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The Genomics Era: From Reference Genomes to Pan-Genomic Approach, 2nd...
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The Genomics Era: From Reference Genomes to Pan-Genomic Approach, 2nd Edition

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (28 February 2025) | Viewed by 5725

Special Issue Editor

Prof. Dr. Chiara Scapoli

E-Mail Website
Guest Editor
Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
Interests: human genetics; complex diseases; statistical genetics; metagenomics; molecular genetics/biomarkers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following a very successful first edition, we are pleased to announce the launch of a second edition of the Special Issue on "The Genomics Era: From Reference Genomes to Pan-Genomic Graphs".

Since entering the "genomic era", up to now, the scientific community has relied on a single "reference" genome for each species, used as the basis for a wide range of genetic analyses. With the number of sequenced genomes steadily increasing, the concept of "reference" genomes has been reconsidered; presently, the idea of using a "pangenome" to describe the complete set of variations in a species appears promising.

This Special Issue of Biomolecules focuses on new insights that pangenomic analyses have brought into a wide range of topics, from microbiology and virology to human genetics, as well as the exploration of pangenomics’ potential in aiding human disease diagnostics.

Studies that investigate pan-genome profiles by defining core genomes up to the reconstruction of accessory genomes across multiple organisms are welcome, as well as those that impliment computational pangenomic approaches and novel statistical methods to highlight the presence of the signature of selection at the genome level. The topics of interest range include metagenomics, illustrating core or dispensable genes potentially related to microbial pathogenicity or niche adaptation; pan-transcriptomics used for a more compact representation of transcriptomes; and human genetics based on linking whole-genome variations to human diversity, diseases, and other related topics.

Both research (in particular) and review articles proposing novelties or overviews, respectively, are welcome.

Prof. Dr. Chiara Scapoli
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • pangenome
  • genome evolution
  • graph-based pangenome
  • core and dispensable genomes
  • human genomics
  • metagenomics
  • transcriptome
  • structural variation

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Related Special Issue

Published Papers (5 papers)

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Research

16 pages, 1222 KiB  
Article
A Pangenomic Approach to Improve Population Genetics Analysis and Reference Bias in Underrepresented Middle Eastern and Horn of Africa Populations
by Adrien Oliva, Rachel Foare, Peter Campbell, Natalie A. Twine, Denis C. Bauer and Angad Singh Johar
Biomolecules 2025, 15(4), 582; https://doi.org/10.3390/biom15040582 - 15 Apr 2025
Viewed by 539
Abstract
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 characterising East African populations, particularly Somalis, by constructing [...] Read more.
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 characterising East African populations, particularly Somalis, by constructing a variation graph using Mozabites from the Human Genome Diversity Project (HGDP) given their ancestral affinity with Somalis. We evaluated the effectiveness of this graph-based reference in estimating effective population sizes (Ne) in Bedouins compared to the hg38 reference and examined its impact on allele frequencies and genome-wide association studies (GWAS). Applying a coalescent model to the graph-based reference produced a Ne estimate of approximately 17 for the Bedouin population, which was significantly lower than the estimate from the hg38 reference (approximately 79,000). Only the graph-based estimate fell within the 95% confidence interval in simulations, indicating improved accuracy. Moreover, graph variants exhibited significantly lower allele frequencies (p-value < 2.2 × 10−16), suggesting potential effects on the interpretation and power of GWAS. Notably, GWAS variants specific to Bedouins derived from the graph showed lower frequencies (p = 0.023) than those obtained from the linear reference. These findings suggest that a pangenomic approach, informed by populations with ancestral affinities such as the Mozabites, provides more accurate estimates of Ne and allele frequencies. This highlights the importance of pangenomic strategies to better capture genetic diversity in underrepresented populations, a critical step towards improving population genetics studies, personalised medicine, and equitable healthcare. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Approach, 2nd Edition)
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18 pages, 3530 KiB  
Article
Comparative Genomics of Bryopsis hypnoides: Structural Conservation and Gene Transfer Between Chloroplast and Mitochondrial Genomes
by Ziwen Liu, Xiao Fan, Yukun Wu, Wei Zhang, Xiaowen Zhang, Dong Xu, Yitao Wang, Ke Sun, Wei Wang and Naihao Ye
Biomolecules 2025, 15(2), 278; https://doi.org/10.3390/biom15020278 - 13 Feb 2025
Viewed by 608
Abstract
Bryopsis hypnoides, a unicellular multinucleate green alga in the genus Bryopsis, plays vital ecological roles and represents a key evolutionary link between unicellular and multicellular algae. However, its weak genetic baseline data have constrained the progress of evolutionary research. In this [...] Read more.
Bryopsis hypnoides, a unicellular multinucleate green alga in the genus Bryopsis, plays vital ecological roles and represents a key evolutionary link between unicellular and multicellular algae. However, its weak genetic baseline data have constrained the progress of evolutionary research. In this study, we successfully assembled and annotated the complete circular chloroplast and mitochondrial genomes of B. hypnoides. The chloroplast genome has a total length of 139,745 bp and contains 59 protein-coding genes, 2 rRNA genes, and 11 tRNA genes, with 31 genes associated with photosynthesis. The mitochondrial genome has a total length of 408,555 bp and contains 41 protein-coding genes, 3 rRNA genes, and 18 tRNA genes, with 18 genes involved in oxidative phosphorylation. Based on the data, we conducted a genetic comparison involving repeat sequences, phylogenetic relationships, codon usage preferences, and gene transfer between the two organellar genomes. The major results highlighted that (1) the chloroplast genome favors A/T repeats, whereas the mitochondrial genome prefers C/G repeats; (2) codon usage preference analysis indicated that both organellar genomes prefer codons ending in A/T, with a stronger bias observed in the chloroplast genome; and (3) sixteen fragments with high sequence identity were identified between the two organellar genomes, indicating potential gene transfer. These findings provide critical insights into the organellar genome characteristics and evolution of B. hypnoides. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Approach, 2nd Edition)
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15 pages, 2085 KiB  
Article
Detection of Possible Resistance Mechanisms in Uropathogenic Escherichia coli Strains Isolated from Kidney Transplant Recipients Based on Whole Genome Sequencing
by Soraya Herrera-Espejo, Alejandro Rubio, Lucía Ceballos-Romero, Jerónimo Pachón, Elisa Cordero, Antonio J. Pérez-Pulido and María Eugenia Pachón-Ibáñez
Biomolecules 2025, 15(2), 260; https://doi.org/10.3390/biom15020260 - 11 Feb 2025
Cited by 1 | Viewed by 708
Abstract
Background: Urinary tract infections are a global health concern, with uropathogenic Escherichia coli (UPEC) accounting for 80–90% of cases. Given the rise in antimicrobial resistance, our aim was to elucidate the genetic mechanisms behind low-level resistance to ciprofloxacin and fosfomycin (LLCR and LLFR) [...] Read more.
Background: Urinary tract infections are a global health concern, with uropathogenic Escherichia coli (UPEC) accounting for 80–90% of cases. Given the rise in antimicrobial resistance, our aim was to elucidate the genetic mechanisms behind low-level resistance to ciprofloxacin and fosfomycin (LLCR and LLFR) in UPEC strains, using whole-genome sequencing (WGS) to identify point mutations in chromosomal and plasmid genes. Methods: A cohort UPEC was collected from kidney transplant recipients at the Virgen del Rocío University Hospital, Spain. Minimum inhibitory concentrations were determined for ciprofloxacin and fosfomycin to categorize strains into LLCR and LLFR. Twenty strains were selected for WGS, with genome annotations. Point mutations were identified and analyzed using alignment tools, and protein stability changes were predicted. Results: LLCR strains exhibited mutations in key quinolone resistance-determining regions of the gyrA gene, in 83% of cases. The qnrS1 plasmid gene was found in 17% of LLCR strains. LLFR strains showed mutations in the glpT and cyaA genes. Mutations in the uhp gene family were linked to the fosfomycin-resistant phenotype, suggesting a multi-step resistance evolution mechanism. Conclusions: This study highlights the complex interplay between chromosomal and plasmid genes in UPEC’s resistance to ciprofloxacin and fosfomycin. The findings contribute to understanding low-level resistance mechanisms and may guide the development of novel therapeutic strategies to combat multidrug-resistant strains. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Approach, 2nd Edition)
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17 pages, 3787 KiB  
Article
Direct On-Chip Diagnostics of Streptococcus bovis/Streptococcus equinus Complex in Bovine Mastitis Using Bioinformatics-Driven Portable qPCR
by Jaewook Kim, Eiseul Kim, Seung-Min Yang, Si Hong Park and Hae-Yeong Kim
Biomolecules 2024, 14(12), 1624; https://doi.org/10.3390/biom14121624 - 18 Dec 2024
Viewed by 980
Abstract
This study introduces an innovative on-site diagnostic method for rapidly detecting the Streptococcus bovis/Streptococcus equinus complex (SBSEC), crucial for livestock health and food safety. Through a comprehensive genomic analysis of 206 genomes, this study identified genetic markers that improved classification and [...] Read more.
This study introduces an innovative on-site diagnostic method for rapidly detecting the Streptococcus bovis/Streptococcus equinus complex (SBSEC), crucial for livestock health and food safety. Through a comprehensive genomic analysis of 206 genomes, this study identified genetic markers that improved classification and addressed misclassifications, particularly in genomes labeled S. equinus and S. lutetiensis. These markers were integrated into a portable quantitative polymerase chain reaction (qPCR) that can detect SBSEC species with high sensitivity (down to 101 or 100 colony-forming units/mL). The portable system featuring a flat chip and compact equipment allows immediate diagnosis within 30 min. The diagnostic method was validated in field conditions directly from cattle udders, farm environments, and dairy products. Among the 100 samples, 51 tested positive for bacteria associated with mastitis. The performance of this portable qPCR was comparable to laboratory methods, offering a reliable alternative to whole-genome sequencing for early detection in clinical, agricultural, and environmental settings. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Approach, 2nd Edition)
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16 pages, 5491 KiB  
Article
In-Depth Genome Characterization and Pan-Genome Analysis of Strain KMM 296, a Producer of Highly Active Alkaline Phosphatase; Proposal for the Reclassification of Cobetia litoralis and Cobetia pacifica as the Later Heterotypic Synonyms of Cobetia amphilecti and Cobetia marina, and Emended Description of the Species Cobetia amphilecti and Cobetia marina
by Olga Nedashkovskaya, Larissa Balabanova, Nadezhda Otstavnykh, Natalia Zhukova, Ekaterina Detkova, Aleksandra Seitkalieva, Evgenia Bystritskaya, Yulia Noskova, Liudmila Tekutyeva and Marina Isaeva
Biomolecules 2024, 14(2), 196; https://doi.org/10.3390/biom14020196 - 6 Feb 2024
Cited by 5 | Viewed by 2053
Abstract
A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of the mussel Crenomytilus grayanus, was investigated in detail due to its ability to produce a highly active alkaline phosphatase CmAP of the structural family [...] Read more.
A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of the mussel Crenomytilus grayanus, was investigated in detail due to its ability to produce a highly active alkaline phosphatase CmAP of the structural family PhoA. A previous taxonomic study allocated the strain to the species Cobetia marina, a member of the family Halomonadaceae of the class Gammaproteobacteria. However, 16S rRNA gene sequencing showed KMM 296’s relatedness to Cobetia amphilecti NRIC 0815T. The isolate grew with 0.5–19% NaCl at 4–42 °C and hydrolyzed Tweens 20 and 40 and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C18:1 ω7c, C12:0 3-OH, C18:1 ω7c, C12:0, and C17:0 cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and also an unidentified aminolipid, phospholipid, and a few unidentified lipids. The major respiratory quinone was Q-8. According to phylogenomic and chemotaxonomic evidence, and the nearest neighbors, the strain KMM 296 represents a member of the species C. amphilecti. The genome-based analysis of C. amphilecti NRIC 0815T and C. litoralis NRIC 0814T showed their belonging to a single species. In addition, the high similarity between the C. pacifica NRIC 0813T and C. marina LMG 2217T genomes suggests their affiliation to one species. Based on the rules of priority, C. litoralis should be reclassified as a later heterotypic synonym of C. amphilecti, and C. pacifica is a later heterotypic synonym of C. marina. The emended descriptions of the species C. amphilecti and C. marina are also proposed. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Approach, 2nd Edition)
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