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PubMed2025

A chromosome-level genome assembly and annotation of Cercis chuniana (Fabaceae).

The genus Cercis L., at the base of the subfamily Cercidoideae of Fabaceae, is known for its ecological adaptability and significant medicinal, ornamental, and economic value. However, the lack of a high-quality genome hinders the understanding of the evolution of Cercis and Fabaceae. In this study, we present a chromosome-level genome of Cercis chuniana by combining Illumina short reads, PacBio HiFi long reads, and Hi-C data. The final genome size is 355.53 Mb, consisting of 12 contigs with a N50 of 42.34 Mb. Notably, 344.24 Mb, corresponding to 96.82% of the genome, was anchored to seven chromosomes. The assembly comprises 24.83% repetitive sequences, including 19.32% long terminal repeats. Additionally, a total of 33,837 protein-coding genes were predicted in the genome, with 32,709 (96.67%) genes successfully annotated. The high-quality genome assembly of C. chuniana not only bridges the existing gap in genomic data and offers important resources for molecular studies of this species, but also provides essential insights for future studies on speciation, functional and comparative genomics within the Fabaceae family.

Genome, Plant↗

PubMed1998

Analysis of EST-driven gene annotation in human genomic sequence.

We have performed a systematic analysis of gene identification in genomic sequence by similarity search against expressed sequence tags (ESTs) to assess the suitability of this method for automated annotation of the human genome. A BLAST-based strategy was constructed to examine the potential of this approach, and was applied to test sets containing all human genomic sequences longer than 5 kb in public databases, plus 300 kb of exhaustively characterized benchmark sequence. At high stringency, 70%-90% of all annotated genes are detected by near-identity to EST sequence; >95% of ESTs aligning with well-annotated sequences overlap a gene. These ESTs provide immediate access to the corresponding cDNA clones for follow-up laboratory verification and subsequent biologic analysis. At lower stringency, up to 97% of annotated genes were identified by similarity to ESTs. The apparent false-positive rate rose to 55% of ESTs among all sequences and 20% among benchmark sequences at the lowest stringency, indicating that many genes in public database entries are unannotated. Approximately half of the alignments span multiple exons, and thus aid in the construction of gene predictions and elucidation of alternative splicing. In addition, ESTs from multiple cDNA libraries frequently cluster over genes, providing a starting point for crude expression profiles. Clone IDs may be used to form EST pairs, and particularly to extend models by associating alignments of lower stringency with high-quality alignments. These results demonstrate that EST similarity search is a practical general-purpose annotation technique that complements pattern recognition methods as a tool for gene characterization.

Base Sequence↗

PubMed2003

ASAP, a systematic annotation package for community analysis of genomes.

ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization (https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm). ASAP facilitates ongoing community annotation of genomes and tracking of information as genome projects move from preliminary data collection through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. ASAP supports three levels of users: public viewers, annotators and curators. Public viewers can currently browse updated annotation information for Escherichia coli K-12 strain MG1655, genome-wide transcript profiles from more than 50 microarray experiments and an extensive collection of mutant strains and associated phenotypic data. Annotators worldwide are currently using ASAP to participate in a community annotation project for the Erwinia chrysanthemi strain 3937 genome. Curation of the E. chrysanthemi genome annotation as well as those of additional published enterobacterial genomes is underway and will be publicly accessible in the near future.

Databases, Genetic↗

PubMed2004

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their experimental generation remains difficult. Consequently, interolog mapping--the transfer of interaction annotation from one organism to another using comparative genomics--is of significant value. Here we quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. Using interaction information from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Helicobacter pylori, we find that protein-protein interactions can be transferred when a pair of proteins has a joint sequence identity >80% or a joint E-value <10(-70). (These "joint" quantities are the geometric means of the identities or E-values for the two pairs of interacting proteins.) We generalize our interolog analysis to protein-DNA binding, finding such interactions are conserved at specific thresholds between 30% and 60% sequence identity depending on the protein family. Furthermore, we introduce the concept of a "regulog"--a conserved regulatory relationship between proteins across different species. We map interologs and regulogs from yeast to a number of genomes with limited experimental annotation (e.g., Arabidopsis thaliana) and make these available through an online database at http://interolog.gersteinlab.org. Specifically, we are able to transfer approximately 90,000 potential protein-protein interactions to the worm. We test a number of these in two-hybrid experiments and are able to verify 45 overlaps, which we show to be statistically significant.

Amino Acid Sequence↗

PubMed2006

Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress.

BACKGROUND: In our previous studies, we found that the sites in prokaryotic genomes which are most susceptible to duplex destabilization under the negative superhelical stresses that occur in vivo are statistically highly significantly associated with intergenic regions that are known or inferred to contain promoters. In this report we investigate how this structural property, either alone or together with other structural and sequence attributes, may be used to search prokaryotic genomes for promoters. RESULTS: We show that the propensity for stress-induced DNA duplex destabilization (SIDD) is closely associated with specific promoter regions. The extent of destabilization in promoter-containing regions is found to be bimodally distributed. When compared with DNA curvature, deformability, thermostability or sequence motif scores within the -10 region, SIDD is found to be the most informative DNA property regarding promoter locations in the E. coli K12 genome. SIDD properties alone perform better at detecting promoter regions than other programs trained on this genome. Because this approach has a very low false positive rate, it can be used to predict with high confidence the subset of promoters that are strongly destabilized. When SIDD properties are combined with -10 motif scores in a linear classification function, they predict promoter regions with better than 80% accuracy. When these methods were tested with promoter and non-promoter sequences from Bacillus subtilis, they achieved similar or higher accuracies. We also present a strictly SIDD-based predictor for annotating promoter sequences in complete microbial genomes. CONCLUSION: In this report we show that the propensity to undergo stress-induced duplex destabilization (SIDD) is a distinctive structural attribute of many prokaryotic promoter sequences. We have developed methods to identify promoter sequences in prokaryotic genomes that use SIDD either as a sole predictor or in combination with other DNA structural and sequence properties. Although these methods cannot predict all the promoter-containing regions in a genome, they do find large sets of potential regions that have high probabilities of being true positives. This approach could be especially valuable for annotating those genomes about which there is limited experimental data.

Bacillus subtilis↗

PubMed2004

Expression profiling of the Leishmania life cycle: cDNA arrays identify developmentally regulated genes present but not annotated in the genome.

As genomic sequencing of Leishmania nears completion, functional analyses that provide a global genetic perspective on biological processes are important. Despite polycistronic transcription, RNA transcript abundance can be measured using microarrays. To provide a resource to evaluate cDNA arrays, we undertook 5' expressed sequence tag analysis of 2183 full-length randomly selected cDNAs from Leishmania major promastigote (days 3, 7, 10 of culture in vitro), and lesion-derived amastigote libraries. PCR-amplified inserts from 1830 of these cDNA representing 1001 unique genes were spotted onto microarrays, and compared internally with PCR-amplified open reading frames (ORFs) from 904 genes representing 842 unique genes annotated in the L. major genome. Microarrays were screened with RNA from procyclic, metacyclic and amastigote populations of L. major. Redundant clones on the array gave highly reproducible results, providing confidence in identification of stage-specific gene expression. Four hundred and thirty unique (i.e. non-redundant) stage-specific genes were identified. A higher percentage of stage-specific gene expression was observed in amastigotes ( approximately 35%) compared to metacyclics ( approximately 12%) for both cDNAs and ORFs, but cDNAs provided a richer source of regulated genes than currently annotated ORFs from the Leishmania genome. In mapping cDNAs onto the Leishmania genome, we noted that approximately 42% aligned to regions not recognised as genes using current predictive annotation tools. These genes are highly represented in our stage-specific genes, and therefore represent important drug targets and vaccine candidates. Careful annotation of cDNAs onto the Leishmania genome will be important before producing the next generation of oligonucleotide arrays based on annotated genes of the genomic sequencing project.

Animals↗

PubMed2001

Experimental annotation of the human genome using microarray technology.

The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

Algorithms↗

PubMed2025

Genome assembly and annotation of the parasitoid jewel wasp Nasonia oneida.

The jewel wasp, Nasonia (Hymenoptera: Pteromalidae), is a well-established model system for evolutionary genetics and host-microbial interactions. Here, we present the genome of N. oneida, a species lacking prior genomic characterization, using 10× Genomics linked-read (400× coverage), Illumina short-read (120× coverage), and transcriptome data (30× coverage). The assembled genome size is 267 Mb, comprising 4,675 scaffolds, with a scaffold N50 of 1 Mb and 98.40% Benchmarking Universal Single-Copy Orthologues (BUSCOs) completeness score. Annotation revealed 32.29% (86.46 Mb) of repetitive sequences and 14,221 protein-coding genes. Comparative genomics of N. oneida with 15 other hymenopteran species validated the presence of 5,939 gene families shared among them, including 3643 single-copy and 2296 multicopy gene families. This study provides the first de novo assembly of N. oneida, providing a significant addition to the growing repertoire of molecular tools for comparative genomics and functional studies to understand the evolution of closely related species as well as the evolution of parasitic wasps.

Animals↗

PubMed1999

Automated genome sequence analysis and annotation.

MOTIVATION: Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. RESULTS: We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. AVAILABILITY: The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac. uk/gqsrv/submit

Amino Acid Sequence↗

PubMed2003

Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes.

Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them. Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of 'functionally interacting' genes. Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display. In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function. The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously. The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones. An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.

Bacterial Proteins↗

PubMed2003

Update on human genome completion and annotations: gene nomenclature.

Why is agreeing on one particular name for each gene important? As one genome after another becomes sequenced, it is imperative to consider the complexity of genes, genetic architecture, gene expression, gene-gene and gene-product interactions and evolutionary relatedness across species. To agree on a particular gene name not only makes one's own research easier, but will also be helpful to the present generation, as well as future generations, of graduate students and postdoctoral fellows who are about to enter genomics research.

Databases, Factual↗

PubMed2025

A high-quality chromosome-level genome assembly and annotation of the giant freshwater prawn (Macrobrachium rosenbergii).

The giant freshwater prawn, Macrobrachium rosenbergii, is native to Southeast Asia and is used in aquacultural practices worldwide. It is considered advantageous because of its rapid growth, high nutritional value, and economic benefits. As one of the three major freshwater aquaculture shrimp sources in China, a high-quality genome resource is of great significance for promoting the germplasm improvement of varieties. This study presents a high-quality chromosome-level genome assembly of M. rosenbergii that was generated by combining PacBio, MGI, and Hi-C reads. The assembled genome was 2.96 Gb in size, with a contig N50 of 0.64 Mb and a scaffold N50 of 55.76 Mb, which was positioned on 59 pseudo-chromosomes. The Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis for genome assembly reached 94.37%. In total, 27,111 protein-coding genes were identified, of which 25,470 were functionally annotated. These results provide a foundation for future research into adaptive evolution, genomics, and molecular breeding in M. rosenbergii.

Animals↗

PubMed2004

3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.

The 3D-GENOMICS database (http://www.sbg.bio. ic.ac.uk/3dgenomics/) provides structural annotations for proteins from sequenced genomes. In August 2003 the database included data for 93 proteomes. The annotations stored in the database include homologous sequences from various sequence databases, domains from SCOP and Pfam, patterns from Prosite and other predicted sequence features such as transmembrane regions and coiled coils. In addition to annotations at the sequence level, several precomputed cross- proteome comparative analyses are available based on SCOP domain superfamily composition. Annotations are available to the user via a web interface to the database. Multiple points of entry are available so that a user is able to: (i) directly access annotations for a single protein sequence via keywords or accession codes, (ii) examine a sequence of interest chosen from a summary of annotations for a particular proteome, or (iii) access precomputed frequency-based cross-proteome comparative analyses.

Amino Acid Sequence↗

PubMed2026

Genome sequencing and annotation of two rhizobacteria with antifungal activity: Pseudomonas tolaasii strain A46 and Pseudomonas palleroriana P61.

Here, we report the draft genome sequences of P. tolaasii A46 and P. palleroriana P61, two rhizobacteria previously shown to inhibit Rhizoctonia solani. These genomic resources will support future efforts to elucidate the molecular basis of fungal suppression and to assess the biocontrol potential of these Pseudomonas strains.

antagonistic rhizobacteria↗

PubMed2001

The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes.

In genome projects of eukaryotic model organisms, a large number of novel genes of unknown function and evolutionary history ("orphans") are being identified. Since many orphans have no known homologs in distant species, it is unclear whether they are restricted to certain taxa or evolve rapidly, either because of a lack of constraints or positive Darwinian selection. Here we use three criteria for the selection of putatively rapidly evolving genes from a single sequence of Drosophila melanogaster. Thirteen candidate genes were chosen from the Adh region on the second chromosome and 1 from the tip of the X chromosome. We succeeded in obtaining sequence from 6 of these in the closely related species D. simulans and D. yakuba. Only 1 of the 6 genes showed a large number of amino acid replacements and in-frame insertions/deletions. A population survey of this gene suggests that its rapid evolution is due to the fixation of many neutral or nearly neutral mutations. Two other genes showed "normal" levels of divergence between species. Four genes had insertions/deletions that destroy the putative reading frame within exons, suggesting that these exons have been incorrectly annotated. The evolutionary analysis of orphan genes in closely related species is useful for the identification of both rapidly evolving and incorrectly annotated genes.

Animals↗

PubMed2026

High-Resolution Chromosome-Level Genome Assembly and Annotation of Triplophysa stewarti, an Endemic Plateau Loach from the Qinghai-Tibet Plateau.

The bottom-dwelling fish Triplophysa stewarti, endemic to the Qinghai-Tibet Plateau, is a valuable model for studying high-altitude adaptation in aquatic ecosystems. However, the lack of a high-quality reference genome has hindered comparative genomic and evolutionary studies within this genus. Here, we present a chromosome-level genome assembly for T. stewarti, generated using PacBio HiFi long-read sequencing and Hi-C scaffolding. The 697.9 Mb assembly is highly continuous (scaffold N50 of 253.58 Mb) and encompasses 25 chromosomes, representing 92.65% of the genome. BUSCO analysis indicated a 98.4% completeness, supporting the high quality of the assembly. We annotated 28,009 protein-coding genes, with 97.04% being functionally assigned across multiple databases (NR, UniProt, KEGG, GO, Pfam and InterPro). Additionally, repetitive elements constituted 42.47% of the genome, and we identified 52,709 non-coding RNAs. This high-quality reference genome provides a fundamental resource for exploring the adaptive evolution, population structure, and conservation genetics of T. stewarti and related species on the Qinghai-Tibet Plateau.

Animals↗

PubMed2026

Chromosome-level genome assembly and annotation of the porcupine fish (Diodon hystrix).

The porcupinefish (Diodon hystrix), a coral reef teleost, is widely distributed in tropical/subtropical waters of the Pacific, Atlantic, Indian Oceans, and Mediterranean Sea. It shares easily recognizable features with pufferfish, such as body inflation and spines. Additionally, its culinary value makes D. hystrix a highly desirable species in many tropical coastal regions, with considerable market potential. However, lack of a high-quality genome hindered further studies on its reproduction, molecular biology, and genomic improvement. Here, we assembled the chromosome-scale genome using PacBio HiFi, ultra-long reads, and Hi-C. Of the 713.62 Mb genome, 98.63% anchored to 23 chromosomes (scaffold N50: 31.52 Mb) with 39.82% repetitive sequences. The assembled genome achieved a BUSCO completeness score of 97.7%, with 23,171 protein-coding genes predicted, 22,221 of which were functionally annotated. Phylogenetic analysis identified D. hystrix's evolutionary relationships with other species in the Tetraodontiformes. In summary, the high-quality genome of D. hystrix sheds light on valuable insights into genome size evolution, and provides a valuable resource for exploiting genomic study and breeding applications in this species.

Animals↗

PubMed2005

A procedure for assessing GO annotation consistency.

MOTIVATION: The Gene Ontology (GO) is widely used to annotate molecular attributes of genes and gene products. Multiple groups undertaking functional annotations of genomes contribute their annotation sets to the GO database resource and these data are subsequently used in comparative functional analysis research. Although GO curators adhere to the same protocols and standards while assigning GO annotations, the specific procedure followed by each annotation group can vary. Since differences in application of annotation standards would dilute the effectiveness of comparative analysis, methods for assessing annotation consistency are essential. The development of methodologies that are broadly applicable for the assessment of GO annotation consistency is an important issue for the comparative genomics community. RESULTS: We have developed a methodology for assessing the consistency of GO annotations provided by different annotation groups. The method is completely general and can be applied to compare any two sets of GO annotations. This is the first attempt to assess cross-species GO annotation consistency. Our method compares annotation sets utilizing the hierarchical structure of the GO to compare GO annotations between orthologous gene pairs. The method produces a report on the annotation consistency and inconsistency for each orthologous pair. We present results obtained by comparing GO annotations for mouse and human gene sets. AVAILABILITY: The complete current MGI_GOA GO annotation consistency report is available online at http://www.spatial.maine.edu/~mdolan/

Animals↗