title: Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae).
abstract: The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages.
  
  
  
  To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. The earliest-diverging clade displayed Hafniomonas laevis and the Crucicarteria, and was followed by the Radicarteria and then by the Chloromonadinia. The latter lineage was sister to two superclades, one consisting of the Oogamochlamydinia and Reinhardtinia and the other of the Caudivolvoxa and Xenovolvoxa. To our surprise, the Jenufa species and the two spine-bearing green algae belonging to the Golenkinia and Treubaria genera were recovered in a highly supported monophyletic group that also included three taxa representing distinct families of the Sphaeropleales (Bracteacoccaceae, Mychonastaceae, and Scenedesmaceae).
  
  
  
  Our phylogenomic study advances our knowledge regarding the circumscription and internal structure of the Chlamydomonadales, suggesting that a previously unrecognized lineage is sister to the Sphaeropleales. In addition, it offers new insights into the flagellar structures of the founding members of both the Chlamydomonadales and Sphaeropleales.
authors.affiliation: Département de Biochimie, de Microbiologie et de Bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 ave de la Médecine, Pavillon Marchand, Québec, QC, G1V 0A6, Canada. claude.lemieux@bcm.ulaval.ca.
authors.forename: Claude
authors.initials: C
authors.lastname: Lemieux
authors.affiliation: Département de Biochimie, de Microbiologie et de Bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 ave de la Médecine, Pavillon Marchand, Québec, QC, G1V 0A6, Canada. antony.vincent.1@ulaval.ca.
authors.forename: Antony T
authors.initials: AT
authors.lastname: Vincent
authors.affiliation: Département de Biochimie, de Microbiologie et de Bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 ave de la Médecine, Pavillon Marchand, Québec, QC, G1V 0A6, Canada. aurelie.labarre.1@ulaval.ca.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Labarre
authors.affiliation: Département de Biochimie, de Microbiologie et de Bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 ave de la Médecine, Pavillon Marchand, Québec, QC, G1V 0A6, Canada. christian.otis@bcm.ulaval.ca.
authors.forename: Christian
authors.initials: C
authors.lastname: Otis
authors.affiliation: Département de Biochimie, de Microbiologie et de Bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 ave de la Médecine, Pavillon Marchand, Québec, QC, G1V 0A6, Canada. monique.turmel@bcm.ulaval.ca.
authors.forename: Monique
authors.initials: M
authors.lastname: Turmel
mesh_terms: D001499:Bayes Theorem; D000460:Chlorophyta / Q000145:classification* / Q000166:cytology / Q000235:genetics*; D018742:DNA, Chloroplast / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics
chemical_list: D018742:DNA, Chloroplast; D012337:RNA, Ribosomal, 18S