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<h4>Introduction</h4>Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant …
Read PDFThe Cypripedioideae subfamily (slipper orchids) exhibits remarkable ecological diversity, spanning temperate to tropical habitats, yet the molecular mechanisms underlying its adaptive radiation remain poorly understood. Chloroplast genomes, with their critical roles in photosynthesis and conserved …
Read PDF<h4>Background</h4><i>Gynostemma pentaphyllum</i> (Thunb.) Makino is an important medicinal plant within the Cucurbitaceae family. Despite its economic and pharmacological importance, genomic resources for this species remain limited.<h4>Methods</h4>We sequenced and assembled the complete mitochondrial genome of <i>G. …
Read PDFBipolaris oryzae, the causal agent of rice brown spot, is a necrotrophic fungus that produces phytotoxic secondary metabolites, yet its genomic basis of pathogenicity remains incompletely defined. We sequenced six South Korean B. oryzae isolates …
Read PDFThe Polygonati Rhizoma have generated significant market attention for their medicinal and culinary applications. However, morphological similarities and ambiguous species boundaries complicate the identification of genera and species, thereby impeding product development and utilization within …
Read PDFHere, we re-examine the high level phylogeny of <i>Pezizomycotina</i> with special attention to the recently proposed phylogenomic hypothesis (Díaz-Escandón et al. 2022) that "morphologically hyperdiverse" <i>Candelariomycetes</i>, <i>Coniocybomycetes</i>, <i>Geoglossomycetes</i>, <i>Lichinomycetes</i>, <i>Sareomycetes</i> and <i>Xylonomycetes</i> (henceforth referred to …
Read PDFTrichosporeae is the largest and most taxonomically difficult tribe of Gesneriaceae due to its diverse morphology. Previous studies have not clarified the phylogenetic relationships within this tribe on several DNA markers, including the generic relationships …
Read PDFTransitions between saprotrophic and biotrophic lifestyles represent pivotal evolutionary events in fungal ecology; however, the genomic and physiological mechanisms underlying such shifts remain poorly understood. The agaric genus <i>Clitopilus</i> (<i>Basidiomycota</i>, <i>Entolomataceae</i>) offers a valuable model …
Read PDFIn this study, we analyzed the evolutionary patterns of tandem repeats in the mitochondrial Control Region (CR) of groupers of the genus Epinephelus. This research was based on a comprehensive survey of Epinephelus mitogenomes available …
Read PDF<h4>Background</h4>Tumor neoantigens are key targets for personalized vaccines and T-cell therapies, yet most pipelines focus on neoantigens derived from SNV/small indel and often yield a limited number of high-quality candidates. SVs are prevalent in tumors …
Read PDF<h4>Background</h4>Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor characterized by rapid progression, early metastasis, and high mortality, with limited effective long-term treatment options. <i>B4GALT1</i>, a β-1,4-galactosyltransferase, has been implicated in the malignant progression …
Read PDFPangenomes are revolutionizing our ability to resolve genomic regions with complex variations<sup>1</sup>. However, existing human pangenomes<sup>2,3</sup>, constrained by small sample sizes, provide limited utility for medical and population genetic applications. Here we generated 1,116 diploid …
Read PDFCYP2C19 and CYP2D6 are involved in the hepatic metabolism of approximately 35-40% of clinically used drugs. We conducted an in vivo phenotyping study encompassing 114 Estonian Biobank participants to evaluate the functional impact of rare …
Read PDFBalanced chromosomal rearrangements (BCRs) refer to a type of chromosomal structural variations without chromosomal gains or losses. BCR carriers may experience fertility issues, including a higher risk of infertility, recurrent miscarriages, or having offspring with …
Read PDF<h4>Background</h4>Foetal chromosomal abnormalities are identified as one of the leading causes of adverse pregnancy outcome in pregnancies that are referred on suspicion of structural abnormalities in the foetus. While various types of genomic analyses can …
Read PDFStructural variants (SVs) are a major type of genetic variation, yet their role in human traits remains largely uncharacterized, primarily due to challenges in genotyping them on a genome-wide scale in large cohorts. Here we …
Read PDFSequencing cohorts with long-read technology is crucial to understand the impact of structural variants (SVs) on complex traits. Here, we obtain 4.86 terabases of HiFi reads with an average read N50 of 16.3 Kb from …
Read PDFInherited retinal diseases (IRDs) are a major cause of visual impairment worldwide, marked by extensive genetic and phenotypic heterogeneity. Recent estimates from the U.S. suggest a prevalence of nearly 1 in 1000 individuals, reflecting both …
Read PDF<h4>Background</h4>Nearly 80% of patients with High grade serous ovarian cancer (HGSOC) will experience recurrence within 5 years, but little is known about the mechanisms that drive this process.<h4>Methods</h4>In this study we used whole genome sequencing …
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