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The classification of orphans is improved by combining searches in both proteomes and genomes
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab). Swedish e-Science Research Center (SeRC), Sweden.ORCID-id: 0000-0002-7115-9751
2017 (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
Abstract [en]

The identification of de novo created genes is important as it provides a glimpse on the evolutionary processes of gene creation. Potential de novo created genes are identified by selecting genes that have no homologs outside a particular species, but for an accurate detection this identification needs to be correct.

Genes without any homologs are often referred to as orphans; in addition to de novo created ones, fast evolving genes or genes lost in all related genomes might also be classified as orphans. The identification of orphans is dependent on: (i) a method to detect homologs and (ii) a database including genes from related genomes.

Here, we set out to investigate how the detection of orphans is influenced by these two factors. Using Saccharomyces cerevisiae we identify that best strategy is to use a combination of searching annotated proteins and a six-frame translation of all ORFs from closely related genomes. Using this strategy we obtain a set of 54 orphans in Drosophila melanogaster and 38 in Drosophila pseudoobscura, significantly less than what is reported in some earlier studies.

Ort, förlag, år, upplaga, sidor
2017.
Nationell ämneskategori
Biologiska vetenskaper
Forskningsämne
biokemi med inriktning mot bioinformatik
Identifikatorer
URN: urn:nbn:se:su:diva-149079DOI: 10.1101/185983OAI: oai:DiVA.org:su-149079DiVA, id: diva2:1158350
Tillgänglig från: 2017-11-20 Skapad: 2017-11-20 Senast uppdaterad: 2020-02-20Bibliografiskt granskad
Ingår i avhandling
1. Orphan Genes Bioinformatics: Identification and properties of de novo created genes
Öppna denna publikation i ny flik eller fönster >>Orphan Genes Bioinformatics: Identification and properties of de novo created genes
2017 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2017
Nyckelord
bioinformatics, de novo, orphans, evolutionary genetics
Nationell ämneskategori
Biologiska vetenskaper
Forskningsämne
biokemi med inriktning mot bioinformatik
Identifikatorer
urn:nbn:se:su:diva-149168 (URN)978-91-7797-085-9 (ISBN)978-91-7797-086-6 (ISBN)
Disputation
2018-01-12, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (Engelska)
Opponent
Handledare
Anmärkning

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

Tillgänglig från: 2017-12-20 Skapad: 2017-11-20 Senast uppdaterad: 2017-12-20Bibliografiskt granskad

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Av författaren/redaktören
Basile, WalterSalvatore, MarcoElofsson, Arne
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Institutionen för biokemi och biofysikScience for Life Laboratory (SciLifeLab)
Biologiska vetenskaper

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