Special Issue "Structure and Evolution of Genome"

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

Deadline for manuscript submissions: closed (30 November 2015)

Special Issue Editor

Guest Editor
Prof. Dr. Alexander Bolshoy

Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Haifa, Israel
Website | E-Mail
Interests: comparative genomics; molecular evolution; computational virology; machine-learning algorithms for sequence analysis

Special Issue Information

Dear Colleagues,

The present Special Issue of Life is devoted to a relatively new field of science, Evolutionary Genomics. In principle, we welcome all kind of manuscripts related to any question that can be asked about the evolution of genomes. Here are some examples:

  • How do genomes, or parts of genomes, change in size during evolution?
  • Why do some species have more coding DNA (that is, more genes or longer genes) than other species?
  • Why do some species have more non-coding DNA than others?
  • Which genes are unique to each species, and which genes are shared with other species?
  • How are genes arranged in a genome?
  • The evolution and arrangement of splicing enhancers and silencers
  • When have genomic changes have occurred?

Prof. Dr. Alexander Bolshoy
Guest Editor

Manuscript Submission Information

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Keywords

  • gene structure evolution
  • genome rearrangements
  • GC-content
  • origin of ORFans
  • chromatin structure
  • splicing codes

Published Papers (5 papers)

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Research

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Open AccessArticle
Gene-Family Extension Measures and Correlations
Received: 2 June 2016 / Revised: 18 July 2016 / Accepted: 18 July 2016 / Published: 3 August 2016
PDF Full-text (984 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that [...] Read more.
The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that size of gene family and size of genome are positively correlated. Additionally, it was found that several atypical microbes deviated from the observed general trend. In this study, we reexamined these associations on a larger dataset consisting of 1484 prokaryotic genomes and using several ranking approaches. We applied ranking methods in such a way that genomes with lower numbers of gene copies would have lower rank. Until now only simple ranking methods were used; we applied the Kemeny optimal aggregation approach as well. Regression and correlation analysis were utilized in order to accurately quantify and characterize the relationships between measures of paralog indices and genome size. In addition, boxplot analysis was employed as a method for outlier detection. We found that, in general, all paralog indexes positively correlate with an increase of genome size. As expected, different groups of atypical prokaryotic genomes were found for different types of paralog quantities. Mycoplasmataceae and Halobacteria appeared to be among the most interesting candidates for further research of evolution through gene duplication. Full article
(This article belongs to the Special Issue Structure and Evolution of Genome)
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Open AccessArticle
Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals
Received: 18 March 2016 / Revised: 28 June 2016 / Accepted: 12 July 2016 / Published: 15 July 2016
Cited by 4 | PDF Full-text (1058 KB) | HTML Full-text | XML Full-text
Abstract
The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which [...] Read more.
The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important. Full article
(This article belongs to the Special Issue Structure and Evolution of Genome)
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Graphical abstract

Open AccessArticle
Support Values for Genome Phylogenies
Received: 7 December 2015 / Revised: 3 February 2016 / Accepted: 23 February 2016 / Published: 7 March 2016
Cited by 1 | PDF Full-text (599 KB) | HTML Full-text | XML Full-text
Abstract
We have recently developed a distance metric for efficiently estimating the number of substitutions per site between unaligned genome sequences. These substitution rates are called “anchor distances” and can be used for phylogeny reconstruction. Most phylogenies come with bootstrap support values, which are [...] Read more.
We have recently developed a distance metric for efficiently estimating the number of substitutions per site between unaligned genome sequences. These substitution rates are called “anchor distances” and can be used for phylogeny reconstruction. Most phylogenies come with bootstrap support values, which are computed by resampling with replacement columns of homologous residues from the original alignment. Unfortunately, this method cannot be applied to anchor distances, as they are based on approximate pairwise local alignments rather than the full multiple sequence alignment necessary for the classical bootstrap. We explore two alternatives: pairwise bootstrap and quartet analysis, which we compare to classical bootstrap. With simulated sequences and 53 human primate mitochondrial genomes, pairwise bootstrap gives better results than quartet analysis. However, when applied to 29 E. coli genomes, quartet analysis comes closer to the classical bootstrap. Full article
(This article belongs to the Special Issue Structure and Evolution of Genome)
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Open AccessArticle
Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch
Received: 17 December 2015 / Revised: 20 January 2016 / Accepted: 25 January 2016 / Published: 29 January 2016
Cited by 2 | PDF Full-text (1356 KB) | HTML Full-text | XML Full-text
Abstract
A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a [...] Read more.
A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragment of an amino acid sequence and by a phylogenetic profile of a protein. No such integral clustering with the corresponding functions can be found in the public domain. The putative regulons of the transcription factors Ycf28 and Ycf29 encoded in the plastids were identified using the clustering and the database. A regulation of translation initiation was proposed for the ycf24 gene in plastids of certain red algae and apicomplexans as well as a regulation of a putative gene in apicoplasts of Babesia spp. and Theileria parva. The conserved regulation of the ycf24 gene expression and specificity alternation of the transcription factor Ycf28 were shown in the plastids. A phylogenetic tree of plastids was generated for the rhodophytic branch. The hypothesis of the origin of apicoplasts from the common ancestor of all apicomplexans from plastids of red algae was confirmed. Full article
(This article belongs to the Special Issue Structure and Evolution of Genome)
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Other

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Open AccessOpinion
Ultra Large Gene Families: A Matter of Adaptation or Genomic Parasites?
Received: 9 May 2016 / Revised: 27 June 2016 / Accepted: 20 July 2016 / Published: 8 August 2016
Cited by 5 | PDF Full-text (1317 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly) deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution [...] Read more.
Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly) deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution of ultra large gene families on long and short evolutionary time scales. In particular, we focus on a family of NACHT-domain and leucine-rich-repeat-containing (NLR)-genes, which we previously found in large numbers to occupy one chromosome arm of the zebrafish genome. We were interested to see whether such a tight clustering is characteristic for ultra large gene families. Our data reconfirm that most gene family inflations are lineage-specific, but we can only identify very few gene clusters. Based on our observations we hypothesise that, beyond a certain size threshold, ultra large gene families continue to proliferate in a mechanism we term “run-away evolution”. This process might ultimately lead to the failure of genomic integrity and drive species to extinction. Full article
(This article belongs to the Special Issue Structure and Evolution of Genome)
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