Abstract
Prochlorococcus marinus, one of the most abundant marine cyanobacteria in the global ocean, is classified into low‐light (LL) and high‐light (HL) adapted ecotypes. These two adapted ecotypes differ in their ecophysiological characteristics, especially whether adapted for growth at high‐light or low‐light intensities. However, some evolutionary relationships of Prochlorococcus phylogeny remain to be resolved, such as whether the strains SS120 and MIT9211 form a monophyletic group. We use the Natural Vector (NV) method to represent the sequence in order to identify the phylogeny of the Prochlorococcus. The natural vector method is alignment free without any model assumptions. This study added the covariances of amino acids in protein sequence to the natural vector method. Based on these new natural vectors, we can compute the Hausdorff distance between the two clades which represents the dissimilarity. This method enables us to systematically analyze both the dataset of ribosomal proteomes and the dataset of 16s‐23s rRNA sequences in order to reconstruct the phylogeny of Prochlorococcus. Furthermore, we apply classification to inspect the relationship of SS120 and MIT9211. From the reconstructed phylogenetic trees and classification results, we may conclude that the SS120 does not cluster with MIT9211. This study demonstrates a new method for performing phylogenetic analysis. The results confirm that these two strains do not form a monophyletic clade in the phylogeny of Prochlorococcus.
Highlights
The oceans play an important role in global nutrient cycling and climate regulation
We develop a new natural vector method which adds the covariances of amino acids to the existing natural vector method (Deng et al, 2011) and use it infer the phylogeny of Prochlorococcus with increased accuracy
Our mathematical approach characterizes the protein sequence as a new natural vector according to the information in the sequence
Summary
The oceans play an important role in global nutrient cycling and climate regulation. The genus Prochlorococcus is a marine cyanobacteria that dominates most tropical and temperate oceans (Kettler et al, 2007; Moore, Rocap, & Chisholm, 1998; Murata et al, 2017; Partensky, Hess, & Vaulot, 1999). The alignment-free natural vector method has been widely used in studying the evolutionary of virus and bacteria (Deng, Yu, Liang, He, & Yau, 2011; Povolotskaya & Kondrashov, 2010; Tian et al, 2015; Yau, Yu, & He, 2008; Yu, Cheng, He, & Yau, 2011; Yu, He, & Yau, 2013c; Yu et al, 2013a,b; Zhao, Wan, He, & Yau, 2016) This method is based on the normalized distribution of amino acids in protein sequence without any model assumption. In order to illustrate the results clearly, we add the classification of the 12 Prochlorococcus strains to analyze the similarity of SS120 and MIT9211
Sign-in/Register to view highlights & summary 
Published Version (
Free)
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.
