Tracing the Evolution of the Plastome and Mitogenome in the Chloropicophyceae Uncovered Convergent tRNA Gene Losses and a Variant Plastid Genetic Code

GBE Tracing the Evolution of the Plastome and Mitogenome in the Chloropicophyceae Uncovered Convergent tRNA Gene Losses and a Variant Plastid Genetic Code Monique Turmel1, Adriana Lopes dos Santos2,3, Christian Otis1, Roxanne Sergerie1, and Claude Lemieux1,* 1 2 Asian School of the Environment, Nanyang Technological University, Singapore 3 CNRS, Sorbonne Universite, UMR 7144 Station Biologique de Roscoff, Roscoff, France *Corresponding author: E-mail: . Accepted: March 30, 2019 Data deposition: This project has been deposited at GenBank under the accessions MK085986-MK086011. Abstract The tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (Chloropicon and Chloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/ contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with the trnI(cau) and trnL(uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance of trnI(cau) from the plastome in the Chloroparvula lineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine in Chloroparvula. This noncanonical genetic code has not previously been uncovered in plastids. Key words: prasinophyte green algae, Picocystis salinarum, chloroplast genome, mitochondrial genome, phylogenomic analyses, AUA codon reassignment. Introduction Prasinophytes constitute a paraphyletic assemblage of unicellular, morphologically diversified, and predominantly marine green algae at the base of the Chlorophyta (Lemieux et al. 2014; Sym 2015; Leliaert et al. 2016). Apart from the tiny algae belonging to the Mamiellophyceae, which are well known for their important contributions to phytoplankton communities and to primary productivity (Rii et al. 2016), at least four other prasinophyte lineages (Prasinococcales, Pycnococcaceae, Chloropicophyceae, and Picocystophyceae) comprise species of small size (5 lm in diameter). A highly reduced, coccoid growth form is thought to confer a distinct advantage to planktonic green algae because the resulting higher surface area-to-volume ratio enhances the efficiency of nutrient uptake and also because a reduced size helps to escape predators and promotes buoyancy (Potter et al. 1997; Grimsley et al. 2015; Sym 2015). Analyses of 18S rRNA metabarcoding data sets have demonstrated that the distribution pattern and habitat of prasinophytes in marine waters vary markedly depending upon the lineage and species examined (Rii et al. 2016; Lopes dos Santos, Gourvil, et al. 2017; Tragin and Vaulot 2018). The members of the three genera found in ß The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Genome Biol. Evol. 11(4):1275–1292. doi:10.1093/gbe/evz074 Advance Access publication April 1, 2019 1275 Departement de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Integrative et des Systèmes, Universite Laval, Quebec City, Quebec, Canada GBE Turmel et al. 1276 of core chlorophytes (Turmel and Lemieux 2018). As revealed by gene mapping on evolutionary trees, the plastome sustained losses of many genes several times independently during the evolution of prasinophyte picoalgae (Turmel and Lemieux 2018). Because the nuclear genomes of mamiellalean picoalgae also feature a reduced size and a high gene density (Grimsley et al. 2015), it appears that miniaturization of both the nuclear genome and plastome occurred along cell reduction during evolution. The Chloropicon primus plastome is currently the sole organelle genome reported for the Chloropicophyceae and at 64.3 kb, it is the smallest plastome documented among photosynthetic green algae (Lemieux et al. 2014). Unlike the plastomes of the picoalgae Ostreococcus tauri, Micromonas commode, and Picocystis salinarum, it has not retained the large inverted repeat (IR) encoding the rRNA genes, a feature commonly found in green algae and land plants (forming together the Viridiplantae or Chloroplastida). Despite the widespread occurrence of the IR, however, multiple independent events of losses were inferred in the Chlorophyta (at least four losses in prasinophytes, seven in the Trebouxiophyceae, three in the Ulvophyceae, and two in the Chlorophyceae) (Turmel and Lemieux 2018). As observed for other picoalgae, the plastome gene order of Chloropicon primus is substantially scrambled relative to most other prasinophyte plastomes (Lemieux et al. 2014). Within the Mamiellales order, however, the Ostreococcus and Micromonas plastomes are highly similar in size and gene content and are essentially colinear. To date, complete or almost complete mitogenome sequences are available for only five prasinophyte picoalgae, which represent the Mamiellales, Prasinococcales, and Pycnococcaceae (Robbens et al. 2007; Worden et al. 2009; Turmel et al. 2010; Moreau et al. 2012; Pombert et al. 2013). They show important variation in size (24.3 kb in Pycnococcus provasolii to 54.5 kb in Prasinoderma coloniale) and gene content (36 in Pycnococcus to 63 in Ostreococcus and Micromonas), but no general trend toward a reduced gene complement when they are compared to the mitogenomes of Nephroselmis (45.2 kb, 66 genes) (Turmel et al. 1999a), Pyramimonas parkeae (NIES254: 53.4 kb, 58 genes; SCCAP K-0007: 43.3 kb, 59 genes) (Hrda et al. 2017; Satjarak et al. 2017), and Cymbomonas tetramitiformis (73.5 kb, 56 genes) (Satjarak et al. 2017). As d (...truncated)