Abstract
The first complete genome that was sequenced at the beginning of the sequencing era was that of a phage, since then researchers throughout the world have been steadily describing and publishing genomes from a wide array of phages, uncovering the secrets of the most abundant and diverse biological entities known to man. Currently, we are experiencing an unprecedented rate of novel bacteriophage discovery, which can be seen from the fact that the amount of complete bacteriophage genome entries in public sequence repositories has more than doubled in the past 3 years and is steadily growing without showing any sign of slowing down. The amount of publicly available phage genome-related data can be overwhelming and has been summarized in literature before but quickly becomes out of date. Thus, the aim of this paper is to briefly outline currently available phage diversity data for public acknowledgment that could possibly encourage and stimulate future “depth” studies of particular groups of phages or their gene products.
Highlights
The first completely sequenced genome of a bacteriophage (MS2) was reported as early as 1976 (Fiers et al, 1976), it is due to the recent advancements in the throughput of sequencing technology and the growth of their affordability along with the development of omics approaches that have really pushed the limits of many studies in a range of biological fields, including the phage diversity research field (Goodwin et al, 2016)
Despite the self-explanatory fact that a metaviromics approach might be the fastest way to “mine” potentially useful phage genes from the environmental samples, broadening our understanding of the phage pangenome and pinpointing protein candidates for detailed phage-derived product studies, it strictly limits the possibilities of in-depth studies of a particular phage as a microbiological entity (Schoenfeld et al, 2010)
The amount of data generated during metagenomic studies have pushed phage researchers to develop and constantly improve tools that try to partly overcome some of these difficulties and make in silico predictions for some of the aforementioned unknown information purely from the sequencing data, but the positive predictive value of the algorithms used shows that these methods are still hypothetical for most of the novel candidate phage sequences for which no culture is present
Summary
The first completely sequenced genome of a bacteriophage (MS2) was reported as early as 1976 (Fiers et al, 1976), it is due to the recent advancements in the throughput of sequencing technology and the growth of their affordability along with the development of omics approaches that have really pushed the limits of many studies in a range of biological fields, including the phage diversity research field (Goodwin et al, 2016). 4,783 of the entries were found to be either sequences of the same phage under different accession numbers or phages falling over the current phage species percent identity demarcation criterion It was noted at this point, that at least 110 out of the deduplicated sequences represented archaeal viruses rather than bacteriophages (Abedon and Murray, 2013) and were, respectively, excluded, leaving 8,239 complete bacteriophage genomes for our phage genome overview. When comparing complete phage genome counts for phages infecting a particular bacterial genera, Mycobacterium phages are the most prominent among phages infecting other bacterial genera, with 1,328 phages that possibly represent a phage species It is evident within the phage community that this number is a result of the tremendous dedication of the staff involved in “Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES)” and their ability to masterfully involve undergraduates in what becomes their first bacteriophage diversity research endeavor (Jordan et al, 2014). Categorized, “small-sized” (100 kbp) genomes of phages are mostly found within a 150– 175 kbp size range (Figure 1C)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
