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The classification of orphans is improved by combining searches in both proteomes and genomes
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203Article in journal (Refereed) Submitted
Abstract [en]

The detection of genes without homologs (“orphans”) in other species is important, as it provides a glimpse on the evolutionary processes that create novel genes. However, for an unbiased view of such de novo gene creation the detection of these genes needs to be accurate. The estimation of the conservation, and in general the age determination of any gene, is dependent on two factors: (i) a method to detect homologs in a genome and (ii) a set of related genomes. Here, we set out to investigate how the detection of orphans is influenced be these factors. We show that when using multiple genomes and six-frame translations of complete genomes the number of orphans is significantly reduced, when compared with earlier studies. Given these premises we obtain a strict set of 34 orphan Saccharomyces cerevisiae genes, and show that the number of orphans in Drosophila melanogaster and Drosophila pseudoobscura can be reduced to only 30 and 17, respectively.

Place, publisher, year, edition, pages
2017.
National Category
Biological Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
URN: urn:nbn:se:su:diva-149079OAI: oai:DiVA.org:su-149079DiVA, id: diva2:1158350
Available from: 2017-11-20 Created: 2017-11-20 Last updated: 2017-11-29Bibliographically approved
In thesis
1. Orphan Genes Bioinformatics: Identification and properties of de novo created genes
Open this publication in new window or tab >>Orphan Genes Bioinformatics: Identification and properties of de novo created genes
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Even today, many genes are without any known homolog. These "orphans" are found in all species, from Viruses to Prokaryotes and Eukaryotes. For a portion of these genes, we might simply not have enough data to find homologs yet. Some of them are imported from taxonomically distant organisms via lateral transfer; others have homologs, but mutated beyond the point of recognition.

However, a sizeable fraction of orphan genes is unambiguously created via "de novo" mechanisms. The study of such novel genes can contribute to our understanding of the emergence of functional novelty and the adaptation of species to new ecological niches.

In this work, we first survey the field of orphan studies, and illustrate some of the common issues. Next, we analyze some of the intrinsic properties of orphans proteins, including secondary structure elements and Intrinsic Structural Disorder; specifically, we observe that in young proteins the relationship between these properties and the G+C content of their coding sequence is stronger than in older proteins.

We then tackle some of the methodological problems often found in orphan studies. We find that using evolutionarily close species, and sensitive, state-of-the art homology recognition methods is instrumental to the identification of a set of orphans enriched in de novo created ones.

Finally, we compare how intrinsic disorder is distributed in bacteria versus eukaryota. Eukaryotic proteins are longer and more disordered; the difference is to be attributed primarily to eukaryotic-specific domains and linker regions. In these sections of the proteins, a higher frequency of the disorder-promoting amino acid Serine can be observed in Eukaryotes.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2017
Keywords
bioinformatics, de novo, orphans, evolutionary genetics
National Category
Biological Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-149168 (URN)978-91-7797-085-9 (ISBN)978-91-7797-086-6 (ISBN)
Public defence
2018-01-12, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Manuscript.

Available from: 2017-12-20 Created: 2017-11-20 Last updated: 2017-12-20Bibliographically approved

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