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Life: Computational Genomics
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Life: Computational Genomics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (15 September 2021) | Viewed by 29752

Special Issue Editors

Prof. Dr. Yuriy Lvovich Orlov

E-Mail Website
Guest Editor
Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
Interests: medical genomics; e-health; bioinformatics; systems biology
Special Issues, Collections and Topics in MDPI journals
Dr. Anastasia A. Anashkina

E-Mail Website
Guest Editor
Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
Interests: structural bioinformatics; biophysics; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue collects papers on systems biology applications, computational genomics and bioinformatics methods in life sciences.

Based on the readers’ interest in computational genomics and systems biology, we continue publication in this area based on novel technological approaches, gene networks and proteomics analysis. Here, we focus on bioinformatics and systems biology approaches in model organisms.

Topics of the Special Issue include:

  • Computational genomics in model organisms for biotechnology;
  • Bioinformatics approaches for life sciences;
  • Applications of genomics research in plant science;
  • Systems biology and networks;
  • Interdisciplinary research in genomics.

The current collection continues the series of post-conference Special Issues, presenting the highlights from the meetings on genetics and systems biology that were held in Russia at the BGRS-2020 and SIBS-2020 symposia.

BGRS (Bioinformatics of Genome Regulation and Structure) 2020 https://bgrssb.icgbio.ru/2020/
This is future event (in Russian)
http://way2drug.com/dr/symp_bcadd_2021.php

We also welcome novel materials beyond the conferences’ discussion.
 
Prof. Dr. Yuriy Lvovich Orlov
Dr. Anastasia A. Anashkina
Guest Editors

Manuscript Submission Information

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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. Life 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.

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Published Papers (10 papers)

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Editorial

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4 pages, 197 KiB  
Editorial
Life: Computational Genomics Applications in Life Sciences
by Yuriy L. Orlov and Anastasia A. Anashkina
Life 2021, 11(11), 1211; https://doi.org/10.3390/life11111211 - 9 Nov 2021
Cited by 3 | Viewed by 1863
Abstract
This Special Issue, “Life: Computational Genomics”, presents research articles on systems biology applications, computational genomics, and bioinformatics methods in life sciences [...] Full article
(This article belongs to the Special Issue Life: Computational Genomics)

Research

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17 pages, 4272 KiB  
Article
Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and Gnetum Species
by Avi Titievsky, Yuliya A. Putintseva, Elizaveta A. Taranenko, Sofya Baskin, Natalia V. Oreshkova, Elia Brodsky, Alexandra V. Sharova, Vadim V. Sharov, Julia Panov, Dmitry A. Kuzmin, Leonid Brodsky and Konstantin V. Krutovsky
Life 2021, 11(11), 1234; https://doi.org/10.3390/life11111234 - 15 Nov 2021
Cited by 3 | Viewed by 3386
Abstract
Repetitive elements (RE) and transposons (TE) can comprise up to 80% of some plant genomes and may be essential for regulating their evolution and adaptation. The “repeatome” information is often unavailable in assembled genomes because genomic areas of repeats are challenging to assemble [...] Read more.
Repetitive elements (RE) and transposons (TE) can comprise up to 80% of some plant genomes and may be essential for regulating their evolution and adaptation. The “repeatome” information is often unavailable in assembled genomes because genomic areas of repeats are challenging to assemble and are often missing from final assembly. However, raw genomic sequencing data contain rich information about RE/TEs. Here, raw genomic NGS reads of 10 gymnosperm species were studied for the content and abundance patterns of their “repeatome”. We utilized a combination of alignment on databases of repetitive elements and de novo assembly of highly repetitive sequences from genomic sequencing reads to characterize and calculate the abundance of known and putative repetitive elements in the genomes of 10 conifer plants: Pinus taeda, Pinus sylvestris, Pinus sibirica, Picea glauca, Picea abies, Abies sibirica, Larix sibirica, Juniperus communis, Taxus baccata, and Gnetum gnemon. We found that genome abundances of known and newly discovered putative repeats are specific to phylogenetically close groups of species and match biological taxa. The grouping of species based on abundances of known repeats closely matches the grouping based on abundances of newly discovered putative repeats (kChains) and matches the known taxonomic relations. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
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18 pages, 3419 KiB  
Article
Stochastic Effects in Retrotransposon Dynamics Revealed by Modeling under Competition for Cellular Resources
by Sergey Pavlov, Vitaly V. Gursky, Maria Samsonova, Alexander Kanapin and Anastasia Samsonova
Life 2021, 11(11), 1209; https://doi.org/10.3390/life11111209 - 9 Nov 2021
Cited by 3 | Viewed by 1950
Abstract
Transposons are genomic elements that can relocate within a host genome using a ‘cut’- or ‘copy-and-paste’ mechanism. They make up a significant part of many genomes, serve as a driving force for genome evolution, and are linked with Mendelian diseases and cancers. Interactions [...] Read more.
Transposons are genomic elements that can relocate within a host genome using a ‘cut’- or ‘copy-and-paste’ mechanism. They make up a significant part of many genomes, serve as a driving force for genome evolution, and are linked with Mendelian diseases and cancers. Interactions between two specific retrotransposon types, autonomous (e.g., LINE1/L1) and nonautonomous (e.g., Alu), may lead to fluctuations in the number of these transposons in the genome over multiple cell generations. We developed and examined a simple model of retrotransposon dynamics under conditions where transposon replication machinery competed for cellular resources: namely, free ribosomes and available energy (i.e., ATP molecules). Such competition is likely to occur in stress conditions that a malfunctioning cell may experience as a result of a malignant transformation. The modeling revealed that the number of actively replicating LINE1 and Alu elements in a cell decreases with the increasing competition for resources; however, stochastic effects interfere with this simple trend. We stochastically simulated the transposon dynamics in a cell population and showed that the population splits into pools with drastically different transposon behaviors. The early extinction of active Alu elements resulted in a larger number of LINE1 copies occurring in the first pool, as there was no competition between the two types of transposons in this pool. In the other pool, the competition process remained and the number of L1 copies was kept small. As the level of available resources reached a critical value, both types of dynamics demonstrated an increase in noise levels, and both the period and the amplitude of predator–prey oscillations rose in one of the cell pools. We hypothesized that the presented dynamical effects associated with the impact of the competition for cellular resources inflicted on the dynamics of retrotransposable elements could be used as a characteristic feature to assess a cell state, or to control the transposon activity. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
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11 pages, 249 KiB  
Article
Study of Early Onset Schizophrenia: Associations of GRIN2A and GRIN2B Polymorphisms
by Evgeniya G. Poltavskaya, Olga Yu. Fedorenko, Elena G. Kornetova, Anton J. M. Loonen, Alexander N. Kornetov, Nikolay A. Bokhan and Svetlana A. Ivanova
Life 2021, 11(10), 997; https://doi.org/10.3390/life11100997 - 22 Sep 2021
Cited by 18 | Viewed by 2783
Abstract
Background: Schizophrenia is a complex mental disorder with a high heritability. Dysfunction of the N-methyl-D-aspartate (NMDA)-type glutamate receptors may be involved in the pathogenesis of schizophrenia. In this study, we examined the contribution of GRIN2A and GRIN2B (Glutamate Ionotropic Receptor NMDA Type Subunit [...] Read more.
Background: Schizophrenia is a complex mental disorder with a high heritability. Dysfunction of the N-methyl-D-aspartate (NMDA)-type glutamate receptors may be involved in the pathogenesis of schizophrenia. In this study, we examined the contribution of GRIN2A and GRIN2B (Glutamate Ionotropic Receptor NMDA Type Subunit 2A/2B) polymorphisms to the clinical features of schizophrenia, such as the leading symptoms, the type of course, and the age of onset. Methods: A population of 402 Russian patients with schizophrenia from the Siberian region was investigated. Genotyping of seventeen single-nucleotide polymorphisms (SNPs) in GRIN2A and GRIN2B was performed using QuantStudio™ 3D Digital PCR System Life Technologies amplifier using TaqMan Validated SNP Genotyping Assay kits (Applied Biosystems). The results were analyzed using Chi-square and the Fisher’s exact tests. Results: We found an association of GRIN2A rs7206256 and rs11644461 and GRIN2B rs7313149 with the early onset (before the age of 18 years old) schizophrenia. We did not reveal any associations of GRIN2A and GRIN2B polymorphisms with leading (positive vs. negative) symptoms or type of course (continuous vs. episodic) of schizophrenia. Conclusions: In the study, we confirmed the involvement of the GRIN2A and GRIN2B genes in the early onset of schizophrenia in a Russian population of the Siberian region. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
9 pages, 980 KiB  
Communication
Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations
by Alexander Igoshin, Nikolay Yudin, Ruslan Aitnazarov, Andrey A. Yurchenko and Denis M. Larkin
Life 2021, 11(9), 959; https://doi.org/10.3390/life11090959 - 13 Sep 2021
Cited by 10 | Viewed by 3095
Abstract
Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes [...] Read more.
Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
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16 pages, 2799 KiB  
Article
Genomic and Ancestral Variation Underlies the Severity of COVID-19 Clinical Manifestation in Individuals of European Descent
by Priyanka Upadhyai, Gokul Suresh, Rahul Parit and Ranajit Das
Life 2021, 11(9), 921; https://doi.org/10.3390/life11090921 - 5 Sep 2021
Cited by 4 | Viewed by 3484
Abstract
The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by a wide spectrum of clinical phenotypes ranging from asymptomatic to symptomatic with mild or moderate presentation and severe disease. COVID-19 susceptibility, severity and recovery have [...] Read more.
The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by a wide spectrum of clinical phenotypes ranging from asymptomatic to symptomatic with mild or moderate presentation and severe disease. COVID-19 susceptibility, severity and recovery have demonstrated high variability worldwide. Variances in the host genetic architecture may underlie the inter-individual and population-scale differences in COVID-19 presentation. We performed a genome-wide association analysis employing the genotyping data from AncestryDNA for COVID-19 patients of European descent and used asymptomatic subjects as the control group. We identified 621 genetic variants that were significantly distinct between asymptomatic and acutely symptomatic COVID-19 patients (multiple-testing corrected p-value < 0.001). These variants were found to be associated with pathways governing host immunity, such as interferon, interleukin and cytokine signalling, and known COVID-19 comorbidities, such as obesity and cholesterol metabolism. Further, our ancestry analysis revealed that the asymptomatic COVID-19 patients possess discernibly higher proportions of the Ancestral North Eurasian (ANE) and Eastern Hunter-Gatherer (EHG) ancestry, which was introduced to Europe through Bell Beaker culture (Yamnaya related) and lower fractions of Western Hunter-Gatherer (WHG) ancestry, while severely symptomatic patients have higher fractions of WHG and lower ANE/EHG ancestral components, thereby delineating the likely ancestral differences between the two groups. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
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14 pages, 1587 KiB  
Article
Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia
by Siroj Bakoev, Anatoly Kolosov, Faridun Bakoev, Olga Kostyunina, Nekruz Bakoev, Timofey Romanets, Olga Koshkina and Lyubov Getmantseva
Life 2021, 11(8), 861; https://doi.org/10.3390/life11080861 - 22 Aug 2021
Cited by 6 | Viewed by 2377
Abstract
Intensive selection raises the efficiency of pig farming considerably, but it also promotes the accumulation of homozygosity, which can lead to an increase in inbreeding and the accumulation of deleterious variation. The analysis of segments homozygous-by-descent (HBD) and non-HBD segments in purebred and [...] Read more.
Intensive selection raises the efficiency of pig farming considerably, but it also promotes the accumulation of homozygosity, which can lead to an increase in inbreeding and the accumulation of deleterious variation. The analysis of segments homozygous-by-descent (HBD) and non-HBD segments in purebred and crossbred pigs is of great interest. Research was carried out on 657 pigs, of which there were Large White (LW, n = 280), Landrace (LR, n = 218) and F1 female (♂LR × ♀LW) (F1, n = 159). Genotyping was performed using the GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc., USA). To identify HBD segments and estimate autozygosity (inbreeding coefficient), we used the multiple HBD classes model. LW pigs exhibited 50,420 HBD segments, an average of 180 per animal; LR pigs exhibited 33,586 HBD segments, an average of 154 per animal; F1 pigs exhibited 21,068 HBD segments, an average of 132 per animal. The longest HBD segments in LW were presented in SSC1, SSC13 and SSC15; in LR, in SSC1; and in F1, in SSC15. In these segments, 3898 SNPs localized in 1252 genes were identified. These areas overlap with 441 QTLs (SSC1—238 QTLs; SSC13—101 QTLs; and SSC15—102 QTLs), including 174 QTLs for meat and carcass traits (84 QTLs—fatness), 127 QTLs for reproduction traits (100 QTLs—litter traits), 101 for production traits (69 QTLs—growth and 30 QTLs—feed intake), 21 QTLs for exterior traits (9 QTLs—conformation) and 18 QTLs for health traits (13 QTLs—blood parameters). Thirty SNPs were missense variants. Whilst estimating the potential for deleterious variation, six SNPs localized in the NEDD4, SEC11C, DCP1A, CCT8, PKP4 and TENM3 genes were identified, which may show deleterious variation. A high frequency of potential deleterious variation was noted for LR in DCP1A, and for LW in TENM3 and PKP4. In all cases, the genotype frequencies in F1 were intermediate between LR and LW. The findings presented in our work show the promise of genome scanning for HBD as a strategy for studying population history, identifying genomic regions and genes associated with important economic traits, as well as deleterious variation. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
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15 pages, 3885 KiB  
Article
RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints
by Bo Song, Mengyun Jiang and Lei Gao
Life 2021, 11(7), 701; https://doi.org/10.3390/life11070701 - 16 Jul 2021
Cited by 10 | Viewed by 3424
Abstract
Ribo-seq, also known as ribosome profiling, refers to the sequencing of ribosome-protected mRNA fragments (RPFs). This technique has greatly advanced our understanding of translation and facilitated the identification of novel open reading frames (ORFs) within untranslated regions or non-coding sequences as well as [...] Read more.
Ribo-seq, also known as ribosome profiling, refers to the sequencing of ribosome-protected mRNA fragments (RPFs). This technique has greatly advanced our understanding of translation and facilitated the identification of novel open reading frames (ORFs) within untranslated regions or non-coding sequences as well as the identification of non-canonical start codons. However, the widespread application of Ribo-seq has been hindered because obtaining periodic RPFs requires a highly optimized protocol, which may be difficult to achieve, particularly in non-model organisms. Furthermore, the periodic RPFs are too short (28 nt) for accurate mapping to polyploid genomes, but longer RPFs are usually produced with a compromise in periodicity. Here we present RiboNT, a noise-tolerant ORF predictor that can utilize RPFs with poor periodicity. It evaluates RPF periodicity and automatically weighs the support from RPFs and codon usage before combining their contributions to identify translated ORFs. The results demonstrate the utility of RiboNT for identifying both long and small ORFs using RPFs with either good or poor periodicity. We implemented the pipeline on a dataset of RPFs with poor periodicity derived from membrane-bound polysomes of Arabidopsis thaliana seedlings and identified several small ORFs (sORFs) evolutionarily conserved in diverse plant species. RiboNT should greatly broaden the application of Ribo-seq by minimizing the requirement of RPF quality and allowing the use of longer RPFs, which is critical for organisms with complex genomes because these RPFs can be more accurately mapped to the position from which they were derived. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
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8 pages, 391 KiB  
Article
Genomic Regions and Candidate Genes Linked to Capped Hock in Pig
by Lyubov Getmantseva, Maria Kolosova, Faridun Bakoev, Anna Zimina and Siroj Bakoev
Life 2021, 11(6), 510; https://doi.org/10.3390/life11060510 - 31 May 2021
Cited by 5 | Viewed by 2212
Abstract
Capped hock affects the exterior of pedigree pigs, making them unsalable and resulting in a negative impact on the efficiency of pig-breeding centers. The purpose of this paper was to carry out pilot studies aimed at finding genomic regions and genes linked to [...] Read more.
Capped hock affects the exterior of pedigree pigs, making them unsalable and resulting in a negative impact on the efficiency of pig-breeding centers. The purpose of this paper was to carry out pilot studies aimed at finding genomic regions and genes linked to the capped hock in pigs. The studies were carried out on Landrace pigs (n = 75) and Duroc pigs (n = 70). To identify genomic regions linked to capped hock in pigs, we used smoothing FST statistics. Genotyping was performed with GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc, San Diego, CA, USA). The research results showed 70 SNPs linked to capped hock in Landrace (38 SNPs) and Duroc (32 SNPs). The identified regions overlapped with QTLs related with health traits (blood parameters) and meat and carcass traits (fatness). In total, 31 genes were identified (i.e., 17 genes in Landrace, 14 genes in Durocs). Three genes appeared in both the Landrace and Duroc groups, including A2ML1 (SSC5), ROBO2 (SSC13), and MSI1 (SSC14). We identified genomic regions directly or indirectly linked to capped hock, which thus might contribute to identifying genetic variants and using them as genetic markers in pig breeding. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
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19 pages, 8576 KiB  
Systematic Review
A Minimum Set of Physiological Parameters to Diagnose Obstructive Sleep Apnea Syndrome Using Non-Invasive Portable Monitors. A Systematic Review
by Ángel Serrano Alarcón, Natividad Martínez Madrid and Ralf Seepold
Life 2021, 11(11), 1249; https://doi.org/10.3390/life11111249 - 17 Nov 2021
Cited by 8 | Viewed by 2970
Abstract
Introduction. Despite its high accuracy, polysomnography (PSG) has several drawbacks for diagnosing obstructive sleep apnea (OSA). Consequently, multiple portable monitors (PMs) have been proposed. Objective. This systematic review aims to investigate the current literature to analyze the sets of physiological parameters captured by [...] Read more.
Introduction. Despite its high accuracy, polysomnography (PSG) has several drawbacks for diagnosing obstructive sleep apnea (OSA). Consequently, multiple portable monitors (PMs) have been proposed. Objective. This systematic review aims to investigate the current literature to analyze the sets of physiological parameters captured by a PM to select the minimum number of such physiological signals while maintaining accurate results in OSA detection. Methods. Inclusion and exclusion criteria for the selection of publications were established prior to the search. The evaluation of the publications was made based on one central question and several specific questions. Results. The abilities to detect hypopneas, sleep time, or awakenings were some of the features studied to investigate the full functionality of the PMs to select the most relevant set of physiological signals. Based on the physiological parameters collected (one to six), the PMs were classified into sets according to the level of evidence. The advantages and the disadvantages of each possible set of signals were explained by answering the research questions proposed in the methods. Conclusions. The minimum number of physiological signals detected by PMs for the detection of OSA depends mainly on the purpose and context of the sleep study. The set of three physiological signals showed the best results in the detection of OSA. Full article
(This article belongs to the Special Issue Life: Computational Genomics)
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