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31 pages, 5816 KiB

Open AccessArticle

A Method for the Structure-Based, Genome-Wide Analysis of Bacterial Intergenic Sequences Identifies Shared Compositional and Functional Features

by Leonardo Lenzini, Francesca Di Patti, Roberto Livi, Marco Fondi, Renato Fani and Alessio Mengoni

Genes 2019, 10(10), 834; https://doi.org/10.3390/genes10100834 - 22 Oct 2019

Viewed by 2774

Abstract

In this paper, we propose a computational strategy for performing genome-wide analyses of intergenic sequences in bacterial genomes. Following similar directions of a previous paper, where a method for genome-wide analysis of eucaryotic Intergenic sequences was proposed, here we developed a tool for [...] Read more.

In this paper, we propose a computational strategy for performing genome-wide analyses of intergenic sequences in bacterial genomes. Following similar directions of a previous paper, where a method for genome-wide analysis of eucaryotic Intergenic sequences was proposed, here we developed a tool for implementing similar concepts in bacteria genomes. This allows us to (i) classify intergenic sequences into clusters, characterized by specific global structural features and (ii) draw possible relations with their functional features. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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11 pages, 1696 KiB

Open AccessArticle

Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites

by Yaqing Ou and James O. McInerney

Genes 2019, 10(9), 648; https://doi.org/10.3390/genes10090648 - 28 Aug 2019

Cited by 2 | Viewed by 4348

Abstract

The formation of new genes by combining parts of existing genes is an important evolutionary process. Remodelled genes, which we call composites, have been investigated in many species, however, their distribution across all of life is still unknown. We set out to examine [...] Read more.

The formation of new genes by combining parts of existing genes is an important evolutionary process. Remodelled genes, which we call composites, have been investigated in many species, however, their distribution across all of life is still unknown. We set out to examine the extent to which genomes from cells and mobile genetic elements contain composite genes. We identify composite genes as those that show partial homology to at least two unrelated component genes. In order to identify composite and component genes, we constructed sequence similarity networks (SSNs) of more than one million genes from all three domains of life, as well as viruses and plasmids. We identified non-transitive triplets of nodes in this network and explored the homology relationships in these triplets to see if the middle nodes were indeed composite genes. In total, we identified 221,043 (18.57%) composites genes, which were distributed across all genomic and functional categories. In particular, the presence of composite genes is statistically more likely in eukaryotes than prokaryotes. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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14 pages, 1413 KiB

Open AccessArticle

GWEHS: A Genome-Wide Effect Sizes and Heritability Screener

by Eugenio López-Cortegano and Armando Caballero

Genes 2019, 10(8), 558; https://doi.org/10.3390/genes10080558 - 24 Jul 2019

Cited by 3 | Viewed by 3956

Abstract

During the last decade, there has been a huge development of Genome-Wide Association Studies (GWAS), and thousands of loci associated to complex traits have been detected. These efforts have led to the creation of public databases of GWAS results, making a huge source [...] Read more.

During the last decade, there has been a huge development of Genome-Wide Association Studies (GWAS), and thousands of loci associated to complex traits have been detected. These efforts have led to the creation of public databases of GWAS results, making a huge source of information available on the genetic background of many diverse traits. Here we present GWEHS (Genome-Wide Effect size and Heritability Screener), an open-source online application to screen loci associated to human complex traits and diseases from the NHGRI-EBI GWAS Catalog. This application provides a way to explore the distribution of effect sizes of loci affecting these traits, as well as their contribution to heritability. Furthermore, it allows for making predictions on the change in the expected mean effect size, as well as in the heritability as new loci are found. The application enables inferences on whether the additive contribution of loci expected to be discovered in the future will be able to explain the estimates of familial heritability for the different traits. We illustrate the use of this tool, compare some of the results obtained with those from a previous meta-analysis, and discuss its uses and limitations. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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15 pages, 2306 KiB

Open AccessArticle

Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes

by Charley G. P. McCarthy and David A. Fitzpatrick

Genes 2019, 10(7), 521; https://doi.org/10.3390/genes10070521 - 10 Jul 2019

Cited by 12 | Viewed by 8148

Abstract

Although the pan-genome concept originated in prokaryote genomics, an increasing number of eukaryote species pan-genomes have also been analysed. However, there is a relative lack of software intended for eukaryote pan-genome analysis compared to that available for prokaryotes. In a previous study, we [...] Read more.

Although the pan-genome concept originated in prokaryote genomics, an increasing number of eukaryote species pan-genomes have also been analysed. However, there is a relative lack of software intended for eukaryote pan-genome analysis compared to that available for prokaryotes. In a previous study, we analysed the pan-genomes of four model fungi with a computational pipeline that constructed pan-genomes using the synteny-dependent Pan-genome Ortholog Clustering Tool (PanOCT) approach. Here, we present a modified and improved version of that pipeline which we have called Pangloss. Pangloss can perform gene prediction for a set of genomes from a given species that the user provides, constructs and optionally refines a species pan-genome from that set using PanOCT, and can perform various functional characterisation and visualisation analyses of species pan-genome data. To demonstrate Pangloss’s capabilities, we constructed and analysed a species pan-genome for the oleaginous yeast Yarrowia lipolytica and also reconstructed a previously-published species pan-genome for the opportunistic respiratory pathogen Aspergillus fumigatus. Pangloss is implemented in Python, Perl and R and is freely available under an open source GPLv3 licence via GitHub. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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25 pages, 2331 KiB

Open AccessArticle

Going Deeper into High and Low Phylogenetic Relationships of Protura

by Antonio Carapelli, Yun Bu, Wan-Jun Chen, Francesco Nardi, Chiara Leo, Francesco Frati and Yun-Xia Luan

Genes 2019, 10(4), 292; https://doi.org/10.3390/genes10040292 - 10 Apr 2019

Cited by 7 | Viewed by 5734

Abstract

Proturans are small, wingless, soil-dwelling arthropods, generally associated with the early diversification of Hexapoda. Their bizarre morphology, together with conflicting results of molecular studies, has nevertheless made their classification ambiguous. Furthermore, their limited dispersal capability (due to the primarily absence of wings) and [...] Read more.

Proturans are small, wingless, soil-dwelling arthropods, generally associated with the early diversification of Hexapoda. Their bizarre morphology, together with conflicting results of molecular studies, has nevertheless made their classification ambiguous. Furthermore, their limited dispersal capability (due to the primarily absence of wings) and their euedaphic lifestyle have greatly complicated species-level identification. Mitochondrial and nuclear markers have been applied herein to investigate and summarize proturan systematics at different hierarchical levels. Two new mitochondrial genomes are described and included in a phylum-level phylogenetic analysis, but the position of Protura could not be resolved with confidence due to an accelerated rate of substitution and extensive gene rearrangements. Mitochondrial and nuclear loci were also applied in order to revise the intra-class systematics, recovering three proturan orders and most of the families/subfamilies included as monophyletic, with the exception of the subfamily Acerentominae. At the species level, most morphologically described species were confirmed using molecular markers, with some exceptions, and the advantages of including nuclear, as well as mitochondrial, markers and morphology are discussed. At all levels, an enlarged taxon sampling and the integration of data from different sources may be of significant help in solving open questions that still persist on the evolutionary history of Protura. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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12 pages, 2177 KiB

Open AccessArticle

ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements

by Fei Yuan, Hoa Nguyen and Dan Graur

Genes 2019, 10(3), 181; https://doi.org/10.3390/genes10030181 - 26 Feb 2019

Cited by 6 | Viewed by 3581

Abstract

Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying parallel and convergent replacements involves multiple steps and computational routines, such as multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, [...] Read more.

Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying parallel and convergent replacements involves multiple steps and computational routines, such as multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, topology tests, and simulation of sequence evolution. Here, we present ProtParCon, a Python 3 package that provides a common interface for users to process molecular data and identify parallel and convergent amino acid replacements in orthologous protein sequences. By integrating several widely used programs for computational biology, ProtParCon implements general functions for handling multiple sequence alignment, ancestral-state reconstruction, maximum-likelihood phylogenetic tree inference, and sequence simulation. ProtParCon also contains a built-in pipeline that automates all these sequential steps, and enables quick identification of observed and expected parallel and convergent amino acid replacements under different evolutionary assumptions. The most up-to-date version of ProtParCon, including scripts containing user tutorials, the full API reference and documentation are publicly and freely available under an open source MIT License via GitHub. The latest stable release is also available on PyPI (the Python Package Index). Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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18 pages, 3461 KiB

Open AccessArticle

Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians

by Umberto Esposito, Ranajit Das, Syakir Syed, Mehdi Pirooznia and Eran Elhaik

Genes 2018, 9(12), 625; https://doi.org/10.3390/genes9120625 - 12 Dec 2018

Cited by 13 | Viewed by 10889

Abstract

The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day [...] Read more.

The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, however, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA. Further the high missingness rates in ancient—and oftentimes haploid—DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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17 pages, 2000 KiB

Open AccessArticle

Cryptic Diversity Hidden within the Leafminer Genus Liriomyza (Diptera: Agromyzidae)

by Antonio Carapelli, Abir Soltani, Chiara Leo, Matteo Vitale, Moez Amri and Jouda Mediouni-Ben Jemâa

Genes 2018, 9(11), 554; https://doi.org/10.3390/genes9110554 - 15 Nov 2018

Cited by 8 | Viewed by 4857

Abstract

Leafminer insects of the genus Liriomyza are small flies whose larvae feed on the internal tissue of some of the most important crop plants for the human diet. Several of these pest species are highly uniform from the morphological point of view, meaning [...] Read more.

Leafminer insects of the genus Liriomyza are small flies whose larvae feed on the internal tissue of some of the most important crop plants for the human diet. Several of these pest species are highly uniform from the morphological point of view, meaning molecular data represents the only reliable taxonomic tool useful to define cryptic boundaries. In this study, both mitochondrial and nuclear molecular markers have been applied to investigate the population genetics of some Tunisian populations of the polyphagous species Liriomyza cicerina, one of the most important pest of chickpea cultivars in the whole Mediterranean region. Molecular data have been collected on larvae isolated from chickpea, faba bean, and lentil leaves, and used for population genetics, phylogenetics, and species delimitation analyses. Results point toward high differentiation levels between specimens collected on the three different legume crops, which, according to the species delimitation methods, are also sufficient to define incipient species differentiation and cryptic species occurrence, apparently tied up with host choice. Genetic data have also been applied for a phylogenetic comparison among Liriomyza species, further confirming their decisive role in the systematic studies of the genus. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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Review

Jump to: Research

15 pages, 1023 KiB

Open AccessReview

Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients

by Catarina Branco and Miguel Arenas

Genes 2018, 9(10), 506; https://doi.org/10.3390/genes9100506 - 18 Oct 2018

Cited by 5 | Viewed by 3901

Abstract

Selecting among alternative scenarios of human evolution is nowadays a common methodology to investigate the history of our species. This strategy is usually based on computer simulations of genetic data under different evolutionary scenarios, followed by a fitting of the simulated data with [...] Read more.

Selecting among alternative scenarios of human evolution is nowadays a common methodology to investigate the history of our species. This strategy is usually based on computer simulations of genetic data under different evolutionary scenarios, followed by a fitting of the simulated data with the real data. A recent trend in the investigation of ancestral evolutionary processes of modern humans is the application of genetic gradients as a measure of fitting, since evolutionary processes such as range expansions, range contractions, and population admixture (among others) can lead to different genetic gradients. In addition, this strategy allows the analysis of the genetic causes of the observed genetic gradients. Here, we review recent findings on the selection among alternative scenarios of human evolution based on simulated genetic gradients, including pros and cons. First, we describe common methodologies to simulate genetic gradients and apply them to select among alternative scenarios of human evolution. Next, we review previous studies on the influence of range expansions, population admixture, last glacial period, and migration with long-distance dispersal on genetic gradients for some regions of the world. Finally, we discuss this analytical approach, including technical limitations, required improvements, and advice. Although here we focus on human evolution, this approach could be extended to study other species. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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