The importance of allopolyploidy in plant evolution has been widely recognized. The genetic changes triggered by allopolyploidy, however, are not yet fully understood due to inconsistent phenomena ...reported across diverse species. The construction of synthetic polyploids offers a controlled approach to systematically reveal genomic changes that occur during the process of polyploidy. This study reports the first fully sequenced synthetic allopolyploid constructed from a cross between Cucumis sativus and C. hystrix, with high‐quality assembly. The two subgenomes are confidently partitioned and the C. sativus‐originated subgenome predominates over the C. hystrix‐originated subgenome, retaining more sequences and showing higher homeologous gene expression. Most of the genomic changes emerge immediately after interspecific hybridization. Analysis of a series of genome sequences from several generations (S0, S4–S13) of C. ×hytivus confirms that genomic changes occurred in the very first generations, subsequently slowing down as the process of diploidization is initiated. The duplicated genome of the allopolyploid with double genes from both parents broadens the genetic base of C. ×hytivus, resulting in enhanced phenotypic plasticity. This study provides novel insights into plant polyploid genome evolution and demonstrates a promising strategy for the development of a wide array of novel plant species and varieties through artificial polyploidization.
The first whole‐genome sequence of a synthetic allopolyploid in Cucumis demonstrates significant subgenome dominance. Comparative genomic analyses on interspecific hybrid and different generations of allopolyploids successfully differentiate the divergent roles of hybridization, genome duplication, and diploidization in shaping the genome. Moreover, the merger of two distinct genomes practically creates a novel allopolyploid species with higher fitness.
Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA-mRNA modules in the cucumber fruit expansion are not yet to be investigated. In ...this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.
▶ The investigated data showed a large range of variability of morphological characters among the 39 inbred lines of
C. moschata. ▶ There were various degree correlations among morphological ...characters, making it possible to summarize the diversities of the 20 characters into 3 major principal components: leaf, fruit and flesh quality factor. ▶ The classification based on principal component data was more distinct than that based on standardized original data, because it extracted the major information of genetic divergence among inbred lines and ignored the minor information. ▶ However, the cluster based on standardized original data was more valuable than that based on principle component data in cross breeding for classifying heterotic group, because parent inbred lines whose hybrids displayed significant heterosis in fruit weight, soluble solid and fruit shape were generally located in different clusters or sub-clusters based on standardized original data.
Knowledge of genetic divergence among inbred lines is essential for cross breeding. The objectives of this study were to (1) analyze the level and character of genetic diversity in
C. moschata accessions, and (2) classify the genetic divergence among inbred lines in
C. moschata to assist in selection of parent genotypes for genetic improvement. Twenty agronomic characters were investigated and rich diversities were demonstrated among 39 inbred lines of
C. moschata from China. Various degree correlations among these characters made it possible to summarize the diversities of the twenty characters into 3 major principal components: leaf, fruit and flesh quality factor. Forty-one inbred lines of pumpkin were clustered into four groups based on principal component data, which is more distinct for classification that based on the original data of the 20 characters. However, parent inbred lines whose hybrids displayed significant heterosis in fruit weight, soluble solid and fruit shape were located in different clusters or sub-clusters based on standardized original data. It was suggested that genotypes in the same clusters may represent members of one heterotic group.
SUMMARY
Karyotype dynamics driven by complex chromosome rearrangements constitute a fundamental issue in evolutionary genetics. The evolutionary events underlying karyotype diversity within plant ...genera, however, have rarely been reconstructed from a computed ancestral progenitor. Here, we developed a method to rapidly and accurately represent extant karyotypes with the genus, Cucumis, using highly customizable comparative oligo‐painting (COP) allowing visualization of fine‐scale genome structures of eight Cucumis species from both African‐origin and Asian‐origin clades. Based on COP data, an evolutionary framework containing a genus‐level ancestral karyotype was reconstructed, allowing elucidation of the evolutionary events that account for the origin of these diverse genomes within Cucumis. Our results characterize the cryptic rearrangement hotspots on ancestral chromosomes, and demonstrate that the ancestral Cucumis karyotype (n = 12) evolved to extant Cucumis genomes by hybridizations and frequent lineage‐ and species‐specific genome reshuffling. Relative to the African species, the Asian species, including melon (Cucumis melo, n = 12), Cucumis hystrix (n = 12) and cucumber (Cucumis sativus, n = 7), had highly shuffled genomes caused by large‐scale inversions, centromere repositioning and chromothripsis‐like rearrangement. The deduced reconstructed ancestral karyotype for the genus allowed us to propose evolutionary trajectories and specific events underlying the origin of these Cucumis species. Our findings highlight that the partitioned evolutionary plasticity of Cucumis karyotype is primarily located in the centromere‐proximal regions marked by rearrangement hotspots, which can potentially serve as a reservoir for chromosome evolution due to their fragility.
Significance Statement
To date, elucidating karyotype evolution that has been disrupted by complex chromosome rearrangements remains a major challenge in the study of chromosome evolution. By reconstructing a deduced ancestral chromosome and an evolutionary framework using highly customizable comparative oligo‐painting, we demonstrated the evolutionary histories for eight Cucumis species. Our findings highlight that the evolution of Cucumis genomes is marked by partitioned evolutionary plasticity with the essential function of creating karyotype novelty, expanding our understanding for karyotype evolution.
•Non-pollinated ovary in pumpkin delayed its growth and suffered the aborting process from 2 DPA.•A total of 7536 DEGs were screened during pumpkin fruit set, with 3406 up-regulated and 4130 ...down-regulated.•Genes related to “cell growth, cell division, cell cycle”, “photosynthesis”, “glycometabolism”, “transcription factors” and “plant hormone signal transduction” might play a crucial role during pumpkin fruit set.•qRT-PCR analysis indicated that RNA-seq data was reliable.
Fruit set is a complex biological process, which determines fruit development and production. Little information is available on the fruit set and regulatory mechanism in pumpkin. In an attempt to obtain the candidate genes involved in fruit set and elucidate the regulatory networks, early growth properties of pumpkin fruit were evaluated from anthesis until 4 days post anthesis (DPA) between pollination and non-pollination treatment. The results showed that non-pollinated ovary delayed its growth and suffered the aborting process from 2 DPA, while, pollinated fruit showed an exponential growth from anthesis until 4 DPA, with notable changes in fruit length and diameter. Furthermore, RNA-seq was carried out aimed at identifying differentially expressed genes (DEGs) responsible for fruit set in pumpkin after pollination. The results revealed that a total of 7536 DEGs were screened during pumpkin fruit set after pollination, including 3406 up-regulated and 4130 down-regulated. Of these DEGs, 5180, 1594 and 762 were differentially expressed in PF_2 vs UF_2, PF_2 vs UF_0 and UF_2 vs UF_0, respectively. 644 DEGs related to cell growth, cell division, cell cycle (28), photosynthesis (15), glycometabolism (71), transcription factors (405) and plant hormone signal transduction (125) were analyzed based on functional annotation, which might play a crucial role during pumpkin fruit set. In addition, quantitative real-time PCR (qRT-PCR) analysis of 9 DEGs selected randomly indicated that RNA-seq data was reliable. Taken together, our results will provide useful gene resources for genetic improvement, and lay a theoretical foundation for understanding the molecular mechanism of pumpkin fruit set.
•The growth of ryegrass weakened as tetracycline concentration increased.•Tetracycline triggered strong oxidative stress.•3 metabolic pathways were different under tetracycline in the roots.•11 ...metabolites could have crucial functions to the extension of roots.
Tetracycline is an antibiotic that frequently contaminates the environment. In this study, the growth and metabolites of ryegrass seedlings treated with tetracycline (0, 1, 10 or 100 mg/L) for 5 days were investigated. The results showed that the growth of ryegrass and the concentrations of carotenoid and chlorophyll decreased as the tetracycline concentration increased. Tetracycline increased the production of reactive oxygen species (ROS) and cell permeability and triggered mitochondrial membrane potential loss in the roots of ryegrass. The metabolic profiles of ryegrass differed between the control and tetracycline-treated groups. The contents of glucose, shikimic acid, aconitic acid, serine, lactose, phenylalanine, mannitol, galactose, gluconic acid, asparagine, and glucopyranose were positively correlated with root length and had high variable importance projection values. These compounds may have crucial functions in root extension. Tetracycline also affected aminoacyl-tRNA biosynthesis, nitrogen metabolism, and alanine, aspartate and glutamate metabolism in the roots. Tetracycline may affect root extension by regulating the synthesis/degradation of these metabolites or the activity of their biosynthetic pathways. These results provide an insight into the stress response of ryegrass to tetracycline.
•Vacuum infiltration and sonication can improve the efficiency of transient transformation.•Over-expression of the StNHX1 gene improved the salt tolerance of pumpkin seedlings.•The lower epidermis of ...cotyledon was the optimal tissue for subcellular localization in pumpkin.•The CmPHD1-EGFP fusion protein was detected in the nucleus of cotyledon epidermal cells.
Currently, gene exploration and molecular breeding in pumpkin (Cucurbita moschata Duch.) is a challenging process. There are limited efficient stable transformation methods for pumpkin. Transient transformation is a promising tool for the study of gene function. Here, an efficient Agrobacterium-mediated transient transformation system was developed for gene function studies in pumpkin. In this system, the function of salt-tolerant gene StNHX1 was confirmed by over-expression in germinated seeds. The CmPHD1-EGFP fusion protein was detected in the nucleus of cotyledon epidermal cells. This system can be used to analyze gene function and protein subcellular localization in pumpkin. Its advantages are highly efficient, cost-effective and time-saving (∼14 days). It may play a key role in gene exploration and molecular breeding in pumpkin, especially in large-scale analyses.
Environmental factors, including antibiotics such as tetracycline, can alter biological processes in plants. To ascertain how cell/tissue response to tetracycline, a multi-omic analysis was ...implemented to explore the molecular mechanism of tetracycline influencing the growth of ryegrass root. Tetracycline induced extensive changes in the root metabolome in plants, particularly impacting metabolites of flavonoid metabolic pathways, which were supported through consistent differences between transcriptome and proteome. Cross-comparison between mRNA and protein contents considered the authentication of congruence with related metabolites and revealed changes of several biological processes under tetracycline stress. Overall, we present an undemanding multi-omic strategy to survey the significant influence on the root under tetracycline stress.
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•Tetracycline inhibited the levels of flavonoid metabolites.•Flavonoid metabolic pathway was reduced at the levels of transcription and protein.•Multiomics method was developed and gained consistent results with monomic analysis.
Key message
Two genetic loci,
det-ma
(
CsCEN
) and
det-lb
, showed epistatic interaction on indeterminate/determinate growth of LB in cucumber.
CsSHBY
was identified as the candidate gene for
det-lb
...locus.
Plant architecture depends on the spatial regulation of meristems from both main axis (MA) and lateral branches (LBs). Fate (indeterminate or determinate) of these meristems is a crucial source of architectural diversity determining crop productivity and management.
CENTRORADIALIS
/
TERMINAL FLOWER 1
/
SELF-PRUNING
(
CETS
) gene family have been well known as pivotal regulators for indeterminate/determinate growth of MA. Nevertheless, genes that regulate LB indeterminacy/determinacy remained unclear. Cucumber (
Cucumis sativus
L.) has typical monopodial growth and multiple lateral branches. Both MA and LBs had indeterminate or determinate growth, and indeterminate/determinate growth of LB was controlled by two distinct loci,
det-ma
(
CsCEN
) and
det-lb
. In our study, based on bulked segregant analysis (BSA) method, the
det-lb
locus was mapped on a 60.6 kb region on chromosome 1 harboring only one gene
CsaV3_1G044330
, which encoded a putative vacuolar-sorting protein (designated as
CsSHBY
). Multipoint mutations in
CsSHBY
were identified in D082 and D226, compared with CCMC, including nonsynonymous SNP mutations and a 6-bp deletion in exons. Further, qPCR showed that
CsSHBY
was highly expressed in lateral bud of CCMC, suggesting that
CsSHBY
might play an active role in regulating indeterminate/determinate growth of LB. Genetic analyses showed that
det-ma
(
CsCEN
) had an epistatic effect on
det-lb
(
CsSHBY
), and
CsCEN
could activate
CsSHBY
promoter by Dual luciferase and GUS activity assays. Meanwhile,
Cscen
or
Csshby
was found to influence auxin contents and
CsYUCs
and
CsPINs
expression levels. These findings provided new insights into precisely optimizing plant architecture for yield improvements.
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