Genome最新文献

Successful resistance to disease-causing pathogens is underpinned by properly regulated immune signalling and defence responses in plants. The plant immune system is controlled at multiple levels of gene and protein regulation-from chromatin-associated epigenetic processes to protein post-translational modifications. Optimal fine-tuning of plant immune signalling and responses is important to prevent plant disease development, which is being exacerbated by a globally changing climate. In this review, we focus on how changing climatic factors mechanistically intercept plant immunity at different levels of regulation (chromatin, transcriptional, post-transcriptional, translational, and post-translational). We specifically highlight recent studies that have provided molecular insights into critically important climate-sensitive nodes and mechanisms of the plant immune system. We then propose several potential future directions to build climate-resilient plant disease resistance using cutting-edge biotechnology. Overall, this conceptual understanding and promising biotechnological advances provide a foundational platform towards novel approaches to engineer plant immune resilience.

This review explores the challenges and potential solutions in plant micropropagation and biotechnology. While these techniques have proven successful for many species, certain plants or tissues are recalcitrant and do not respond as desired, limiting the application of these technologies due to unattainable or minimal in vitro regeneration rates. Indeed, traditional in vitro culture techniques may fail to induce organogenesis or somatic embryogenesis in some plants, leading to classification as in vitro recalcitrance. This paper focuses on recalcitrance to somatic embryogenesis due to its promise for regenerating juvenile propagules and applications in biotechnology. Specifically, this paper will focus on epigenetic factors that regulate recalcitrance as understanding them may help overcome these barriers. Transformation recalcitrance is also addressed, with strategies proposed to improve transformation frequency. The paper concludes with a review of CRISPR-mediated genome editing's potential in modifying somatic embryogenesis-related epigenetic status and strategies for addressing transformation recalcitrance.

Traditional taxonomic revisions based on macromorphological and leaf anatomical traits may have limitations in accurately distinguishing certain species within the genus. To improve taxonomic clarity, this study applied DNA barcoding to enhance the understanding of the taxonomy and phylogeny of Baccaurea Lour., a plant genus widely utilized for food, medicine, and building materials. DNA barcode regions, including rbcL, ITS2, and trnH-psbA, were used to analyze 64 samples representing 19 Baccaurea species. Using similarity Basic Local Alignment Search Tool and phylogenetic tree inference, we determined the discriminatory efficiencies of rbcL, ITS2, trnH-psbA, and their combinations rbcL + ITS2 and rbcL + ITS2 + trnH-psbA as 21.1%, 89.5%, 87.5%, 89.5%, and 89.5%, respectively. The Neighbor-Joining tree revealed well-defined, monophyletic species clusters that largely align with phylogenetic positions based on macromorphological features. Notably, our results indicate that Baccaurea parviflora and the synonymized Baccaurea scortechinii are distinct species, recommending the re-establishment of B. scortechinii as a separate species. DNA barcoding is useful in delineating species boundaries, facilitating routine specimen identification, and flagging atypical samples for detailed examination.

Platycarya longipes is a dominant tree species in karst forests. Due to limited genomic information, its exact phylogenetic position within the family Juglandaceae remains unclear. In this study, the complete chloroplast genome (cp genome) of Platycarya longipes was de novo assembled using Illumina reads. This circular cp genome was 158 592 bp in length, consisting of an 88 066 bp large single-copy region, an 18 524 bp small single-copy region, and a total of 26 001 bp derived from a pair of inverted repeats (IRa and IRb), with an average GC content of 36.15%. It accommodated a total of 113 genes, including 80 protein-coding genes, 29 tRNAs, and 4 rRNAs. Additionally, within the genome, 49 long repeats and 66 simple sequence repeats, which could be utilized as molecular markers, were identified. In comparison to the related Platycarya strobilacea, the K_a/K_s substitution rate values of Platycarya longipes exhibited significant divergence, supporting the differentiation between the species. The conserved gene order and structure of the Platycarya longipes cp genome compared to other Juglandaceae members. Phylogenetic analysis using maximum likelihood and Bayesian inference methods with Fagales genomes showed a close relationship between Platycarya longipes and Platycarya strobilacea.

Benzo(a)pyrene produced by food during high-temperature process enters the body through ingestion, which causes food safety issues to the human body. To alleviate the harm of foodborne benzo(a)pyrene to human health, a strain that can degrade benzo(a)pyrene was screened from Kefir, a traditional fermented product in Xinjiang. Bacillus cereus M72-4 is a Gram-positive bacteria sourced from Xinjiang traditional fermented product Kefir; under benzo(a)pyrene stress conditions, there was 69.39% degradation rate of 20 mg/L benzo(a)pyrene by strain M72-4 after incubation for 72 h. The whole genome of M72-4 was sequenced using PacBio sequencing technology in this study. The genome size was 5754 801 bp and a GC content was 35.24%; a total of 5719 coding genes were predicted bioinformatically. Through functional database annotation, it was found that the strain has a total of 219 genes involved in the transportation and metabolism of hydrocarbons, a total of 9 metabolic pathways related to the degradation and metabolism of exogenous substances, and a total of 67 coding genes. According to the Kyoto Encyclopedia of Genes and Genomes database annotation results, a key enzyme related to benzo(a)pyrene degradation, catechol 2,3-dioxygenase, was detected in the genome data of Bacillus cereus M72-4, encoding genes dmpB and xylE, respectively. There are also monooxygenases and dehydrogenases. Therefore, it can be inferred that this strain mainly degrades benzo(a)pyrene through benzoate metabolic.

Nyctimantis pomba is a critically endangered frog that has been the target of conservation programs, including captive breeding to prevent extinction. Data from different scientific fields, including cytogenetics, can be valuable for species conservation efforts. Here, we characterize the karyotype of N. pomba using conventional and molecular cytogenetics and discuss these data in light of the phylogeny of the genus. Nyctimantis pomba had a diploid chromosome number 2n = 24 and exhibited a secondary constriction in one of the homologs of pair 9q, coincident with the rDNA sites. C-banding evidenced pericentromeric blocks on all chromosomes, and CMA₃ staining confirmed that these regions were GC-rich. AT-rich pericentromeric heterochromatin was observed in the long arm of pair 2. (TTAGGG)_n probes labeled the telomeres of all chromosomes, with additional signals at the centromeric regions of some of them. (GA)_n probes hybridized to the terminal regions of all chromosomes and pericentromeric regions of five pairs. These results showed that N. pomba differs from other karyotyped species by the presence of a nucleolar organizer region in pair 9, AT-rich pericentromeric heterochromatin in pair 2, and (TTAGGG)_n signals in the centromeric regions. These variations represent distinct markers of N. pomba and indicate that cytogenetics may be a useful tool for detecting karyotypic differences in reintroduced populations.

Transposable elements play an important role in determining the size and structure of eukaryotic genomes. Represented by several families, the Tc1/mariner superfamily is widely distributed in animal and plant genomes, and its structure has been characterized. Boana is a Neotropical genus of treefrogs, and despite the frequent 2n = 24 chromosomes found in its representatives, the karyotypic organization of the species cannot be considered conserved due to the scarcity of studies focusing on chromosomal mapping of repetitive DNA sequences. Here, Tc1/mariner elements were isolated and mapped on the chromosomes of three Boana species, followed by structural and phylogenetic analysis. The physical mapping revealed dispersed signals in euchromatin with small accumulations in some heterochromatic regions. All Tc1/mariner transposons isolated in this study presented high sequence integrity, suggesting that these elements had a recent invasion phase and are active in the host genomes of these frog species. Boana albopuntata and Boana faber presented a DD36E signature, while Boana prasina showed a new DD37E signature with a similar organizational structure and a close relationship with the known DD36E/Incomer family. These findings improve our understanding of the diversity of Tc1/mariner transposons and their role in the evolution of the hylid frog genome and karyotype.

Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. High intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in this genus. In our study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against the kinetochore protein KNL1 and the cell-cycle dependent posttranslational modifications histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in the newly sequenced species Eleocharis maculosa, Eleocharis geniculata, Eleocharis parodii, Eleocharis elegans, and Eleocharis montana. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was distributed irregularly along the chromatid length in a line-like manner. EmaSAT14 monomers were present in a few copies in few species across the Eleocharis phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus Eleocharis. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.

Recombination, the reciprocal exchange of DNA between homologous chromosomes, is a mandatory step necessary for meiosis progression. Crossovers between homologous chromosomes generate new combinations of alleles and maintain genetic diversity. Due to genetic, epigenetic, and environmental factors, the recombination landscape is highly heterogeneous along the chromosomes and it also differs between populations and between sexes. Here, we investigated recombination characteristics across the 19 chromosomes of the model allopolyploid crop species oilseed rape (Brassica napus L.), using two unique multiparental populations derived from two genetically divergent founder pools, each of which comprised 50 genetically diverse founder accessions. A fully balanced, pairwise chain-crossing scheme was utilized to create each of the two populations. A total of 3213 individuals, spanning five successive generations, were genotyped using a 15K SNP array. We observed uneven distribution of recombination along chromosomes, with some genomic regions undergoing substantially more frequent recombination in both populations. In both populations, maternal recombination events were more frequent than paternal recombination. This study provides unique insight into the recombination landscape at chromosomal level and reveals a maternal-paternal bias for recombination number with implications for breeding.

Brassica napus L. plants are sensitive to water stress conditions throughout their life cycle from seed germination to seed setting. This study aims at identifying quantitative trait loci (QTL) linked to B. napus tolerance to water stress mimicked by applications of 10% polyethylene glycol-6000 (PEG-6000). Two doubled haploid populations, each consisting of 150 genotypes, were used for this research. Plants at the two true leaf stage of development were grown in the absence (control) or presence (stress) of PEG-6000 under controlled environmental conditions for 48 h, and the drought stress index was calculated for each genotype. All genotypes, along with their parents, were genotyped using the Brassica Infinium 90K SNP BeadChip Array. Inclusive composite interval mapping was used to identify QTL. Six QTL and 12 putative QTL associated with water stress tolerance were identified across six chromosomes (A2, A3, A4, A9, C3, and C7). Collectively, 2154 candidate genes for water stress tolerance were identified for all the identified QTL. Among them, 213 genes were identified as being directly associated with water stress (imposed by PEG-6000) tolerance based on nine functional annotations. These results can be incorporated into future breeding initiatives to select plant material with the ability to cope effectively with water stress.