PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data.

Complete mitochondrial genomes (mitogenomes) of plants are valuable resources for nucleocytoplasmic interactions, plant evolution, and plant cytoplasmic male sterile line breeding. However, the complete assembly of plant mitogenomes is challenging due to frequent recombination events and horizontal gene transfers. Previous studies have adopted Illumina, PacBio, and Nanopore sequencing data to assemble plant mitogenomes, but the poor assembly completeness, low sequencing accuracy, and high cost limit the sampling capacity.

Small RNA and Degradome Sequencing Reveal Roles of miRNAs in the Petal Color Fading of Crabapple.

The crabapple is an important woody ornamental plant. The fading of petals during its development significantly affects their ornamental value. Petal color is related to anthocyanin content and miRNAs play an important role in the post-transcriptional regulation of anthocyanin synthesis.

Transcriptome-Wide Identification and Response Pattern Analysis of the NAC Transcription Factor in Response to Pb Stress.

The NAC (NAM-ATAF1/2-CUC) transcription factor family is one of the largest plant-specific transcription factor families, playing an important role in plant growth and development and abiotic stress response. As a short-rotation woody plant, () has high lead (Pb) phytoremediation potential. To understand the role of NAC in Pb tolerance, 53 transcripts were identified using third-generation and next-generation transcriptomic data from exposed to Pb stress, and a phylogenetic analysis revealed 11 subfamilies.

Novel mechanisms for the synthesis of important secondary metabolites in seed revealed by multi-omics data.

Although the detailed biosynthetic mechanism is still unclear, the unique secondary metabolites of , including ginkgolic acids (GAs) and terpene trilactones, have attracted increasing attention for their potent medicinal, physiological and biochemical properties. In particular, GAs have shown great potential in the fields of antibacterial and insecticidal activities, making it urgent to elucidate their biosynthetic mechanism. In this study, we systematically revealed the landscape of metabolic-transcriptional regulation across continuous growth stages of seeds (GBS) based on multi-omics mining and experimental verification, and successfully identified all major types of GAs and terpene trilactones along with more than a thousand kinds of other metabolites.

Assessment of the Impact of Alternative Fixatives on HER2 Detection in Breast Cancer and Gastric Cancer Tumor Specimens.

The type of fixative used for preserving tumor specimens can significantly impact the performance of the immunohistochemistry and in situ hybridization assays used for assessing human epidermal growth factor receptor 2 (HER2) status. This study reports the prevalence of the use of alternative fixatives other than the guideline-recommended 10% neutral buffered formalin (NBF) during HER2 testing in a real-world setting. The effects of alternative fixatives [20% NBF and 10% unbuffered formalin (UBF) fixatives] on HER2 testing of breast cancer (BC) and gastric cancer (GC) cell lines and tissues are also assessed.

Protoplast isolation and transient transformation system for L.

L. has a unique evolutionary status. Owing to its high medicinal and ornamental value, ginkgo has also recently become a research hotspot.

overexpression negatively regulates proanthocyanin biosynthesis.

Flavonoids are important secondary metabolites with extensive pharmacological functions. L. (ginkgo) has attracted extensive attention because of its high flavonoid medicinal value.

Gene Structural Specificity and Expression of Gene Family in .

genes encode transcription factors that affect plant growth and development. is an oil tree species with ornamental value, but there have been few molecular biological studies on the developmental regulation of this species. To explore their possible role in and lay a foundation for subsequent research, 89 genes were identified across the whole genome of for the first time.

Assembly and comparative analysis of the complete mitochondrial genome of using PacBio HiFi sequencing.

L. (willows) is one of the most taxonomically complex genera of flowering plants, including shrubs, tall trees, bushes, and prostrate plants. Despite the high species diversity, only five mitochondrial genomes (mitogenomes) have been released in this genus.

Pedigree reconstruction and genetic analysis of major ornamental characters of ornamental crabapple (Malus spp.) based on paternity analysis.

Ornamental crabapple is an important woody ornamental plant in the Northern Hemisphere. Its flowers, fruits, leaves and tree habit are all important ornamental characters. As there has been no research on the selection of superior parents and phenotypic variation, new varieties of ornamental crabapple are mainly selected from open-pollination progeny.

Genome-Wide Identification of PLATZ Transcription Factors in L. and Their Expression Characteristics During Seed Development.

Plant AT-rich protein and zinc-binding protein (PLATZ) is a class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. PLATZ plays an important role in seed development, water tolerance, and cell proliferation in early plant growth. In this study, 11 s were identified from the ginkgo genome with complete PLATZ-conserved domains, which represents a smaller number compared with angiosperms.

Genome-Wide Identification of the Ginkgo ( L.) Transcription Factor Gene and Characterization of Its Expression.

Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors involved in various transcriptional regulation processes. We identified a total of 37 genes in ginkgo, and based on gene structure and phylogenetic analysis, the gene family was classified into class I (33, with the largest number of Id genes (16)) and class II (4). The ginkgo gene was also analyzed regarding its chromosomal distributions, gene duplications, promoters, and introns/exons.

Effect of the Gene from Masson Pine () on the Development of .

Masson pine () is a core industrial tree species that is used for afforestation in southern China. Previous studies have shown that (s) are involved in the growth and development of various species, but the function of s in Masson pine is unclear. In this research, we cloned and identified Masson pine cDNA (PmARF6).

Effect of Mild and Moderate Hepatic Impairment (Defined by Child-Pugh Classification and National Cancer Institute Organ Dysfunction Working Group Criteria) on Pexidartinib Pharmacokinetics.

Pexidartinib is a novel oral small-molecule tyrosine kinase inhibitor targeting the colony-stimulating factor 1 receptor. Pexidartinib undergoes extensive hepatic metabolism via multiple cytochrome P450 and uridine 5'-diphospho-glucuronosyl transferase enzymes, with ZAAD-1006a as the only major metabolite in human plasma. As pexidartinib is extensively metabolized, hepatic impairment (HI) could lead to increased exposure to pexidartinib.

Identification and Expression Analysis of the -Gene Family.

The gibberellic acid-stimulated () gene family plays an important regulatory role in the growth and development of plants. In this study, we identified 19 genes using bioinformatics-based methods in , and these genes could be divided into three categories based on their phylogenetic relationships. Based on an analysis of the structure and motifs of these genes, it was concluded that class II members are more conserved than class I and class III members are, and the results of collinearity analysis showed that members of class II are collinearly related in poplar.

The reference genome of camellia chekiangoleosa provides insights into camellia evolution and tea oil biosynthesis.

Camellia oil extracted from Camellia seeds is rich in unsaturated fatty acids (UFAs) and secondary metabolites beneficial to human health. However, no oil-tea tree genome has yet been published, which is a major obstacle to investigating the heredity improvement of oil-tea trees. Here, using both Illumina and PicBio sequencing technologies, we present the first chromosome-level genome sequence of the oil-tea tree species Camellia chekiangoleosa Hu.

Overexpression of the Ginkgo biloba WD40 gene GbLWD1-like improves salt tolerance in transgenic Populus.

WD40 transcription factors are an ancient protein family whose members play important roles in plant growth and stress resistance. In this study, a new WD40 gene was cloned from Ginkgo biloba L. via the rapid amplification of cDNA ends (RACE) technique.

Overexpression of Ginkgo BBX25 enhances salt tolerance in Transgenic Populus.

B-box (BBX) genes play important roles in plant growth, light morphogenesis, and environmental stress responses. Ginkgo (Ginkgo biloba L.) is known as a living fossil species that has a strong ability to adapt to environmental changes and tolerate harsh conditions.

Hip Arthroscopic Reduction and Fixation for Adolescent Acetabular Posterior Wall Fracture: A Case Report.

Background: Posterior wall fracture is the most common type of acetabular fracture, the traditional open reduction and fixation through the Kocher-Langenbeck approach required a large incision and extensive muscle and soft tissue dissection, resulting in more blood loss, more complications and delayed recovery after the operation. Hip arthroscopy has been widely used in clinical practice but rarely reported in acetabular fractures.

Case Presentation: We present the case of a 14-year-old boy with acetabular posterior wall fracture who was treated with hip arthroscopy reduction and fixation using anchors.

The complete chloroplast genome of (Hayata) Coh. St. (Theaceae: Ericales) from China based on PacBio and Illumina data.

is an economic plant that can produce high-value edible oil in southern China. Using a combination of PacBio RS and Illumina sequencing platforms, the complete chloroplast genome of was assembled and annotated. This newly deciphered chloroplast genome was 2,731 bp shorter in the gene than the previously published genome.

Overexpression of Provides a Potential to Improve the Content of Epicatechin and Gallocatechin.

The flavonoids in L. () have important medicinal uses due to their antioxidant, antitumor, and blood circulation-promoting effects. However, the genetic mechanisms underlying flavonoid biosynthesis in remain elusive.

Integrative analysis of wood biomass and developing xylem transcriptome provide insights into mechanisms of lignin biosynthesis in wood formation of Pinus massoniana.

Lignin is an important renewable energy source as an excellent new battery fuel and ideal substitutes for the petrochemical industry. However, the molecular mechanism underlying lignin biosynthesis in wood formation of P. massoniana remains unexplored.

ARF family identification in reveals the salt responsive expression of targeted by miR167.

Auxin response factors (s) are important transcription factors (TFs) that are differentially expressed in response to various abiotic stresses. The important roles of s and small RNA- pathways in mediating plant growth and stress responses have emerged in several recent studies. However, no studies on the involvement of s in tamarisk trees, which are resistant to salinity, have been conducted.

Transcriptomic analysis of flower color variation in the ornamental crabapple (Malus spp.) half-sib family through Illumina and PacBio Sequel sequencing.

Ornamental crabapple is an important woody ornamental plant with flower colors ranging from white to pink to red, and the degree of redness is directly related to the anthocyanin content. To explore the molecular mechanism leading to the variation in flower color in ornamental crabapple, transcriptome sequencing using the Illumina and PacBio Sequel platforms revealed the difference in gene expression between the petals of plants with white and red flowers in the half-sib family. In total, the analysis identified 603 differentially expressed genes (DEGs), including 449 upregulated and 154 downregulated genes.