Aspergillus fumigatus is a ubiquitous saprophytic mold and a major pathogen in immunocompromised patients. The effectiveness of triazole compounds, the A. fumigatus first line treatment, is being threatened by a rapid and global emergence of azole re...
Practices related to mitochondrial research have long been hindered by the presence of mitochondrial pseudogenes within the nuclear genome (NUMTs). Even though partially assembled human reference genomes like hg38 have included NUMTs compilation, the...
Closely related Aspergillus section Nigri species are difficult to resolve taxonomically, while short-read comparisons may be influenced by reference-genome choice. We applied reciprocal genome projection to 31 whole-genome sequencing libraries repre...
Background/Objectives: Reference genome choice can introduce systematic bias into cancer transcriptomic analyses, particularly for populations underrepresented in standard references. However, its impact on downstream biological interpretation remain...
The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation stra...
Despite rapid improvements in the accessibility of whole-genome sequencing (WGS), understanding the extent of human genetic variation is limited by the scarce availability of genome sequences from underrepresented populations. Developing the populati...
The Peruvian creole cattle (PCC) is a neglected breed and an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed...
Solanum lycopersicum cv. Pusa Ruby (PR) is a superior tomato cultivar routinely used as a model tomato variety. Here, we report a reference-guided genome assembly for PR, covering 97.6% of the total single-copy genes in the solanales order. The PR ge...
Although Genome Reference Consortium Human Build 38 (GRCh38) was released with improvement over GRCh37, it has not been widely adopted. Several liftover tools have been developed as a convenient approach for GRCh38 implementation. This study aimed to...
Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genom...
Tissue-culture adaptation of viruses can modulate infection. Laboratory passage and bacterial artificial chromosome (BAC)mid cloning of human cytomegalovirus, HCMV, resulted in genomic deletions and rearrangements altering genes encoding the virus en...
Soil-transmitted helminths (STHs) are parasitic nematodes that infect humans, particularly in tropical and subtropical regions, where they contribute substantially to neglected tropical diseases (NTDs). Among them, hookworms (Ancylostoma duodenale, N...
The reference genome serves as a fundamental resource for sheep genetic research and molecular breeding, and iterative improvements in assembly quality have directly driven advances in these fields. A systematic literature review was conducted by ret...
Sparganosis is a neglected food- and water-borne zoonotic disease caused by members of the tapeworm genus Spirometra. More than 1600 human cases have been reported in the literature, primarily in Korea and China; however, the clinical significance of...
As the largest chamber of the ruminant stomach, the rumen not only serves as the principal absorptive surface and nutrient transport pathway from the lumen into the animal, but also plays an important short-chain fatty acid (SCFA) metabolic role in a...
The size of the reference population is critical in order to improve the accuracy of genomic prediction. Indeed, improving genomic prediction accuracy by combining multinational reference populations has proven to be effective. In this study, we inve...
Precision medicine approaches rely on accurate somatic variant detection, where the DNA input into genomic workflows is a key variable. However, there are no gold standard methods for total DNA quantification. In this study, a pentaplex reference gen...
The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we perfo...
Accurate reference genome sequences provide the foundation for modern molecular biology and genomics as the interpretation of sequence data to study evolution, gene expression, and epigenetics depends heavily on the quality of the genome assembly use...
This study introduces a meticulously constructed genome assembly at the chromosome level for the Rosaceae family species Prinsepia uniflora, a traditional Chinese medicinal herb. The final assembly encompasses 1272.71 megabases (Mb) distributed acros...
The genetically modified (GM) maize DBN9936 with a biosafety certificate will soon undergo commercial application. To monitor the safety of DBN9936 maize, three genomic DNA (gDNA) reference materials (RMs) (DBN9936a, DBN9936b, and DBN9936c) were prep...
Lepidopteran insects are an important group of animals, including those used as biochemical and physiological model species in the insect and silk industries as well as others that are major agricultural pests. Therefore, the genome sequences of seve...
Background: Population-specific reference genomes are essential for improving the accuracy and reliability of genomic analyses across diverse human populations. Although Vietnam ranks as the 16th most populous country in the world, with more than 86%...
The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named “Tas...
The flour beetle Tribolium freemani is a sibling species of the model organism and important pest Tribolium castaneum. The two species are so closely related that they can produce hybrid progeny, but the genetic basis of their differences has not bee...
The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comp...
In recent decades, next-generation sequencing (NGS) was developed and brought biology into a new era. Rice, maize, wheat, sorghum and barley are the most important cereal crops and feed most of the world's population. Great progress in the study of c...
Arabidopsis thaliana became the model organism for plant studies because of its small diploid genome, rapid lifecycle and short adult size. Its genome was the first among plants to be sequenced, becoming the reference in plant genomics. However, the...
Recent years have witnessed a surge in the publication of dozens of genome assemblies for Triticeae crops, which have significantly advanced gene-related research in wheat, rye, and triticale. However, this progress has also introduced challenges in...
The availability of large-scale genomic data resources makes it very convenient to mine and analyze genes that are related to important agricultural traits in rice. Pan-genomes have been constructed to provide insight into the genome diversity and fu...
Horizontal transfer of mitochondrial DNA into the nuclear genome generates nuclear mitochondrial sequences (NUMTs), which serve as molecular fossils reflecting long-term mitochondrial–nuclear interactions and genome evolution. However, the biol...
The discovery of novel microRNA (miRNA) and piwi-interacting RNA (piRNA) is an important task for the understanding of many biological processes. Most of the available miRNA and piRNA identification methods are dependent on the availability of the or...
Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasit...
The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is...
The growing availability of genomic resources is changing how genetic diversity is studied in Vitis vinifera L. At the same time, it has become increasingly clear that a single reference genome cannot fully represent the complexity of a species chara...
The Bursaphelenchus mucronatus, which was highly similar with Bursaphelenchus xylophilus in terms of morphological characteristics and biological properties—but had weaker pathogenicity to forests—was a native species often displaced by B...
The relationships between diseases and genetic factors are by no means uniform. Single-gene diseases are caused primarily by rare mutations of specific genes. Although each single-gene disease has a low prevalence, there are an estimated 5000 or more...
The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational...
In various European regions, white lupin (Lupinus albus L) production could increase by autumn sowing of winter-hardy varieties. This study aimed to explore the genetic variation, the genetic architecture, and the genomic prediction of frost resistan...
Any project seeking to deliver a plant or animal reference genome sequence must address the question as to the completeness of the assembly. Given the complexity introduced particularly by the presence of sequence redundancy, a problem which is espec...
The hominid-specific retrotransposon SINE-VNTR-Alu (SVA) is a composite element that has contributed to the genetic variation between individuals and influenced genomic structure and function. SVAs are involved in modulating gene expression and splic...
Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affe...
The current human reference genome (GRCh38), with its superior quality, has contributed significantly to genome analysis. However, GRCh38 may still underrepresent the ethnic genome, specifically for Asians, though exactly what we are missing is still...
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occup...
Genomics plays a crucial role in addressing health disparities, yet most studies rely on the hg38 linear reference genome, limiting the potential of pangenomic approaches, particularly for underrepresented populations. In this study, we focus on char...
The emergence of pangenome graphs represents a paradigm shift in genomics, moving beyond linear reference genomes to embrace the full spectrum of genetic diversity within and across species. These graph-based models provide a unified framework for re...
Genomic selection has transformed animal and plant breeding in advanced economies globally, resulting in economic, social and environmental benefits worth billions of dollars annually. Although genomic selection offers great potential in low- to midd...
The pygmy grasshopper, Zhengitettix transpicula, is a Chinese endemic species with an exceedingly limited distribution and fragile population structure, rendering it vulnerable to extinction. We present a high-continuity, chromosome-scale reference g...
High-quality reference panels are important resources for genotype imputation and genomic selection in dairy goats; however, dairy-goat reference panels remain limited in sample size, population representation, and standardized workflow evaluation. I...
The German cockroach, Blattella germanica, and the American cockroach, Periplaneta americana are the most common and synanthropic household pests of interest to public health. While they have increasingly served as model systems in hemimetabolous ins...
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