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Biomolecules
Special Issues
The Genomics Era: From Reference Genomes to Pan-Genomic Graphs
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The Genomics Era: From Reference Genomes to Pan-Genomic Graphs

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

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 16665

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,

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 pangenomic analyses have brought into a wide range of topics, from microbiology and virology to human genetics, as well as concerning the exploration of pangenomics’ potential in aiding human disease diagnostics.

Studies investigating core and dispensable genomes across multiple disciplines are welcome, as well as researches presenting the implementation of computational pangenomic approaches and novel statistical methods also aimed at highlighting the presence of the signature of selection at the genome level. In detail, the topics of interest range from metagenomics and illustrating core or dispensable genomes potentially related to microbial pathogenicity or niche adaptation, to pantranscriptomics for a more compact representation of transcriptomes, up to the gain of insights regarding human genetics by linking whole genomic 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
  • evolution genomics
  • graph genome
  • metagenomics
  • core and dispensable genomes
  • human genomics
  • transcriptomes

Related Special Issue

Published Papers (5 papers)

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Research

Jump to: Review

18 pages, 12595 KiB  
Article
Validation of an Ultraviolet Light Response Gene Signature for Predicting Prognosis in Patients with Uveal Melanoma
by Carlos A. Orozco, Alejandro Mejía-García, Marcela Ramírez, Johanna González, Luis Castro-Vega, Richard B. Kreider, Silvia Serrano, Alba Lucia Combita and Diego A. Bonilla
Biomolecules 2023, 13(7), 1148; https://doi.org/10.3390/biom13071148 - 19 Jul 2023
Viewed by 2084
Abstract
Uveal melanoma (UVM) is a highly aggressive ocular cancer with limited therapeutic options and poor prognosis particularly for patients with liver metastasis. As such, the identification of new prognostic biomarkers is critical for developing effective treatment strategies. In this study, we aimed to [...] Read more.
Uveal melanoma (UVM) is a highly aggressive ocular cancer with limited therapeutic options and poor prognosis particularly for patients with liver metastasis. As such, the identification of new prognostic biomarkers is critical for developing effective treatment strategies. In this study, we aimed to investigate the potential of an ultraviolet light response gene signature to predict the prognosis of UVM patients. Our approach involved the development of a prognostic model based on genes associated with the cellular response to UV light. By employing this model, we generated risk scores to stratify patients into high- and low-risk groups. Furthermore, we conducted differential expression analysis between these two groups and explored the estimation of immune infiltration. To validate our findings, we applied our methodology to an independent UVM cohort. Through our study, we introduced a novel survival prediction tool and shed light on the underlying cellular processes within UVM tumors, emphasizing the involvement of immune subsets in tumor progression. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Graphs)
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18 pages, 9631 KiB  
Article
Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure
by Xiaolong Kang, Chenglong Li, Shuli Liu, Ransom L. Baldwin VI, George E. Liu and Cong-Jun Li
Biomolecules 2023, 13(7), 1137; https://doi.org/10.3390/biom13071137 - 16 Jul 2023
Cited by 3 | Viewed by 1831
Abstract
Butyrate contributes epigenetically to the changes in cellular function and tissue development of the rumen in ruminant animals, which might be achieved by its genetic or epigenetic regulation of gene expression. To explore the role of butyrate on bovine rumen epithelial function and [...] Read more.
Butyrate contributes epigenetically to the changes in cellular function and tissue development of the rumen in ruminant animals, which might be achieved by its genetic or epigenetic regulation of gene expression. To explore the role of butyrate on bovine rumen epithelial function and development, this study characterized genome-wide H3K27ac modification changes and super-enhancer profiles in rumen epithelial primary cells (REPC) induced with butyrate by ChIP-seq, and analyzed its effects on gene expression and functional pathways by integrating RNA-seq data. The results showed that genome-wide acetylation modification was observed in the REPC with 94,675 and 48,688 peaks in the butyrate treatment and control group, respectively. A total of 9750 and 5020 genes with increased modification (H3K27ac-gain) and decreased modification (H3K27ac-loss) were detected in the treatment group. The super-enhancer associated genes in the butyrate-induction group were involved in the AMPK signaling pathway, MAPK signaling pathway, and ECM-receptor interaction. Finally, the up-regulated genes (PLCG1, CLEC3B, IGSF23, OTOP3, ADTRP) with H3K27ac gain modification by butyrate were involved in cholesterol metabolism, lysosome, cell adhesion molecules, and the PI3K-Akt signaling pathway. Butyrate treatment has the role of genome-wide H3K27ac acetylation on bovine REPC, and affects the changes in gene expression. The effect of butyrate on gene expression correlates with the acetylation of the H3K27ac level. Identifying genome-wide acetylation modifications and expressed genes of butyrate in bovine REPC cells will expand the understanding of the biological role of butyrate and its acetylation. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Graphs)
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28 pages, 6466 KiB  
Article
Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture
by Aaron T. Dossey, Brenda Oppert, Fu-Chyun Chu, Marcé D. Lorenzen, Brian Scheffler, Sheron Simpson, Sergey Koren, J. Spencer Johnston, Kosuke Kataoka and Keigo Ide
Biomolecules 2023, 13(4), 589; https://doi.org/10.3390/biom13040589 - 24 Mar 2023
Cited by 2 | Viewed by 6055
Abstract
Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports [...] Read more.
Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Graphs)
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Review

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26 pages, 16279 KiB  
Review
Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes
by Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu and Pankaj Jaiswal
Biomolecules 2023, 13(9), 1403; https://doi.org/10.3390/biom13091403 - 17 Sep 2023
Cited by 2 | Viewed by 3531
Abstract
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral [...] Read more.
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Graphs)
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33 pages, 7619 KiB  
Review
Multiomics Analysis Reveals Novel Genetic Determinants for Lens Differentiation, Structure, and Transparency
by Joshua Disatham, Lisa Brennan, Ales Cvekl and Marc Kantorow
Biomolecules 2023, 13(4), 693; https://doi.org/10.3390/biom13040693 - 19 Apr 2023
Cited by 4 | Viewed by 2189
Abstract
Recent advances in next-generation sequencing and data analysis have provided new gateways for identification of novel genome-wide genetic determinants governing tissue development and disease. These advances have revolutionized our understanding of cellular differentiation, homeostasis, and specialized function in multiple tissues. Bioinformatic and functional [...] Read more.
Recent advances in next-generation sequencing and data analysis have provided new gateways for identification of novel genome-wide genetic determinants governing tissue development and disease. These advances have revolutionized our understanding of cellular differentiation, homeostasis, and specialized function in multiple tissues. Bioinformatic and functional analysis of these genetic determinants and the pathways they regulate have provided a novel basis for the design of functional experiments to answer a wide range of long-sought biological questions. A well-characterized model for the application of these emerging technologies is the development and differentiation of the ocular lens and how individual pathways regulate lens morphogenesis, gene expression, transparency, and refraction. Recent applications of next-generation sequencing analysis on well-characterized chicken and mouse lens differentiation models using a variety of omics techniques including RNA-seq, ATAC-seq, whole-genome bisulfite sequencing (WGBS), chip-seq, and CUT&RUN have revealed a wide range of essential biological pathways and chromatin features governing lens structure and function. Multiomics integration of these data has established new gene functions and cellular processes essential for lens formation, homeostasis, and transparency including the identification of novel transcription control pathways, autophagy remodeling pathways, and signal transduction pathways, among others. This review summarizes recent omics technologies applied to the lens, methods for integrating multiomics data, and how these recent technologies have advanced our understanding ocular biology and function. The approach and analysis are relevant to identifying the features and functional requirements of more complex tissues and disease states. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Graphs)
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