The Open Bioinformatics Journal




ISSN: 1875-0362 ― Volume 11, 2018
RESEARCH ARTICLE

Long Non-coding RNAs in the Human Genome Acquired by Horizontal Gene Transfer



Rian Pierneef, Frederick J. Clasen, Oliver K. I. Bezuidt, Oleg N. Reva*
Centre for Bioinformatics and Computational Biology (CBCB), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa

Abstract

Background:

Horizontal gene transfer of mobile genetic elements is an essential component of prokaryotic evolution. These insertion events in eukaryotes and particularly in the human genome have been investigated by various methodologies with varying results.

Objective:

In this paper, we implement a sequence composition approach to investigate insertions of genomic islands in the human genome.

Methods:

A modified version of a prokaryotic GI identifier, SeqWord Gene Island Sniffer v.2.0, was used to predict genomic islands in the hg38 version of the human genome.

Results:

Predicted genomic islands were enriched with long non-coding RNAs and also contributed to the acquisition and modification of proteins associated with the immune system and gonad development, albeit to a lesser extent. The estimated rate of acquisition of these genomic islands in vertebrate genomes was non-linear with regards to species divergence times with an acceleration at the time of vertebrate land invasion and during the transition of prosimians to monkeys soon after the Cretaceous-Paleogene extinction.

Conclusion:

The rapid acquisition of non-conserved long non-coding RNAs in the human genome and probably in vertebrata genomes was facilitated by horizontal gene transfer. All predicted human genomic islands and supporting information are freely accessible from http://hislands.bi.up.ac.za.

Keywords: Genomic island, Mobile genetic element, Horizontal gene transfer, Evolution, Long non-coding RNA, Human genome.


Article Information


Identifiers and Pagination:

Year: 2018
Volume: 11
First Page: 182
Last Page: 196
Publisher Id: TOBIOIJ-11-182
DOI: 10.2174/1875036201811010182

Article History:

Received Date: 25/5/2018
Revision Received Date: 31/7/2018
Acceptance Date: 10/8/2018
Electronic publication date: 31/08/2018
Collection year: 2018

Article Metrics:

CrossRef Citations:
0

Total Statistics:

Full-Text HTML Views: 115
Abstract HTML Views: 65
PDF Downloads: 38
ePub Downloads: 93
Total Views/Downloads: 311

Unique Statistics:

Full-Text HTML Views: 83
Abstract HTML Views: 48
PDF Downloads: 30
ePub Downloads: 36
Total Views/Downloads: 197
Geographical View

© 2018 Pierneef et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: (https://creativecommons.org/licenses/by/4.0/legalcode). This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


* Address correspondence to the author at the Centre for Bioinformatics and Computational Biology (CBCB), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa, Tel: +27-12-420-5810, Fax: +27-12-4205800; E-mails: oleg.reva@up.ac.za; reva.oleg@gmail.com


Endorsements



"Open access will revolutionize 21st century knowledge work and accelerate the diffusion of ideas and evidence that support just in time learning and the evolution of thinking in a number of disciplines."


Daniel Pesut
(Indiana University School of Nursing, USA)

"It is important that students and researchers from all over the world can have easy access to relevant, high-standard and timely scientific information. This is exactly what Open Access Journals provide and this is the reason why I support this endeavor."


Jacques Descotes
(Centre Antipoison-Centre de Pharmacovigilance, France)

"Publishing research articles is the key for future scientific progress. Open Access publishing is therefore of utmost importance for wider dissemination of information, and will help serving the best interest of the scientific community."


Patrice Talaga
(UCB S.A., Belgium)

"Open access journals are a novel concept in the medical literature. They offer accessible information to a wide variety of individuals, including physicians, medical students, clinical investigators, and the general public. They are an outstanding source of medical and scientific information."


Jeffrey M. Weinberg
(St. Luke's-Roosevelt Hospital Center, USA)

"Open access journals are extremely useful for graduate students, investigators and all other interested persons to read important scientific articles and subscribe scientific journals. Indeed, the research articles span a wide range of area and of high quality. This is specially a must for researchers belonging to institutions with limited library facility and funding to subscribe scientific journals."


Debomoy K. Lahiri
(Indiana University School of Medicine, USA)

"Open access journals represent a major break-through in publishing. They provide easy access to the latest research on a wide variety of issues. Relevant and timely articles are made available in a fraction of the time taken by more conventional publishers. Articles are of uniformly high quality and written by the world's leading authorities."


Robert Looney
(Naval Postgraduate School, USA)

"Open access journals have transformed the way scientific data is published and disseminated: particularly, whilst ensuring a high quality standard and transparency in the editorial process, they have increased the access to the scientific literature by those researchers that have limited library support or that are working on small budgets."


Richard Reithinger
(Westat, USA)

"Not only do open access journals greatly improve the access to high quality information for scientists in the developing world, it also provides extra exposure for our papers."


J. Ferwerda
(University of Oxford, UK)

"Open Access 'Chemistry' Journals allow the dissemination of knowledge at your finger tips without paying for the scientific content."


Sean L. Kitson
(Almac Sciences, Northern Ireland)

"In principle, all scientific journals should have open access, as should be science itself. Open access journals are very helpful for students, researchers and the general public including people from institutions which do not have library or cannot afford to subscribe scientific journals. The articles are high standard and cover a wide area."


Hubert Wolterbeek
(Delft University of Technology, The Netherlands)

"The widest possible diffusion of information is critical for the advancement of science. In this perspective, open access journals are instrumental in fostering researches and achievements."


Alessandro Laviano
(Sapienza - University of Rome, Italy)

"Open access journals are very useful for all scientists as they can have quick information in the different fields of science."


Philippe Hernigou
(Paris University, France)

"There are many scientists who can not afford the rather expensive subscriptions to scientific journals. Open access journals offer a good alternative for free access to good quality scientific information."


Fidel Toldrá
(Instituto de Agroquimica y Tecnologia de Alimentos, Spain)

"Open access journals have become a fundamental tool for students, researchers, patients and the general public. Many people from institutions which do not have library or cannot afford to subscribe scientific journals benefit of them on a daily basis. The articles are among the best and cover most scientific areas."


M. Bendandi
(University Clinic of Navarre, Spain)

"These journals provide researchers with a platform for rapid, open access scientific communication. The articles are of high quality and broad scope."


Peter Chiba
(University of Vienna, Austria)

"Open access journals are probably one of the most important contributions to promote and diffuse science worldwide."


Jaime Sampaio
(University of Trás-os-Montes e Alto Douro, Portugal)

"Open access journals make up a new and rather revolutionary way to scientific publication. This option opens several quite interesting possibilities to disseminate openly and freely new knowledge and even to facilitate interpersonal communication among scientists."


Eduardo A. Castro
(INIFTA, Argentina)

"Open access journals are freely available online throughout the world, for you to read, download, copy, distribute, and use. The articles published in the open access journals are high quality and cover a wide range of fields."


Kenji Hashimoto
(Chiba University, Japan)

"Open Access journals offer an innovative and efficient way of publication for academics and professionals in a wide range of disciplines. The papers published are of high quality after rigorous peer review and they are Indexed in: major international databases. I read Open Access journals to keep abreast of the recent development in my field of study."


Daniel Shek
(Chinese University of Hong Kong, Hong Kong)

"It is a modern trend for publishers to establish open access journals. Researchers, faculty members, and students will be greatly benefited by the new journals of Bentham Science Publishers Ltd. in this category."


Jih Ru Hwu
(National Central University, Taiwan)


Browse Contents



Advertisements


Webmaster Contact: info@benthamopen.com
Copyright © 2018 Bentham Open