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A Tale of Genes and Genomes

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

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 60808

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Prof. Dr. Mario Ventura

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Guest Editor

Dipartimento Di Biologia, Università degli Studi di Bari, Bari, Italy
Interests: cytogenetics; genome evolution; chromosome evolution; pericentromere; centromere; neocentromere organization and evolution

Prof. Dr. Francesca Antonacci

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Guest Editor

Department of Genetics and Microbiology, Università degli Studi di Bari, Bari, Italy
Interests: structural variation; genomic inversions; segmental duplications; genomic disorders; genome evolution

Special Issue Information

Dear Colleagues,

Variability is the source on which selective pressure acts, allowing genome evolution and adaptation. Large-scale comparative sequencing promises to reconstruct the evolutionary history of the human genome, and to highlight the functional genetic differences between human and other species.

Great interest has been recently focused on sequencing and assembling complex regions of the genome enriched in segmental duplications and repetitive elements, which, on the one hand may significantly contribute to the emergence of novel genes and species diversification, and on the other hand may trigger genomic rearrangements associated with human disease.

In this Special Issue, we are interested in publishing research articles and reviews on genome organization and gene family evolution. In particular, submissions should be focused on the relevant mechanisms of evolutionary change and gene innovations that tell us tales of the species and their organisms.

Prof. Mario Ventura
Prof. Francesca Antonacci
Guest Editors

Manuscript Submission Information

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Keywords

genome structural variations
genome organization
gene families evolution

Published Papers (12 papers)

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Editorial

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4 pages, 167 KiB

Open AccessEditorial

Special Issue: A Tale of Genes and Genomes

by Mario Ventura and Francesca Antonacci

Genes 2021, 12(5), 774; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12050774 - 19 May 2021

Viewed by 1705

Abstract

Variability is the source on which selective pressure acts, allowing genome evolution and adaptation [...] Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

Research

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11 pages, 604 KiB

Open AccessArticle

Multiple FGF4 Retrocopies Recently Derived within Canids

by Kevin Batcher, Peter Dickinson, Kimberly Maciejczyk, Kristin Brzeski, Sheida Hadji Rasouliha, Anna Letko, Cord Drögemüller, Tosso Leeb and Danika Bannasch

Genes 2020, 11(8), 839; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11080839 - 23 Jul 2020

Cited by 11 | Viewed by 3469

Abstract

Two transcribed retrocopies of the fibroblast growth factor 4 (FGF4) gene have previously been described in the domestic dog. An FGF4 retrocopy on chr18 is associated with disproportionate dwarfism, while an FGF4 retrocopy on chr12 is associated with both disproportionate dwarfism and intervertebral disc disease (IVDD). In this study, whole-genome sequencing data were queried to identify other FGF4 retrocopies that could be contributing to phenotypic diversity in canids. Additionally, dogs with surgically confirmed IVDD were assayed for novel FGF4 retrocopies. Five additional and distinct FGF4 retrocopies were identified in canids including a copy unique to red wolves (Canis rufus). The FGF4 retrocopies identified in domestic dogs were identical to domestic dog FGF4 haplotypes, which are distinct from modern wolf FGF4 haplotypes, indicating that these retrotransposition events likely occurred after domestication. The identification of multiple, full length FGF4 retrocopies with open reading frames in canids indicates that gene retrotransposition events occur much more frequently than previously thought and provide a mechanism for continued genetic and phenotypic diversity in canids. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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22 pages, 4622 KiB

Open AccessArticle

Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum

by Umar Akram, Yuhan Song, Chengzhen Liang, Muhammad Ali Abid, Muhammad Askari, Aye Aye Myat, Mubashir Abbas, Waqas Malik, Zulfiqar Ali, Sandui Guo, Rui Zhang and Zhigang Meng

Genes 2020, 11(7), 803; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11070803 - 16 Jul 2020

Cited by 25 | Viewed by 4455

Abstract

Cotton is an important economic crop affected by different abiotic stresses at different developmental stages. Salinity limits the growth and productivity of crops worldwide. Na⁺/H⁺ antiporters play a key role during the plant development and in its tolerance to salt stress. The aim of the present study was a genome-wide characterization and expression pattern analysis under the salinity stress of the sodium-proton antiporter (NHX) of Gossypium barbadense in comparison with Gossypium hirsutum. In G. barbadense, 25 NHX genes were identified on the basis of the Na⁺_H⁺ exchanger domain. All except one of the G. barbadense NHX transporters have an Amiloride motif that is a known inhibitor of Na⁺ ions in plants. A phylogenetic analysis inferred three classes of GbNHX genes—viz., Vac (GbNHX1, 2 and 4), Endo (GbNHX6), and PM (GbNHX7). A high number of the stress-related cis-acting elements observed in promoters show their role in tolerance against abiotic stresses. The Ka/Ks values show that the majority of GbNHX genes are subjected to strong purifying selection under the course of evolution. To study the functional divergence of G. barbadense NHX transporters, the real-time gene expression was analyzed under salt stress in the root, stem, and leaf tissues. In G. barbadense, the expression was higher in the stem, while in G. hirsutum the leaf and root showed a high expression. Moreover, our results revealed that NHX2 homologues in both species have a high expression under salinity stress at higher time intervals, followed by NHX7. The protein-protein prediction study revealed that GbNHX7 is involved in the CBL-CIPK protein interaction pathway. Our study also provided valuable information explaining the molecular mechanism of Na⁺ transport for the further functional study of Gossypium NHX genes. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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15 pages, 842 KiB

Open AccessArticle

Investigating Human Mitochondrial Genomes in Single Cells

by Maria Angela Diroma, Angelo Sante Varvara, Marcella Attimonelli, Graziano Pesole and Ernesto Picardi

Genes 2020, 11(5), 534; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11050534 - 11 May 2020

Cited by 5 | Viewed by 3079

Abstract

Mitochondria host multiple copies of their own small circular genome that has been extensively studied to trace the evolution of the modern eukaryotic cell and discover important mutations linked to inherited diseases. Whole genome and exome sequencing have enabled the study of mtDNA in a large number of samples and experimental conditions at single nucleotide resolution, allowing the deciphering of the relationship between inherited mutations and phenotypes and the identification of acquired mtDNA mutations in classical mitochondrial diseases as well as in chronic disorders, ageing and cancer. By applying an ad hoc computational pipeline based on our MToolBox software, we reconstructed mtDNA genomes in single cells using whole genome and exome sequencing data obtained by different amplification methodologies (eWGA, DOP-PCR, MALBAC, MDA) as well as data from single cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) in which mtDNA sequences are expected as a byproduct of the technology. We show that assembled mtDNAs, with the exception of those reconstructed by MALBAC and DOP-PCR methods, are quite uniform and suitable for genomic investigations, enabling the study of various biological processes related to cellular heterogeneity such as tumor evolution, neural somatic mosaicism and embryonic development. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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21 pages, 2111 KiB

Open AccessArticle

Evolution of the Human Chromosome 13 Synteny: Evolutionary Rearrangements, Plasticity, Human Disease Genes and Cancer Breakpoints

by Rita Scardino, Vanessa Milioto, Anastasia A. Proskuryakova, Natalia A. Serdyukova, Polina L. Perelman and Francesca Dumas

Genes 2020, 11(4), 383; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11040383 - 01 Apr 2020

Cited by 12 | Viewed by 3551

Abstract

The history of each human chromosome can be studied through comparative cytogenetic approaches in mammals which permit the identification of human chromosomal homologies and rearrangements between species. Comparative banding, chromosome painting, Bacterial Artificial Chromosome (BAC) mapping and genome data permit researchers to formulate hypotheses about ancestral chromosome forms. Human chromosome 13 has been previously shown to be conserved as a single syntenic element in the Ancestral Primate Karyotype; in this context, in order to study and verify the conservation of primate chromosomes homologous to human chromosome 13, we mapped a selected set of BAC probes in three platyrrhine species, characterised by a high level of rearrangements, using fluorescence in situ hybridisation (FISH). Our mapping data on Saguinus oedipus, Callithrix argentata and Alouatta belzebul provide insight into synteny of human chromosome 13 evolution in a comparative perspective among primate species, showing rearrangements across taxa. Furthermore, in a wider perspective, we have revised previous cytogenomic literature data on chromosome 13 evolution in eutherian mammals, showing a complex origin of the eutherian mammal ancestral karyotype which has still not been completely clarified. Moreover, we analysed biomedical aspects (the OMIM and Mitelman databases) regarding human chromosome 13, showing that this autosome is characterised by a certain level of plasticity that has been implicated in many human cancers and diseases. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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20 pages, 1825 KiB

Open AccessArticle

Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing

by Daniela C. Soto, Colin Shew, Mira Mastoras, Joshua M. Schmidt, Ruta Sahasrabudhe, Gulhan Kaya, Aida M. Andrés and Megan Y. Dennis

Genes 2020, 11(3), 276; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11030276 - 04 Mar 2020

Cited by 10 | Viewed by 8229

Abstract

Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two additional Pan troglodytes verus individuals, one of whom carries 13% admixture from Pan troglodytes troglodytes. We performed optical mapping of both individuals followed by nanopore sequencing of one individual. Filtering for larger variants (>10 kbp) and combined with genotyping of SVs using short-read data from the Great Ape Genome Project, we identified 425 deletions and 59 inversions, of which 88 and 36, respectively, were novel. Compared with gene expression in humans, we found a significant enrichment of chimpanzee genes with differential expression in lymphoblastoid cell lines and induced pluripotent stem cells, both within deletions and near inversion breakpoints. We examined chromatin-conformation maps from human and chimpanzee using these same cell types and observed alterations in genomic interactions at SV breakpoints. Finally, we focused on 56 genes impacted by SVs in >90% of chimpanzees and absent in humans and gorillas, which may contribute to chimpanzee-specific features. Sequencing a greater set of individuals from diverse subspecies will be critical to establish the complete landscape of genetic variation in chimpanzees. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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24 pages, 8889 KiB

Open AccessArticle

Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates

by Flavia Angela Maria Maggiolini, Ludovica Mercuri, Francesca Antonacci, Fabio Anaclerio, Francesco Maria Calabrese, Nicola Lorusso, Alberto L’Abbate, Melanie Sorensen, Giuliana Giannuzzi, Evan E. Eichler, Claudia Rita Catacchio and Mario Ventura

Genes 2020, 11(2), 213; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11020213 - 18 Feb 2020

Cited by 6 | Viewed by 4213

Abstract

POTE (prostate, ovary, testis, and placenta expressed) genes belong to a primate-specific gene family expressed in prostate, ovary, and testis as well as in several cancers including breast, prostate, and lung cancers. Due to their tumor-specific expression, POTEs are potential oncogenes, therapeutic targets, and biomarkers for these malignancies. This gene family maps within human and primate segmental duplications with a copy number ranging from two to 14 in different species. Due to the high sequence identity among the gene copies, specific efforts are needed to assemble these loci in order to correctly define the organization and evolution of the gene family. Using single-molecule, real-time (SMRT) sequencing, in silico analyses, and molecular cytogenetics, we characterized the structure, copy number, and chromosomal distribution of the POTE genes, as well as their expression in normal and disease tissues, and provided a comparative analysis of the POTE organization and gene structure in primate genomes. We were able, for the first time, to de novo sequence and assemble a POTE tandem duplication in marmoset that is misassembled and collapsed in the reference genome, thus revealing the presence of a second POTE copy. Taken together, our findings provide comprehensive insights into the evolutionary dynamics of the primate-specific POTE gene family, involving gene duplications, deletions, and long interspersed nuclear element (LINE) transpositions to explain the actual repertoire of these genes in human and primate genomes. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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14 pages, 2516 KiB

Open AccessArticle

Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2

by Feichen Shen and Jeffrey M. Kidd

Genes 2020, 11(2), 141; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11020141 - 29 Jan 2020

Cited by 11 | Viewed by 4599

Abstract

Gene duplication is a major mechanism for the evolution of gene novelty, and copy-number variation makes a major contribution to inter-individual genetic diversity. However, most approaches for studying copy-number variation rely upon uniquely mapping reads to a genome reference and are unable to distinguish among duplicated sequences. Specialized approaches to interrogate specific paralogs are comparatively slow and have a high degree of computational complexity, limiting their effective application to emerging population-scale data sets. We present QuicK-mer2, a self-contained, mapping-free approach that enables the rapid construction of paralog-specific copy-number maps from short-read sequence data. This approach is based on the tabulation of unique k-mer sequences from short-read data sets, and is able to analyze a 20X coverage human genome in approximately 20 min. We applied our approach to newly released sequence data from the 1000 Genomes Project, constructed paralog-specific copy-number maps from 2457 unrelated individuals, and uncovered copy-number variation of paralogous genes. We identify nine genes where none of the analyzed samples have a copy number of two, 92 genes where the majority of samples have a copy number other than two, and describe rare copy number variation effecting multiple genes at the APOBEC3 locus. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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18 pages, 2407 KiB

Open AccessArticle

The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes

by Dong In Kim, Wataru Kai, Sho Hosoya, Mana Sato, Aoi Nozawa, Miwa Kuroyanagi, Yuka Jo, Satoshi Tasumi, Hiroaki Suetake, Yuzuru Suzuki and Kiyoshi Kikuchi

Genes 2019, 10(12), 1027; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10121027 - 10 Dec 2019

Cited by 7 | Viewed by 4386

Abstract

Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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25 pages, 33304 KiB

Open AccessArticle

Genome-Wide Distribution, Expression and Function Analysis of the U-Box Gene Family in Brassica oleracea L.

by Dengke Hu, Qinqin Xie, Qianying Liu, Tonghong Zuo, Hecui Zhang, Yizhong Zhang, Xiaoping Lian and Liquan Zhu

Genes 2019, 10(12), 1000; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10121000 - 02 Dec 2019

Cited by 16 | Viewed by 3877

Abstract

The plant U-box (PUB) protein family plays an important role in plant growth and development. The U-box gene family has been well studied in Arabidopsis thaliana, Brassica rapa, rice, etc., but there have been no systematic studies in Brassica oleracea. In this study, we performed genome-wide identification and evolutionary analysis of the U-box protein family of B. oleracea. Firstly, based on the Brassica database (BRAD) and the Bolbase database, 99 Brassica oleracea PUB genes were identified and divided into seven groups (I–VII). The BoPUB genes are unevenly distributed on the nine chromosomes of B. oleracea, and there are tandem repeat genes, leading to family expansion from the A. thaliana genome to the B. oleracea genome. The protein interaction network, GO annotation, and KEGG pathway enrichment analysis indicated that the biological processes and specific functions of the BoPUB genes may mainly involve abiotic stress. RNA-seq transcriptome data of different pollination times revealed spatiotemporal expression specificity of the BoPUB genes. The differential expression profile was consistent with the results of RT-qPCR analysis. Additionally, a large number of pollen-specific cis-acting elements were found in promoters of differentially expressed genes (DEG), which verified that these significantly differentially expressed genes after self-pollination (SP) were likely to participate in the self-incompatibility (SI) process, including gene encoding ARC1, a well-known downstream protein of SI in B. oleracea. Our study provides valuable information indicating that the BoPUB genes participates not only in the abiotic stress response, but are also involved in pollination. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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Review

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40 pages, 829 KiB

Open AccessReview

An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

by Tanguy Lallemand, Martin Leduc, Claudine Landès, Carène Rizzon and Emmanuelle Lerat

Genes 2020, 11(9), 1046; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11091046 - 04 Sep 2020

Cited by 56 | Viewed by 13901

Abstract

Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences. Indeed, these bioinformatic approaches differ according to the underlying duplication mechanism. Hence, understanding the specificity of the duplicated genes of interest is a great asset for tool selection and should be taken into account when exploring a biological question. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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28 pages, 5102 KiB

Open AccessReview

Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals

by Rachele Antonacci, Serafina Massari, Giovanna Linguiti, Anna Caputi Jambrenghi, Francesco Giannico, Marie-Paule Lefranc and Salvatrice Ciccarese

Genes 2020, 11(6), 624; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11060624 - 05 Jun 2020

Cited by 25 | Viewed by 4226

Abstract

T lymphocytes are the principal actors of vertebrates’ cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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