Advances in cancer genomics and precision oncology.

Background: Next-generation sequencing has revolutionized genome science over the last two decades. Indeed, the wealth of sequence information on our genome has deepened our understanding on cancer. Cancer is a genetic disease caused by genetic or epigenetic alternations that affect the expression of genes that control cell functions, particularly cell growth and division.

Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types.

Background: Plant senescence is the process of physiological maturation of plants and is important for crop yield and quality. Senescence is controlled by several factors, such as temperature and photoperiod. However, the molecular basis by which these genes promote senescence in soybeans is not well understood.

Review of the technology used for structural characterization of the GMO genome using NGS data.

The molecular characterization of genetically modified organisms (GMOs) is essential for ensuring safety and gaining regulatory approval for commercialization. According to CODEX standards, this characterization involves evaluating the presence of introduced genes, insertion sites, copy number, and nucleotide sequence structure. Advances in technology have led to the increased use of next-generation sequencing (NGS) over traditional methods such as Southern blotting.

Comparative analysis of the transcriptomes from regenerated plants and root explants of endangered Oplopanax elatus.

Background: Oplopanax elatus is a plant of therapeutic significance in oriental medicine; however, its mass cultivation is limited owing to the difficulties in propagating it from seeds.

Methods: In this study, we investigated the transcriptome profiles and transcriptional regulatory factors expressed during plantlet regeneration from root tissues of the endangered O. elatus.

Contents of paeoniflorin and albiflorin in two Korean landraces of Paeonia lactiflora and characterization of paeoniflorin biosynthesis genes in peony.

Background And Research Purpose: Paeoniflorin and albiflorin are monoterpene glycosides that exhibit various medicinal properties in Paeonia species. This study explored the terpene biosynthesis pathway and analyzed the distribution of these compounds in different tissues of two Korean landraces of Paeonia lactiflora to gain insights into the biosynthesis of monoterpene glycosides in P. lactiflora and their potential applications.

The MYB-CC Transcription Factor PHOSPHATE STARVATION RESPONSE-LIKE 7 (PHL7) Functions in Phosphate Homeostasis and Affects Salt Stress Tolerance in Rice.

Inorganic phosphate (Pi) homeostasis plays an important role in plant growth and abiotic stress tolerance. Several MYB-CC transcription factors involved in Pi homeostasis have been identified in rice (). PHOSPHATE STARVATION RESPONSE-LIKE 7 (PHL7) is a class II MYC-CC protein, in which the MYC-CC domain is located at the N terminus.

Cellular Morphology and Transcriptome Comparative Analysis of Bunge Sprouts Cultured In Vitro under Different LED Light.

, the major components of which are saponins, flavonoids, and polysaccharides, has been established to have excellent pharmacological activity. After ginseng, it is the second most used medicinal plant. To examine the utility of as a sprout crop for plant factory cultivation, we sought to establish a functional substance control model by comparing the transcriptomes of sprouts grown in sterile, in vitro culture using LED light sources.

Isolation and Characterization of the Genes Involved in the Berberine Synthesis Pathway in Asian Blue Cohosh, .

, commonly named Asian blue cohosh, is a perennial herb in the family Berberidaceae. It has traditionally been used for folk medicine in China. We isolated berberine from the leaves, stem, roots, and fruits of , and this is the first report on berberine in this species.

Comparative Transcriptomics for Genes Related to Berberine and Berbamine Biosynthesis in Berberidaceae.

Berberine and berbamine are bioactive compounds of benzylisoquinoline alkaloids (BIAs) present in species. The contents of berbamine are 20 times higher than berberine in leaf tissues in three closely related species: and . This is the first report on the quantification of berberine compared to the berbamine in the species.

Identifying Terpenoid Biosynthesis Genes in via Full-Length cDNA Sequencing.

The annual herb L. produces anti-inflammatory and biologically active substances such as triterpenoids, tannins, and polyphenols, and it is used in traditional Chinese medicine. Of these bioactive compounds, terpenoids, also called isoprenoids, are major secondary metabolites in .

Genome-wide identification of 194 G protein-coupled receptor (GPCR) genes from the water flea Daphnia magna.

In crustaceans, G protein-coupled receptors (GPCRs) are the largest transmembrane receptor family and function by mediating various environmental stimuli in cells. Understanding GPCR signaling is crucial to better understanding of crustacean endocrinology. GPCRs evolved from early eukaryotes, and genome-wide identification of GPCRs in a particular taxon can provide insight into evolutionary tendencies and adaptive strategies of GPCR response to environmental stimuli.

Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean.

In cultivated plants, shoot morphology is an important factor that influences crop economic value. However, the effects of gene expression patterns on shoot morphology are not clearly understood. In this study, the molecular mechanism behind shoot morphology (including leaf, stem, and node) was analyzed using RNA sequencing to compare weedy (creeper) and cultivar (stand) growth types obtained in F derived from a cross of wild and cultivated soybeans.

Characterization of transcription factor genes related to cold tolerance in Brassica napus.

Brassica napus is the third most important oilseed crop in the world; however, in Korea, it is greatly affected by cold stress, limiting seed growth and production. Plants have developed specific stress responses that are generally divided into three categories: cold-stress signaling, transcriptional/post-transcriptional regulation, and stress-response mechanisms. Large numbers of functional and regulatory proteins are involved in these processes when triggered by cold stress.

Rice module enhances drought tolerance by regulation of flavonoid biosynthesis genes.

Plants have evolved sophisticated defense systems to enhance drought tolerance. These include the microRNA (miRNA) group of small noncoding RNAs that act as post-transcriptional regulators; however, details of the mechanisms by which they confer drought tolerance are not well understood. Here, we show that , a member of - gene family, is mainly expressed in response to drought stress and regulates the transcript levels of () and in rice ().

Identification of resurrection genes from the transcriptome of dehydrated and rehydrated .

is a lycophyta species that survives under extremely dry conditions via the mechanism of resurrection. This phenomenon involves the regulation of numerous genes that play vital roles in desiccation tolerance and subsequent rehydration. To identify resurrection-related genes, we analyzed the transcriptome between dehydration conditions and rehydration conditions of .

Unraveling the complexity of faba bean (Vicia faba L.) transcriptome to reveal cold-stress-responsive genes using long-read isoform sequencing technology.

Faba bean (Vicia faba L.), a globally important grain legume providing a stable source of dietary protein, was one of the earliest plant cytogenetic models. However, the lack of draft genome annotations and unclear structural information on mRNA transcripts have impeded its genetic improvement.

Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize.

Background: Genome wide association studies (GWAS) have been widely used to identify QTLs underlying quantitative traits in humans and animals, and they have also become a popular method of mapping QTLs in many crops, including maize. Advances in high-throughput genotyping technologies enable construction of high-density linkage maps using SNP markers.

Objectives: High-density genetic mapping must precede to find molecular markers associated with a particular trait.

Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean).

Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes.

Gene Expression and Isoform Identification of PacBio Full-Length cDNA Sequences for Berberine Biosynthesis in .

is a medicinal plant containing berberine, which is a bioactive compound of the benzylisoquinoline alkaloid (BIA) class. BIA is widely used in the food and drug industry for its health benefits. To investigate the berberine biosynthesis pathway, gene expression analysis was performed in leaves, flowers, and fruits at different stages of growth.

Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops.

Global population growth and climate change are posing increasing challenges to the production of a stable crop supply using current agricultural practices. The generation of genetically modified (GM) crops has contributed to improving crop stress tolerance and productivity; however, many regulations are still in place that limit their commercialization. Recently, alternative biotechnology-based strategies, such as gene-edited (GE) crops, have been in the spotlight.

The complete chloroplast genome of a Korean endemic species , Nakai.

In this study, we report the complete chloroplast (cp) genome of and its relation with other species within the Fabaceae family. The cp genome was 154,870 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (25,866 bp) separated by a large (85,037 bp) and small (18,101 bp) single-copy (SC) region. The genome encodes a total of 84 protein-coding genes, 35 tRNA genes, and 8 rRNA genes.

The complete chloroplast genome of a fern genus .

In this study, we report the complete chloroplast (cp) genome of , a fern member, and comparative analysis with its related family members. The cp genome was 155,983 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (25,614 bp) separated by a large (82,769 bp) and small (21,986 bp) single-copy (SC) region. The genome encodes a total of 88 protein-coding genes, 35 tRNA genes, and 8 rRNA genes.

The complete chloroplast genome of a .

is one of the diverse members of the fern group and medicinally important genus. In Korea, the natural resources of are being exhausted by excessive exploitation and require urgent conservation. In this study, the complete chloroplast genome of was generated, and its structure was compared with that of other members of same family.