Special Issue "Feature Paper 2012"

Guest Editor
Prof. Dr. J. Peter W. Young
Department of Biology, University of York, Heslington, York YO10 5DD, UK
Website: http://www.york.ac.uk/biology/research/ecology-evolution/j-peter-w-young/
E-Mail: jpy1@york.ac.uk
Phone: +44 1904 328630
Fax: +44 1904 328505
Interests: bacterial genomes; population genetics; phylogenomics; phylogenetics; genome projects; genetic diversity

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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 quarterly 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 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Type of Paper: Review
Title: Origins of Entirely New Genes
Author: Kenji Ikehara
Affiliation: Nara Study Center of The Open University of Japan; E-Mail: sc58059@cc.nara-wu.ac.jp
Abstract: Two main theories have been proposed for the origins of new genes. One is the duplication theory proposed by S. Ohno (1970) and the other is the exon shuffling theory provided by Gilbert et al. (1997). But, it must be pointed out that both theories are insufficient for explaining the origins of new genes, since the ideas require pre-existing ancestor genes. On the other hand, I have proposed another hypothesis for creation of entirely new genes or the first family genes, suggesting that they were created from non-stop frames on anti-sense sequences of GC-rich genes or GC-NSF(a), and of double-stranded GC-rich (SNS)n and (GNC)n genes in the respective eras of the universal, SNS and GNC genetic codes, where S and N mean G or C and one of four nucleotides, respectively. In parallel, I have presented protein 0th-order structures or specific amino acid compositions, in which random joining of amino acids could produce water-soluble globular proteins at a high probability, such as 10 amino acids encoded by SNS and GNC-encoding [GADV]-amino acids, where [GADV] means glycine [G], alanine [A], aspartic acid [D] and valine [V]. In this review, I will discuss on the principle and the reason why entirely new genes could be produced from those anti-sense sequences of the GC-rich genes, base on a view point of the protein 0th-order structures, which contribute to form globular proteins with slightly flexible structures more than extant proteins.

Type of Paper: Article
Title: Ancestral Prokaryotic Genome Reconstruction at the Gene and Replicon Scales
Authors: Kuan Yang, Lenwood S. Heath, and Joao C. Setubal
Affiliation: Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748  sala 911, 05508-000 São Paulo, SP, Brazil; E-Mail: joao.c.setubal@gmail.com
Abstract: While a large number of computational methods exist for gene-centric phylogenyanalysis, not much has been done for detailed ancestral genome reconstruction. Accurate ancestral genome reconstruction can be understood as a phylogenetic study with more de-tails than a phylogenetic tree reconstruction. We developed a new computational system (REGEN) for ancestral bacterial genome reconstruction at both gene and replicon level. RE-GEN reconstructs gene content, a set of contiguous gene runs, and replicon structure for each genome. Furthermore, along each branch of the phylogenetic tree, it reconstructs possible evolutionary events, including gene level events such as insertion and deletion, and replicon level events such as replicon fission and fusion. The reconstruction can be carried out using either the maximum parsimony or maximum likelihood method. The system has been extensively evaluated using both real and simulated data and applied to a group of species in the Rhizobiales order in α-proteobacteria. To the authors knowledge, this system is the first attempt to perform model-free neighboring gene pairs based ancestral genome reconstruction supporting both maximum parsimony and maximum likelihood methods at both gene and replicon scales.