetry in the NUPT/NUMT occurrence, which accumulated during allopolyploid wheat evolution. Our findings provide insight into the dynamic evolutionary fates of organelle-derived nuclear DNA in plants.

Cucurbits are an important vegetable crop of the gourd family. Unfortunately, gummy stem blight (GSB) causes a major fungal disease on Cucurbitaceous vegetable crops. It is also known as black root when affecting fruits, and it is found all over the world. GSB is caused by the fungal pathogen Didymella bryoniae. Research efforts have investigated the different developmental stages and various parts of Cucurbits affected with this disease. In the present paper, we have completed a systematic review for the disease’s symptomatic, pathogenic microbes, resistance resources, resistance inheritance regularity, molecular biology and genomic study of resistance gene and control method, etc., on Cucurbits. This review provides the background and rationale for future studies aiming to address the issues existing in gummy stem blight research and development.

Cytonuclear disruption may accompany allopolyploid evolution as a consequence of the merger of different nuclear genomes in a cellular environment having only one set of progenitor organellar genomes. One path to reconcile potential cytonuclear mismatch is biased expression for maternal gene duplicates (homoeologs) encoding proteins that target to plastids and/or mitochondria. Assessment of this transcriptional form of cytonuclear coevolution at the level of individual cells or cell types remains unexplored. Using single-cell (sc-) and single-nucleus (sn-) RNAseq data from eight tissues in three allopolyploid species, we characterized cell type–specific variations of cytonuclear coevolutionary homoeologous expression and demonstrated the temporal dynamics of expression patterns across development stages during cotton fiber development. Our results provide unique insights into transcriptional cytonuclear coevolution in plant allopolyploids at the single-cell level.

Plants have the salient biological property of totipotency, i.e., the capacity to regenerate a whole plant from virtually any kind of fully differentiated somatic cells after a process of dedifferentiation. This property has been well-documented by successful plant regeneration from tissue cultures of diverse plant species. However, the accumulation of somaclonal variation, especially karyotype alteration, during the tissue culture process compromises cell totipotency. In this respect, Chinese ginseng (Panax ginseng C. A. Mey.) is an exception in that it shows little decline in cell totipotency accompanied by remarkable chromosomal stability even after prolonged tissue cultures. However, it remains unclear whether chromosomal level stability necessarily couples with molecular genetic stability at the nucleotide sequence level, given that the two types of stabilities are generated by largely distinct mechanisms. Here, we addressed this issue by genome-wide comparisons at the single-base resolution of long-term tissue culture-regenerated P. ginseng plants. We identified abundant single nucleotide polymorphisms (SNPs) that have accumulated in cultured ginseng callus and are retained in the process of plant regeneration. These SNPs did not occur at random but showed differences among chromosomes and biased regional aggregation along a given chromosome. In addition, our results demonstrate that, compared with the overall genes, genes related to processes of cell totipotency and chromosomal stability possess lower mutation rates at both coding and flanking regions. In addition, collectively, the mutated genes exhibited higher expression levels than non-mutated genes and are significantly enriched in fundamental biological processes, including cellular component organization, development, and reproduction. These attributes suggest that the precipitated molecular level genetic variations during the process of regeneration in P. ginseng are likely under selection to fortify normal development. As such, they likely did not undermine chromosomal stability and totipotency of the long-term ginseng cultures.

Spuriopimpinella brachycarpa (2n = 2x = 22), a perennial Apiaceae herb traditionally consumed in Northeast China, is rich in bioactive compounds such as flavonoids and terpenoids and possesses both medicinal and comestible value. However, the metabolic mechanisms underlying these traits remain unclear due to the lack of genomic resources. Here, we present the first chromosome-level genome assembly of S. brachycarpa (4.12 Gb; scaffold N50 = 358.95 Mb; 11 chromosomes). Comparative genomics analysis revealed two postdivergence whole-genome duplication (WGD) events in Apiaceae and a close phylogenetic relationship between S. brachycarpa and Daucus carota (carrot). Metabolomic profiling indicated that flavonoids, dominated by flavanols and flavones, are most actively synthesized in leaves, with their biosynthesis likely regulated by the MYB transcription factor SbraChr11G00348720.1. Terpenoids, primarily monoterpenes and sesquiterpenes, accumulated predominantly under cultivated conditions, demonstrating habitat-specific patterns. Transcriptomic analysis further identified two key terpene synthase genes—SbraChr6G00204720.1 (TPS-a subfamily) and SbraChr3G00078100.1 (TPS-b subfamily)—associated with sesquiterpene and monoterpene biosynthesis, respectively. By integrative genomic, transcriptomic, and metabolomic data, this study systematically elucidates the biosynthesis basis of major secondary metabolites in S. brachycarpa and provides a valuable genetic resource for comparative genomics and molecular breeding in Apiaceae crops.

Breeding of cucumber for protected cultivation requires improvement of multiple complex horticultural traits, but studies combining multi-trait association mapping with genomic prediction in the same breeding panel remain limited. We evaluated 208 cucumber inbred lines independently developed from diverse source materials collected across China. Sixteen agronomic traits covering vegetative growth, reproductive development, fruit characteristics, yield, and disease resistance were measured over two consecutive growing seasons, and whole-genome resequencing uncovered 580,151 high-quality single nucleotide polymorphisms (SNPs). Genome-wide association analysis detected 89 significantly associated loci (SALs) for 15 traits, including 10 genomic regions shared by two or more traits. Beyond the known CsFT and Tu/CsDULL loci, numerous additional SALs were identified, yielding 19 candidate genes for further investigation of the corresponding traits in cucumber. Genomic prediction accuracies using rrBLUP were evaluated for nine quantitative traits and were variable among traits, with fruit length, fruit shape index, and fruit neck length showing relatively high prediction accuracies. Together, these results have furthered our understanding of the genetic architecture and genomic predictability of cucumber agronomic traits and laid a foundation for integrating locus-specific and genome-wide information for future breeding strategies.