Modified CTAB protocols for high-molecular-weight DNA extractions from ferns

Integration of GWAS and Co-Expression Network Analysis Identified Main Genes Responsible for Nitrogen Uptake Traits in Seedling Waxy Corn

Background/Objectives: Waxy corn has a unique taste and flavor that a majority of consumers love, and the market application prospect is broad. Nitrogen plays an important role in the growth and development of waxy corn. Exploring the key genes that affect nitrogen absorption can lay a foundation for improving the quality of waxy corn. Methods: In this study, a total of 534 local waxy corn inbred lines were used to perform genome-wide association studies (GWAS) to mine the significant Quantitative Trait Nucleotides (QTNs) for nitrogen content of waxy corn at seedling stage in two different environments. The Weighted Gene Co-Expression Network Analysis (WGCNA) nitrogen response co-expression network was also constructed to explore the differences of gene expression patterns and the co-expression relationship between transcription factors and functional genes to find candidate genes significantly associated with nitrogen uptake in waxy corn. Results: A total of 97 significant associations (LOD-value ≥ 3) were detected between SNPs and nitrate content traits under single and multi-environment conditions. Fifty-four candidate genes were identified around the significant SNPs in about a 20 Kb region. Combined with nitrogen response differential co-expression network analysis, 17 out of the 54 candidate genes were identified in the nitrogen response module, among which 4 main genes (Zm00001d029012, Zm00001d034035, Zm00001d007890, and Zm00001d045097) were repeatedly detected in multiple environments. Conclusions: This study jointly identified four stable and heritable candidate genes involved in the nitrogen metabolism process through GWAS and co-expression network analysis. The results of this study provide theoretical guidance for further elucidating the genetic mechanism of nitrogen efficiency in waxy corn and breeding new germplasm of waxy corn.

Revealing the Genetic Diversity and Population Structure of Garlic Resource Cultivars and Screening of Core Cultivars Based on Specific Length Amplified Fragment Sequencing (SLAF-Seq)

Garlic is an important vegetable and condiment that has good medical and health care effects. At present, the origin of Chinese garlic and its association with other types of quality are limited to the molecular marker level, and there are few reports at the genome level. Therefore, this study is based on the specific length amplified fragment sequencing (SLAF-seq) of 102 copies of garlic germplasm resources, the group structure, and further screening of the core germplasm. SLAF-seq of 102 garlic cultivars yielded 1949.85 Mb of clean data and 526,432,275 SNPs. Through principal component analysis, evolutionary tree, population structure, and genetic relationship analysis, all garlic cultivars were divided into 3 groups. Among them, Group 1 contains 45 Chinese cultivars and 1 Egyptian cultivar, which are distributed mainly in the coastal and central areas of China. Group 2 contains 36 Chinese cultivars and 1 U.S. cultivar, which are distributed mainly in Northwest China. Group 3 contains 19 Chinese cultivars, which are distributed mainly in Xinjiang, China. The genetic diversity results indicate that the fixation index (Fst) values of Group 1 and Group 2 are lower than those of Group 1 and Group 3 and that the diversity of nucleotides (π) of Group 3 is greater than those of Group 2 and Group 1. Finally, the 30 parts of the cultivars were used as the core germplasms, and there was no difference between the two cultivars in terms of core quality. In summary, this study provides tags for the determination of garlic molecular markers and genotypes and provides a theoretical basis for subsequent resource protection and utilization, genetic positioning of important agronomic traits, and molecular marking agglomeration breeding.

A Novel Preservative Film with a Pleated Surface Structure and Dual Bioactivity Properties for Application in Strawberry Preservation due to Its Efficient Apoptosis of Pathogenic Fungal Cells

Botrytis cinerea (B. cinerea) and Colletotrichum gloeosporioides (C. gloeosporioides) were isolated from the decaying strawberry tissue. The antifungal properties of Monarda didyma essential oil (MEO) and its nanoemulsion were confirmed, demonstrating complete inhibition of the pathogens at concentrations of 0.45 μL/mL (0.37 mg/mL) and 10 μL/mL, respectively. Thymol, a primary component of MEO, was determined as an antimicrobial agent with IC50 values of 34.51 (B. cinerea) and 53.40 (C. gloeosporioides) μg/mL. Hippophae rhamnoides oil (HEO) was confirmed as a potent antioxidant, leading to the development of a thymol-HEO-chitosan film designed to act as an antistaling agent. The disease index and weight loss rate can be reduced by 90 and 60%, respectively, with nutrients also being well-preserved, offering an innovative approach to preservative development. Studies on the antifungal mechanism revealed that thymol could bind to FKS1 to disrupt the cell wall, causing the collapse of mitochondrial membrane potential and a burst of reactive oxygen species.

Organellar phylogenomics of Ophioglossaceae fern genera

Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.

Cationic and anionic detergent buffers in sequence yield high-quality genomic DNA from diverse plant species

Because of the heterogeneity among seedlings of outbreeding species, the use of seedling tissues as a source of DNA is unsuitable for the genomic characterization of elite germplasms. High-quality DNA, free of RNA, proteins, polysaccharides, secondary metabolites, and shearing, is mandatory for downstream molecular biology applications, especially for next-generation genome sequencing and pangenome analysis aiming to capture the complete genetic diversity within a species. The study aimed to accomplish an efficient protocol for the extraction of high-quality DNA suitable for diverse plant species/tissues. We describe a reliable, and consistent protocol suitable for the extraction of DNA from 42 difficult-to-extract plant species belonging to 33 angiosperm (monocot and dicot) families, including tissues such as seeds, roots, endosperm, and flower/fruit tissues. The protocol was first optimized for the outbreeding recalcitrant trees viz., Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera, which are rich in proteins, polysaccharides, and secondary metabolites, and the quality of the extracted DNA was confirmed by downstream applications. Nine procedures were attempted to extract high-quality, impurities-free DNA from these three plant species. Extraction of the ethanol-precipitated DNA from cetyltrimethylammonium bromide (CTAB) protocol using sodium dodecyl sulfate (SDS) buffer, i.e., the extraction using a cationic (CTAB) detergent followed by an anionic (SDS) detergent was the key for high yield and high purity (1.75-1.85 against A260/280 and an A260/230 ratio of >2) DNA. A vice versa extraction procedure, i.e., SDS buffer followed by CTAB buffer, and also CTAB buffer followed by CTAB, did not yield good-quality DNA. PCR (using different primers) and restriction endonuclease digestion of the DNA extracted from these three plants validated the protocol. The accomplishment of the genome of P. cineraria using the DNA extracted using the modified protocol confirmed its applicability to genomic studies. The optimized protocol successful in extracting high-quality DNA from diverse plant species/tissues extends its applicability and is useful for accomplishing genome sequences of elite germplasm of recalcitrant plant species with quality reads.

Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales

Premise

We present approaches used to generate long-read Nanopore sequencing reads for the Liliales and demonstrate how modifications to standard protocols directly impact read length and total output. The goal is to help those interested in generating long-read sequencing data determine which steps may be necessary for optimizing output and results.

Methods

Four species of Calochortus (Liliaceae) were sequenced. Modifications made to sodium dodecyl sulfate (SDS) extractions and cleanup protocols included grinding with a mortar and pestle, using cut or wide-bore tips, chloroform cleaning, bead cleaning, eliminating short fragments, and using highly purified DNA.

Results

Steps taken to maximize read length can decrease overall output. Notably, the number of pores in a flow cell is correlated with the overall output, yet we did not see an association between the pore number and the read length or the number of reads produced.

Discussion

Many factors contribute to the overall success of a Nanopore sequencing run. We showed the direct impact that several modifications to the DNA extraction and cleaning steps have on the total sequencing output, read size, and number of reads generated. We show a tradeoff between read length and the number of reads and, to a lesser extent, the total sequencing output, all of which are important factors for successful de novo genome assembly.

What is the "modified" CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

Cetyltrimethylammonium bromide (CTAB)-based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among plant species has necessitated optimization. Research articles often cite a "modified" CTAB protocol without explicitly stating how the protocol had been altered, creating non-reproducible studies. Furthermore, the various modifications that have been applied to the CTAB protocol have not been rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed the literature for modified CTAB protocols used for the isolation of plant DNA. We found that every stage of the CTAB protocol has been modified, and we summarized those modifications to provide recommendations for extraction optimization. Future genomic studies will rely on optimized CTAB protocols. Our review of the modifications that have been used, as well as the protocols we provide here, could better standardize DNA extractions, allowing for repeatable and transparent studies.