Biology subjects

Ghelfi, A.

Publications and source records attributed to Ghelfi, A..

8 recordsLinked to original sources

bioRxiv2024

Hayai-Annotation v3.0: A functional gene prediction tool that integrates orthologs and gene ontology for network analysis

Hayai-Annotation v3, an R-package integrated with the R-Shiny browser interface, utilizes two methods for functional annotation: DIAMOND for sequence alignment using UniProtKB Plants as the database, and OrthoLoger, the official OrthoDB tool for ortholog inferences. The GO enrichment accuracy was assessed by a CAFA-evaluator, demonstrating that Hayai-Annotation v3s accuracy was comparable to that of the benchmark, BLAST2GO. We here propose a method to explore genome evolution and adaptation from a different perspective, by creating networks and heatmaps correlating orthologs with gene ontology (molecular function and biological process) from their co-occurrence tables. This approach enhances the ability to infer functions of uncharacterized genes by associating orthologs with gene ontology terms and the ability to visualize the distribution of gene numbers correlated with co-occurrence patterns across different species. To our knowledge, this is the first attempt to correlate orthologs with GO (MF and BP) to construct a gene network, providing a comprehensive, cross-species view of gene distribution and function. Hayai-Annotation v3 not only retains the convenience of previous versions but also enhances ortholog analysis functionality, allowing for evolutionary insights from gene sequences. Hayai-Annotation v3 is expected to contribute significantly to the future development of plant genome analysis.

bioinformatics↗

bioRxiv2023

Benchmarking Hayai-Annotation Plants: A Re-evaluation Using Standard Evaluation Metrics

The rapid growth of next-generation sequencing (NGS) technology has led to a surge in the determination of whole genome sequences in plants. This has created a need for functional annotation of newly predicted gene sequences in the assembled genomes. To address this, "Hayai-Annotation Plants" was developed as a gene functional annotation tool for plant species. In this report, we compared Hayai-Annotation Plants with Blast2GO and TRAPID, focusing on the three primary gene-ontology (GO) domains: Biological Process (BP), Molecular Function (MF), and Cellular Component (CC). Using the Arabidopsis thaliana GO annotation as a benchmark, we evaluated each tool using two approaches: the area under the precision-recall curve (AUC-PR) and the metrics used at the critical assessment of functional annotation (CAFA). In the latter case, a CAFA-evaluator, was used to determine the F-score, weighted F-score, and S-score for each domain. Hayai-Annotation Plants showed better performances in all three GO domains. Our results thus reaffirm the effectiveness of Hayai-Annotation Plants for functional gene annotation in plant species. In this era of extensive whole genome sequencing, Hayai-Annotation Plants will serve as a valuable tool that facilitates simplified and accurate gene function annotation for numerous users, thereby making a significant contribution to plant research.

bioinformatics↗

bioRxiv2021

Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in family Gentianaceae

Eustoma grandiflorum (Raf.) Shinn., is an annual herbaceous plant native to the southern United States, Mexico, and the Greater Antilles. It has a large flower with a variety of colors and an important flower crop. In this study, we established a chromosome-scale de novo assembly of E. grandiflorum by integrating four genomic and genetic approaches: (1) Pacific Biosciences (PacBio) Sequel deep sequencing, (2) error correction of the assembly by Illumina short reads, (3) scaffolding by chromatin conformation capture sequencing (Hi-C), and (4) genetic linkage maps derived from an F2 mapping population. The 36 pseudomolecules and unplaced 64 scaffolds were created with total length of 1,324.8 Mb. Full-length transcript sequencing was obtained by PacBio Iso-Seq sequencing for gene prediction on the assembled genome, Egra_v1. A total of 36,619 genes were predicted on the genome as high confidence HC) genes. Of the 36,619, 25,936 were annotated functions by ZenAnnotation. Genetic diversity analysis was also performed for nine commercial E. grandiflorum varieties bred in Japan, and 254,205 variants were identified. This is the first report of the construction of reference genome sequences in E. grandiflorum as well as in the family Gentianaceae.

genomics↗

bioRxiv2021

Genome features of common vetch (Vicia sativa) in natural habitats

Wild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch (Vicia sativa) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1,243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. These findings suggest that high heterozygosity at the population level would be required for wild plants to survive under natural conditions while allowing important gene loci to be fixed to adapt the conditions. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement. HighlightSequence analysis of the common vetch (Vicia sativa) genome and SNP genotyping across natural populations revealed nucleotide diversity levels associated with native population environments.

genomics↗

bioRxiv2020

KusakiDB v1.0: a novel approach for validation and completeness of protein orthologous groups

Plants have quite a low coverage in the major protein databases despite their roughly 350,000 species. Moreover, the agricultural sector is one of the main categories in bioeconomy. In order to manipulate and/or engineer plant-based products, it is important to understand the essential fabric of an organism, its proteins. Therefore, we created KusakiDB, which is a database of orthologous proteins, in plants, that correlates three major databases, OrthoDB, UniProt and RefSeq. KusakiDB has an orthologs assessment and management tools in order to compare orthologous groups, which can provide insights not only under an evolutionary point of view but also evaluate structural gene prediction quality and completeness among plant species. KusakiDB could be a new approach to reduce error propagation of functional annotation in plant species. Additionally, this method could, potentially, bring to light some orthologs unique to a few species or families that could have evolved at a high evolutionary rate or could have been a result of a horizontal gene transfer. Availability and ImplementationThe software is implemented in R. It is available at http://pgdbjsnp.kazusa.or.jp/app/kusakidb and at https://hub.docker.com/r/ghelfi/kusakidb under the MIT license. Contactandreaghelfi@kazusa.or.jp Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2020

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype

Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single molecule real-time sequencing data followed by a HiC analysis was employed. The resultant haplotype-phased sequences consisted of 3,779 sequences (2.256 Gb in length and N50 of 1.5 Mb), and 18 pseudomolecules comprising 1.08 Gb scaffold sequences along with a high-density SNP genetic linkage map. Using the genome sequence data obtained from two breeding populations, the SNPs linked to double flower loci (Djo and Dsu), were discovered for each breeding population. DNA markers J01 linked to Djo and S01 linked to Dsu were developed, and these could be used successfully to distinguish the recessive double flower allele for each locus respectively. The LEAFY gene was suggested as the causative gene for Dsu, since frameshift was specifically observed in double flower accession with dsu. The genome information obtained in this study will facilitate a wide range of genomic studies on hydrangea in the future.

genomics↗

bioRxiv2019

Phased genome sequence of an interspecific hybrid flowering cherry, Somei-Yoshino (Cerasus x yedoensis)

We report the phased genome sequence of an interspecific hybrid, the flowering cherry Somei-Yoshino (Cerasus x yedoensis). The sequence was determined by single-molecule real-time sequencing technology and assembled using a trio-binning strategy in which allelic variation was resolved to obtain phased sequences. The resultant assembly consisting of two haplotype genomes spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between two genome sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherry varieties suggested that Somei-Yoshino is derived from a cross between C. spachiana and either C. speciose or its derivative. Transcriptome data for flowering date revealed comprehensive changes in gene expression in floral bud development toward flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

genomics↗

bioRxiv2018

Hayai-Annotation Plants: an ultra-fast and comprehensive gene annotation system in plants

Hayai-Annotation Plants is a browser-based interface for an ultra-fast and accurate gene annotation system for plant species using R. The pipeline combines the sequence-similarity searches, using USEARCH against UniProtKB (taxonomy Embryophyta), with a functional annotation step. Hayai-Annotation Plants provides five layers of annotation: 1) gene name; 2) gene ontology terms consisting of its three main domains (Biological Process, Molecular Function, and Cellular Component); 3) enzyme commission number; 4) protein existence level; 5) and evidence type. In regard to speed and accuracy, Hayai-Annotation Plants annotated Arabidopsis thaliana (Araport11, representative peptide sequences) within five minutes with an accuracy of 96.4 %.\n\nAvailability and ImplementationThe software is implemented in R and runs on Macintosh and Linux systems. It is freely available at https://github.com/kdri-genomics/Hayai-Annotation-Plants under the GPLv3 license.

bioinformatics↗