Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution

Molecular Phylogenetics and Evolution
Karolina FučíkováLouise A Lewis

Abstract

Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny - yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution.

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Citations

Oct 12, 2016·BMC Evolutionary Biology·Joana F CostaHeroen Verbruggen
May 10, 2017·Proceedings of the National Academy of Sciences of the United States of America·Melissa S RothKrishna K Niyogi
Nov 9, 2017·International Journal of Molecular Sciences·Geng-Ming LinChung-Der Hsiao
Jan 11, 2019·Genome Biology and Evolution·Tereza ŠevcíkováMarek Eliáš
Jan 31, 2019·Molecular Biology and Evolution·Emmanuel NoutahiBernd Franz Lang
Feb 7, 2019·Systematic Biology·Suman NeupanePaul O Lewis
Oct 17, 2019·Genome Biology and Evolution·David Žihala, Marek Eliáš
May 31, 2019·PeerJ·Karolina FučíkováLouise A Lewis
Nov 7, 2021·Molecular Phylogenetics and Evolution·Luo ChenXiao-Quan Wang

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