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Prostate cancer (PCa) remains a major global health concern, with a subset of patients progressing to aggressive disease despite advances in diagnosis and treatment. Epithelial-mesenchymal transition (EMT) plays a pivotal role in tumor invasion, metastasis, …
Read PDFAccurate inference of absolute copy numbers beyond simple gains and losses from single-cell chromatin accessibility (scATAC-seq) data remains challenging, thereby obscuring the distinction between genetic and epigenetically driven oncogenic dependencies. Here, we present TeaCNV, a …
Read PDFMost evolutionary studies on pancreatic cancer rely on bulk sequencing, yet clonal evolution happens at the single-cell level. We used single-nucleus DNA sequencing to study 137,491 single nuclei from 24 pancreatic neoplasms reflecting various clinical …
Read PDFAssay for transposase-accessible chromatin using sequencing (ATAC-seq) is a cornerstone for epigenomic profiling, yet its potential for genomic characterization remains poorly explored. Here, we systematically benchmarked bulk ATAC-seq against whole-genome sequencing (WGS) to assess its …
Read PDFThe chemical phenotype (chemotype) of <i>Cannabis sativa</i> is defined by the ratio of cannabidiolic acid (CBDA) to Δ9-tetrahydrocannabinolic acid (THCA). Although the Mendelian segregation of these traits suggests a single-locus biallelic system, recent sequencing and …
Read PDF<h4>Objectives</h4>Through a genomics-based approach analyzing gene expression levels and adaptive immune receptor recombinations, we sought to determine whether MYC amplification was associated with a worse outcome and reduced immunogenicity.<h4>Methods</h4>MYC copy numbers and the presence of …
Read PDF<h4>Motivation</h4>The integration of tumour imaging data and molecular sequencing information can advance our understanding of cancer biology by combining complementary perspectives of tumour phenotype and genotype. However, integrating multi-modal data across heterogeneous and high-dimensional data …
Read PDFGenetic disorders impacting vision affect millions of individuals worldwide, including age-related macular degeneration (common) and inherited retinal disorders (rare). There is an incomplete understanding of the impact of genetic variation on gene expression in the …
Read PDF<h4>Background</h4>The genus Solanum is a diverse group of flowering plants with significant economic importance. Within this genus, the subgenus Leptostemonum, comprising spiny solanums, is particularly noteworthy due to its high species diversity and endemism. Solanum …
Read PDF<h4>Background</h4>Elatostema, one of the largest genera in Urticaceae, comprises approximately 570 species. The taxonomic delimitation of Elatostema and its closely related genera, Elatostematoides and Procris and the infrageneric classification of Elatostema, have historically been challenging. …
Read PDFAnalyzing genomic variants in large datasets composed of short-read sequencing data is a process that requires multiple steps and computational tools, which makes it a complicated task that is difficult to reproduce across projects and …
Read PDFLonicera L. is one of the largest and economically significant genera in the family Caprifoliaceae Juss., with a controversial taxonomy. To contribute to its molecular taxonomy, we sequenced the plastomes of Lonicera species: Lonicera caerulea …
Read PDF<h4>Background</h4>The columbine genus (Aquilegia) contains many species with horticultural and pharmaceutical importance. However, a well-resolved phylogeny for this genus remains lacking owing to recent and rapid radiation. We obtained plastomes of 75 Aquilegia species and …
Read PDFBACKGROUND: Comparative genomics and plastome phylogenomics have advanced significantly in recent years, highlighting the diversity, possible admixture, and non-neutral evolution of the predominantly considered non-recombinant chloroplast genomes in angiosperms. The grass genus Brachypodium serves as …
Read PDFThe plastid genome (plastome) represents an indispensable molecular resource for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genomes, accurately and efficiently annotating and utilizing plastome sequences remain …
Read PDFIn recent years, plant genotyping has been shifting from the accumulation of whole-genome data toward their effective use in breeding programs This review examines key genotyping platforms, including single-nucleotide polymorphism (SNP) arrays, reduced-representation sequencing methods …
Read PDFChloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino acid production, and stress responses. The genus Passiflora, known for its species diversity and dynamic chloroplast (cp) genome evolution, …
Read PDF<h4>Premise</h4>Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. …
Read PDFWe report the mitochondrial genome of <i>Cicindela</i> (<i>Cicindela</i>) <i>transbaicalica</i> Motschulsky, 1844, based on a specimen from Hulunbuir, Inner Mongolia, China. The 16,505 bp genome contains 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes, …
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