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Bioinformatics and Population Genomics
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Bioinformatics and Population Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (20 May 2023) | Viewed by 7926

Special Issue Editors

Dr. Nima Rafati

E-Mail Website
Guest Editor
Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
Interests: NGS; genomics; comparative genomics; transcriptomics; small and large variant analyses; gwas
Dr. Dag Ahrén

E-Mail Website
Guest Editor
Department of Biology, Lund University, 221 00 Lund, Sweden
Interests: genomics; NGS; bioinformatician; evolution; NBIS; National Bioinformatics Infrastructure Sweden; bioinformatics; metagenomics

Special Issue Information

Dear Colleagues,

Studying genetic factors underlying phenotypic variation among populations has been the cornerstone of population genetics. In light of recent developments in sequencing technologies, the scope of these studies has dramatically changed, transforming it to an interdisciplinary field that integrates bioinformatic tools to analyze and manage large biological data. Both theoretical and computational methods are required to understand mechanisms producing and maintaining genetic diversity among populations. Population genetics studies can identify loci involved in adaptation or variants responsible for inbreeding depression. Moreover, these findings can be applied for wildlife conservation. This Special Issue aims to highlight recent discoveries and theoretical frameworks.

We are interested in studies that describe the causes of adaptation as a result of domestication, invasion of non-native species, and climate change as well as disease susceptibility at the genome level by developing and applying novel bioinformatics tools. 

Dr. Nima Rafati
Dr. Dag Ahrén
Guest Editors

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. Genes 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 2600 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

  • new discoveries and recent breakthroughs in population genetics and genomics
  • bioinformatics tools and statistical frameworks in the field of population genetics
  • novel methods for genotyping and sequencing
  • best practice for study design, library preparation, sequencing, and filtering for bioinformatics data analysis
  • application of population genetics to animal and plant breeding
  • role of gene–gene interaction in adaptation
  • integrative analyses of omics data for characterizing population differentiation
  • adaptation to environmental changes
  • dynamics of populations in response to environmental stress
  • adaptation from standing genetic variation
  • population genetics and risk prediction of diseases

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Published Papers (3 papers)

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Research

14 pages, 9034 KiB  
Article
Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker
by Kaifen Zhang, Yongdong Zhou, Weihua Song, Lihua Jiang and Xiaojun Yan
Genes 2023, 14(7), 1508; https://doi.org/10.3390/genes14071508 - 24 Jul 2023
Cited by 3 | Viewed by 1936
Abstract
Larimichthys crocea (also known as the large yellow croaker) is one of the most economically important marine fishes in China, and research on the ecology and genetics of this species is of immense significance. In this study, we performed restriction site-associated DNA sequencing [...] Read more.
Larimichthys crocea (also known as the large yellow croaker) is one of the most economically important marine fishes in China, and research on the ecology and genetics of this species is of immense significance. In this study, we performed restriction site-associated DNA sequencing (RAD-seq) of 54 individuals collected from four sites in China to analyze the genetic structure and diversity of large yellow croaker at the genome level. It revealed that the large yellow croaker populations in the Ningde and Zhoushan coastal waters can be clearly distinguished. Different genetic diversity indices were used to analyze the genetic diversity of the large yellow croaker, which showed that there was a differentiation trend between the wild and farmed populations in Ningde. Moreover, we identified genetically differentiated genomic regions between the populations. GO gene enrichment analysis identified genes that are related to fatty acid metabolism and growth. These findings enhance our understanding of genetic differentiation and adaptation to different living environments, providing a theoretical basis for the preservation and restoration of the genetic resources of the large yellow croaker. Full article
(This article belongs to the Special Issue Bioinformatics and Population Genomics)
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18 pages, 5702 KiB  
Article
Comparative Analysis of CRISPR-Cas Systems in Pseudomonas Genomes
by Ángel Parra-Sánchez, Laura Antequera-Zambrano, Gema Martínez-Navarrete, Vanessa Zorrilla-Muñoz, José Luis Paz, Ysaias J. Alvarado, Lenin González-Paz and Eduardo Fernández
Genes 2023, 14(7), 1337; https://doi.org/10.3390/genes14071337 - 25 Jun 2023
Cited by 4 | Viewed by 2245
Abstract
Pseudomonas is a bacterial genus with some saprophytic species from land and others associated with opportunistic infections in humans and animals. Factors such as pathogenicity or metabolic aspects have been related to CRISPR-Cas, and in silico studies into it have focused more on [...] Read more.
Pseudomonas is a bacterial genus with some saprophytic species from land and others associated with opportunistic infections in humans and animals. Factors such as pathogenicity or metabolic aspects have been related to CRISPR-Cas, and in silico studies into it have focused more on the clinical and non-environmental setting. This work aimed to perform an in silico analysis of the CRISPR-Cas systems present in Pseudomonas genomes. It analyzed 275 complete genomic sequences of Pseudomonas taken from the NCBI database. CRISPR loci were obtained from CRISPRdb. The genes associated with CRISPR (cas) and CAS proteins, and the origin and diversity of spacer sequences, were identified and compared by BLAST. The presence of self-targeting sequences, PAMs, and the conservation of DRs were visualized using WebLogo 3.6. The CRISPR-like RNA secondary structure prediction was analyzed using RNAFold and MFold. CRISPR structures were identified in 19.6% of Pseudomonas species. In all, 113 typical CRISPR arrays with 18 putative cas were found, as were 2050 spacers, of which 52% showed homology to bacteriophages, 26% to chromosomes, and 22% to plasmids. No potential self-targeting was detected within the CRISPR array. All the found DRs can form thermodynamically stable secondary RNA structures. The comparison of the CRISPR/Cas system can help understand the environmental adaptability of each evolutionary lineage of clinically and environmentally relevant species, providing data support for bacterial typing, traceability, analysis, and exploration of unconventional CRISPR. Full article
(This article belongs to the Special Issue Bioinformatics and Population Genomics)
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18 pages, 3800 KiB  
Article
An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis
by Ranran Zhang, Jiaming Xue, Mengyu Tan, Dezhi Chen, Yuanyuan Xiao, Guihong Liu, Yazi Zheng, Qiushuo Wu, Miao Liao, Meili Lv, Shengqiu Qu and Weibo Liang
Genes 2023, 14(4), 865; https://doi.org/10.3390/genes14040865 - 4 Apr 2023
Cited by 7 | Viewed by 2396
Abstract
Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high [...] Read more.
Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform. The sizes of markers and amplicons ranged between 11–81 bp and 123–198 bp, respectively. The sensitivity was 0.25 ng, and the calling results were consistent with Sanger sequencing and the Integrative Genomics Viewer (IGV). It showed measurable polymorphism among sequenced 137 Southwest Chinese Han individuals. No significant deviations in the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were found at all MHs after Bonferroni correction. Furthermore, the specificity was 1:40 for simulated two-person mixtures, and the detection rates of highly degraded single samples and mixtures were 100% and 93–100%, respectively. Moreover, animal DNA testing was incomplete and low depth. Overall, our MPS-based 50-plex MH panel is a powerful forensic tool that provides a strong supplement and enhancement for some existing panels. Full article
(This article belongs to the Special Issue Bioinformatics and Population Genomics)
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