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PubMed2002

Computational comparison of human genomic sequence assemblies for a region of chromosome 4.

Much of the available human genomic sequence data exist in a fragmentary draft state following the completion of the initial high-volume sequencing performed by the International Human Genome Sequencing Consortium (IHGSC) and Celera Genomics (CG). We compared six draft genome assemblies over a region of chromosome 4p (D4S394-D4S403), two consecutive releases by the IHGSC at University of California, Santa Cruz (UCSC), two consecutive releases from the National Centre for Biotechnology Information (NCBI), the public release from CG, and a hybrid assembly we have produced using IHGSC and CG sequence data. This region presents particular problems for genomic sequence assembly algorithms as it contains a large tandem repeat and is sparsely covered by draft sequences. The six assemblies differed both in terms of their relative coverage of sequence data from the region and in their estimated rates of misassembly. The CG assembly method attained the lowest level of misassembly, whereas NCBI and UCSC assemblies had the highest levels of coverage. All assemblies examined included <60% of the publicly available sequence from the region. At least 6% of the sequence data within the CG assembly for the D4S394-D4S403 region was not present in publicly available sequence data. We also show that even in a problematic region, existing software tools can be used with high-quality mapping data to produce genomic sequence contigs with a low rate of rearrangements.

Chromosomes, Human, Pair 4↗

PubMed2024

Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats.

INTRODUCTION: Comprehensive genomic resources offer insights into biological features, including traits/disease-related genetic loci. The current reference genome assembly for the domestic cat (Felis catus), Felis_Catus_9.0 (felCat9), derived from sequences of the Abyssinian cat, may inadequately represent the general cat population, limiting the extent of deducible genetic variations. OBJECTIVES: The goal was to develop Anicom American Shorthair 1.0 (AnAms1.0), a reference-grade chromosome-scale cat genome assembly. METHODS: In contrast to prior assemblies relying on Abyssinian cat sequences, AnAms1.0 was constructed from the sequences of more popular American Shorthair breed, which is related to more breeds than the Abyssinian cat. By combining advanced genomics technologies, including PacBio long-read sequencing and Hi-C- and optical mapping data-based sequence scaffolding, we compared AnAms1.0 to existing Felidae genome assemblies (20 scaffolds, scaffolds N50 > 150 Mbp). Homology-based and ab initio gene annotation through Iso-Seq and RNA-Seq was used to identify new coding genes and splice variants. RESULTS: AnAms1.0 demonstrated superior contiguity and accuracy than existing Felidae genome assemblies. Using AnAms1.0, we identified over 1.5 thousand structural variants and 29 million repetitions compared to felCat9. Additionally, we identified > 1,600 novel protein-coding genes. Notably, olfactory receptor structural variants and cardiomyopathy-related variants were identified. CONCLUSION: AnAms1.0 facilitates the discovery of novel genes related to normal and disease phenotypes in domestic cats. The analyzed data are publicly accessible on Cats-I (https://cat.annotation.jp/), which we established as a platform for accumulating and sharing genomic resources to discover novel genetic traits and advance veterinary medicine.

Animals↗

PubMed2026

Chromosome-level de novo assembly of the nuclear and mitochondrial genomes of Arcopilus aureus, a filamentous fungus with multifaceted ecological and economic roles.

The filamentous fungus Arcopilus aureus (Sordariale: Chaetomiaceae) is notable for its multi-domain significance across agriculture, medicine, and industry. In this study, we generated a chromosome-level nuclear genome and a complete circular mitogenome for A. aureus by integrating data from next-generation sequencing, PacBio HiFi, and Hi-C technologies. The final nuclear genome assembly spans 33.77 Mb (GC content: 57.67%), and was organized into seven chromosomal-sized scaffolds (only one gap) with an N50 size of 5.09 Mb and BUSCO completeness of 95.91%. A total of 10,282 protein-coding genes, 228 non-coding RNAs, and ~1.77 Mb of repetitive elements were predicted in the nuclear genome. By contrast, the mitogenome of A. aureus is 33,820 bp in length, with a GC content of 25.96%. It harbors 15 typical mitochondrial protein-coding genes, one unidentified ORF, two rRNAs (small subunit rns and large subunit rnl), and 28 tRNAs. This high-quality genome assembly provides a valuable resource for understanding the ecology, genetics, and evolution of A. aureus, which facilitates elucidating its mechanisms of biocontrol, infection, and metabolite synthesis.

Genome, Mitochondrial↗

PubMed2025

Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline.

Whole genome sequencing (WGS) is pivotal for the molecular characterization of Chlamydia trachomatis (Ct)-the leading bacterial cause of sexually transmitted infections and infectious blindness worldwide. Ct WGS can inform epidemiologic, public health and outbreak investigations of these human-restricted pathogens. However, challenges persist in generating high-quality genomes for downstream analyses given its obligate intracellular nature and difficulty with in vitro propagation. No single tool exists for the entirety of Ct genome assembly, necessitating the adaptation of multiple programs with varying success. Compounding this issue is the absence of reliable Ct reference strain genomes. We, therefore, developed CtGAP-Chlamydia trachomatisGenome Assembly Pipeline-as an integrated 'one-stop-shop' pipeline for assembly and characterization of Ct genome sequencing data from various sources including isolates, in vitro samples, clinical swabs and urine. CtGAP, written in Snakemake, enables read quality statistics output, adapter and quality trimming, host read removal, de novo and reference-guided assembly, contig scaffolding, selective ompA, multi-locus-sequence and plasmid typing, phylogenetic tree construction, and recombinant genome identification. Twenty Ct reference genomes were also generated. Successfully validated on a diverse collection of 363 samples containing Ct, CtGAP represents a novel pipeline requiring minimal bioinformatics expertise with easy adaptation for use with other bacterial species.

Chlamydia trachomatis↗

PubMed2005

Management and visualization of whole genome shotgun assemblies using SAM.

We have designed and implemented a system to manage whole genome shotgun sequences and whole genome sequence assembly data flow. The Sequence Assembly Manager (SAM) consists primarily of a MySQL relational database and Perl applications designed to easily manipulate and coordinate the analysis of sequence information and to view and report genome assembly progress through its Common Gateway Interface (CGI) web interface. The application includes a tool to compare sequence assemblies to fingerprint maps that has been used successfully to improve and validate both maps and sequence assemblies of the Rhodococcus sp.RHAI and Cryptococcus neoformans WM276 genomes.

Algorithms↗

PubMed1994

A flexible approach to genome map assembly.

A major goal of the Human Genome Project is to construct detailed physical maps of the human genome. A physical map is an assignment of DNA fragments to their locations on the genome. Complete maps of large genomes require the integration of many kinds of experimental data, each with its own forms of noise and experimental error. To facilitate this integration, we are developing a flexible approach to map assembly based on logic programming and data visualization. Logic programming provides a convenient and mathematically rigorous way of reasoning about data, while data visualization provides layout algorithms for assembling and displaying genome maps. To demonstrate the approach, this paper describes numerous rules for map assembly implemented in a data-visualization system called Hy+. Using these rules, we have successfully assembled contigs (partial maps) from real and simulated mapping data-data that is noisy, imprecise and contradictory. The main advantage of the approach is that it allows a user to rapidly develop, implement and test new rules for genome map assembly, with a minimum of programming effort.

Chromosome Mapping↗

PubMed2025

Whole-genome sequencing-based pathogen characterization for streptococcal infection directly from positive blood culture samples.

Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. Consequently, public health laboratories can benefit from assays that directly process blood culture samples without requiring submission of clinical isolates to determine additional pathogen features not identified by clinical tests, such as vaccine serotype and bacterial genomic relatedness, for surveillance and outbreak response purposes. In partnership with the Minnesota Active Bacterial Core surveillance (ABCs) site, we identified blood culture samples positive for ABCs streptococcal pathogens and characterized them by a direct whole-genome sequencing from blood culture (dWGS) assay. The dWGS results were compared with the results of a reference method (WGS of isolates from the same cultures) to evaluate concordance in pathogen features and genome assemblies. Of the 97 eligible blood culture samples, 83 (86%) passed dWGS quality control criteria and were subjected to a total of 655 dWGS-based tests, which yielded 651 (99.3%) evaluable results. The percent agreement with reference results was 100% (83/83) for M protein gene (emm)/capsular types and 100% (81/81) for multilocus sequencing types. For genotypic antimicrobial susceptibility testing prediction, the percent prediction agreement was 100% (487/487), false resistant prediction rate was 0% (0/417), and the false susceptible prediction rate was 0% (0/66). Assemblies of pathogen genomes from the same patient differed by 1.08 ± 1.68 (mean ± SD) sites per genome. The dWGS assay can extract high-quality, important streptococcal strain characteristics directly from positive blood culture samples to support evolving public health needs.IMPORTANCEWhole-genome sequencing (WGS) technologies have emerged as a transformative toolkit used by public health microbiology laboratories to detect and characterize pathogens. The surveillance of bacterial diseases often relies on clinical laboratories to submit pathogen isolates to regional or national public health laboratories, which have the capacity to routinely conduct WGS-based strain characterization. Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. The study evaluated a direct whole-genome sequencing from blood culture (dWGS) assay that directly processes blood culture samples. The dWGS assay recovered high quality, important streptococcal strain characteristics, including vaccine serotypes and whole-genome assemblies, without requiring submission of clinical isolates. Thus, the dWGS assay represents a promising tool for addressing the evolving needs of public health laboratories in the metagenomics era.

Humans↗

PubMed2025

The genome sequence of a flea beetle, Altica lythri Aubé, 1843.

We present a genome assembly from a female specimen of Altica lythri (flea beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). This was a triploid specimen and one subgenome was assembled. The genome sequence has a total length of 1,003.51 megabases. Most of the assembly (82.29%) is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 18.39 kilobases. Gene annotation of this assembly on Ensembl identified 18,969 protein-coding genes.

Altica lythri↗

PubMed2006

A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits.

BACKGROUND: A number of different quantitative trait loci (QTL) for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6). Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as well as their mutual connections are required to efficiently identify genes and gene variants responsible for genetic variation of phenotypic traits. A comprehensive high-resolution gene-rich map linking densely spaced bovine markers and genes to the annotated human genome sequence is required as a framework to facilitate this approach for the region on BTA6 carrying the QTL. RESULTS: Therefore, we constructed a high-resolution radiation hybrid (RH) map for the QTL containing chromosomal region of BTA6. This new RH map with a total of 234 loci including 115 genes and ESTs displays a substantial increase in loci density compared to existing physical BTA6 maps. Screening the available bovine genome sequence resources, a total of 73 loci could be assigned to sequence contigs, which were already identified as specific for BTA6. For 43 loci, corresponding sequence contigs, which were not yet placed on the bovine genome assembly, were identified. In addition, the improved potential of this high-resolution RH map for BTA6 with respect to comparative mapping was demonstrated. Mapping a large number of genes on BTA6 and cross-referencing them with map locations in corresponding syntenic multi-species chromosome segments (human, mouse, rat, dog, chicken) achieved a refined accurate alignment of conserved segments and evolutionary breakpoints across the species included. CONCLUSION: The gene-anchored high-resolution RH map (1 locus/300 kb) for the targeted region of BTA6 presented here will provide a valuable platform to guide high-quality assembling and annotation of the currently existing bovine genome sequence draft to establish the final architecture of BTA6. Hence, a sequence-based map will provide a key resource to facilitate prospective continued efforts for the selection and validation of relevant positional and functional candidates underlying QTL for milk production and growth-related traits mapped on BTA6 and on similar chromosomal regions from evolutionary closely related species like sheep and goat. Furthermore, the high-resolution sequence-referenced BTA6 map will enable precise identification of multi-species conserved chromosome segments and evolutionary breakpoints in mammalian phylogenetic studies.

Animals↗

PubMed2005

A tool for analyzing mate pairs in assemblies (TAMPA).

The current generation of genome assembly programs uses distance and orientation relationships of paired end reads of clones (mate pairs) to order and orient contigs. Mate pair data can also be used to evaluate and compare assemblies after the fact. Earlier work employed a simple heuristic to detect assembly problems by scanning across an assembly to locate peak concentrations of unsatisfied mate pairs. TAMPA is a novel, computational geometry-based approach to detecting assembly breakpoints by exploiting constraints that mate pairs impose on each other. The method can be used to improve assemblies and determine which of two assemblies is correct in the case of sequence disagreement. Results from several human genome assemblies are presented.

Algorithms↗

PubMed2002

A first-generation EST RH comparative map of the porcine and human genome.

We have constructed a first-generation EST radiation hybrid comparative map of the porcine genome by assigning 1,058 markers to the IMpRH(7000) panel. Chromosomal localization was determined with a 2pt LOD of 4.8 for 984 markers, using the IMpRH mapping tool. Annotated ESTs represent 46.2% or 489 of the markers. Marker distribution was not stochastic and ranged from 0.41 for SSC8 to 1.77 for SSC12, respectively. Two hundred fifty-one markers assigned to the physical map of the pig did not find a homologous sequence in V22 of the human genome assembly, indicative of gaps in the assembled human genome sequence. The comparative porcine/human map covers 3,290 MB, or 98.3% of the presumed size of the human genome. However, 60 breakpoints were identified between chromosomes, as well as 90 micro-rearrangements within synteny groups. Six porcine chromosomes-SSC2, 5, 6, 7, 12, and 14-correspond to the three gene-richest human chromosomes, HSA17, 19, and 22, and show above average marker density. Porcine Chrs 1, 8, 11, and X display a low DNA/marker ratio and correspond to the 'genome deserts' on HSA 18, 4, 13, and X.

Animals↗

PubMed2006

Identification of susceptibility and protective major histocompatibility complex haplotypes in canine diabetes mellitus.

Diabetes mellitus occurs spontaneously in dogs, which is believed to have an autoimmune component and to be a model of human latent autoimmune diabetes of adults (LADA). Some dog breeds (e.g. Samoyed) are particularly predisposed, whereas others (e.g. Boxer) are highly resistant. With the completion of the Dog Genome Assembly, comparative genomic studies of complex diseases in dogs, including diabetes, could provide an important investigative approach into such disorders. Type 1 diabetes in humans is strongly associated with major histocompatibility complex (MHC) class II polymorphisms. We have investigated whether canine dog leucocyte antigen (DLA) class II haplotypes are associated with diabetes. DNA from 460 cases and 1047 controls were genotyped for DLA-DRB1, DLA-DQA1 and DLA-DQB1 using sequence-based typing. Three DLA haplotypes, DRB1*009/DQA1*001/DQB1*008, DRB1*015/DQA1*0061/DQB1*023 and DRB1*002/DQA1*009/DQB1*001, were found at significantly increased frequency in cases with diabetes compared with controls. One DLA-DQ haplotype, DQA1*004/DQB1*013, was significantly reduced in cases with diabetes. Further analysis showed that DQA1 alleles carrying arginine at codon 55 of DQA1 were increased in dogs with diabetes. To our knowledge, this is the first report of a comparative study of MHC and diabetes in a non-rodent species. Since no laboratory model of LADA exists and dogs and humans share similar environments, further research into canine diabetes is warranted.

Alleles↗

PubMed2004

MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly.

MapLinker is an analysis tool, as well as a browsing interface, that facilitates integration of whole genome sequence assembly with a clone-based physical map. Using the locations of sequence markers on the physical map, MapLinker generates a tentative sequence map of the genome that serves to verify the map and to guide genome-wide finishing.

Algorithms↗

PubMed2006

Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies.

Mobile elements represent a relatively new class of markers for the study of human evolution. Long interspersed elements (LINEs) belong to a group of retrotransposons comprising approximately 21% of the human genome. Young LINE-1 (L1) elements that have integrated recently into the human genome can be polymorphic for insertion presence/absence in different human populations at particular chromosomal locations. To identify putative novel L1 insertion polymorphisms, we computationally compared two draft assemblies of the whole human genome (Public and Celera Human Genome assemblies). We identified a total of 148 potential polymorphic L1 insertion loci, among which 73 were candidates for novel polymorphic loci. Based on additional analyses we selected 34 loci for further experimental studies. PCR-based assays and DNA sequence analysis were performed for these 34 loci in 80 unrelated individuals from four diverse human populations: African-American, Asian, Caucasian, and South American. All but two of the selected loci were confirmed as polymorphic in our human population panel. Approximately 47% of the analyzed loci integrated into other repetitive elements, most commonly older L1s. One of the insertions was accompanied by a BC200 sequence. Collectively, these mobile elements represent a valuable source of genomic polymorphism for the study of human population genetics. Our results also suggest that the exhaustive identification of L1 insertion polymorphisms is far from complete, and new whole genome sequences are valuable sources for finding novel retrotransposon insertion polymorphisms.

Alleles↗

PubMed2026

Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.

BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE. RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE. CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.

Animals↗

PubMed2026

Whole-genome characterization and phylogenetic placement of Fusarium oxysporum f. sp. vasinfectum isolates.

Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (Fov), remains a persistent threat to cotton production worldwide. Among the known races, Fov race 4 and its extra-virulent variants cause particularly severe losses in Upland cotton. Although several Fov genome assemblies have been assigned to races, the genomic diversity and evolutionary relationships among pathogenic and non-pathogenic isolates associated with cotton outbreaks remain poorly understood at the whole-genome level. This study addressed these gaps by generating and comparing high-quality genome assemblies of four Fusarium isolates collected from Texas cotton fields: two pathogenic (TX17-24 and TX18-9) and two non-pathogenic (TX17-6 and TX18-6). Draft assemblies were generated using Oxford Nanopore long reads and polished with Illumina reads. Comparative genomic analyses showed that pathogenic isolates possessed larger genomes and more conserved orthologous families, whereas non-pathogenic isolates contained more unique genes. Analyses of predicted secreted effectors, transposable elements, and carbohydrate-active enzymes further distinguished pathogenic and non-pathogenic lineages, suggesting roles in virulence adaptation and genome plasticity. Phylogenomic analyses using k-mer-based, assembly- and alignment-free methods incorporated all available long-read Fov genomes and revealed substantial genetic diversity within races 1 and 4, clustering isolates into multiple sublineages. These findings show that Fov race diversification is underestimated when based on traditional classification schemes and may be shaped by host specialization, geographic separation, or horizontal gene transfer. This work advances our understanding of the genomic diversity and evolutionary dynamics of Fov and establishes a foundation for improved race identification and characterization of Fusarium wilt pathogenesis in cotton.

Fusarium oxysporum↗

PubMed2026

Whole-genome sequences of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea.

The Micrapis subgenus, which includes the black dwarf honey bee (Apis andreniformis) and the red dwarf honey bee (Apis florea), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo genome assemblies for both species, generated using a hybrid sequencing approach combining Oxford Nanopore Technologies long reads with Illumina short reads. The final assemblies are highly contiguous, with contig N50 values of 5.0 Mb (A. andreniformis) and 4.3 Mb (A. florea), representing a major improvement over the previously published A. florea genome. Genome completeness assessments indicate high quality, with BUSCO scores exceeding 98.5% using the Hymenoptera database and k-mer analyses supporting base-level accuracy. Repeat annotation revealed a relatively low repetitive sequence content (∼6%), consistent with other Apis species. Using RNA sequencing data, we annotated 12,189 genes for A. andreniformis and 12,207 genes for A. florea, with ∼98% completeness in predicted proteomes. These genome assemblies provide a valuable resource for comparative and functional genomic studies, with the potential to offer new insights into the genetic basis of dwarf honey bee adaptations.

Male↗

PubMed2002

Computational comparison of two mouse draft genomes and the human golden path.

BACKGROUND: The availability of both mouse and human draft genomes has marked the beginning of a new era of comparative mammalian genomics. The two available mouse genome assemblies, from the public mouse genome sequencing consortium and Celera Genomics, were obtained using different clone libraries and different assembly methods. RESULTS: We present here a critical comparison of the two latest mouse genome assemblies. The utility of the combined genomes is further demonstrated by comparing them with the human 'golden path' and through a subsequent analysis of a resulting conserved sequence element (CSE) database, which allows us to identify over 6,000 potential novel genes and to derive independent estimates of the number of human protein-coding genes. CONCLUSION: The Celera and public mouse assemblies differ in about 10% of the mouse genome. Each assembly has advantages over the other: Celera has higher accuracy in base-pairs and overall higher coverage of the genome; the public assembly, however, has higher sequence quality in some newly finished bacterial artificial chromosome clone (BAC) regions and the data are freely accessible. Perhaps most important, by combining both assemblies, we can get a better annotation of the human genome; in particular, we can obtain the most complete set of CSEs, one third of which are related to known genes and some others are related to other functional genomic regions. More than half the CSEs are of unknown function. From the CSEs, we estimate the total number of human protein-coding genes to be about 40,000. This searchable publicly available online CSEdb will expedite new discoveries through comparative genomics.

Animals↗