title: Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes.
abstract: The phylogenetic branching order of the green algal groups that gave rise to land plants remains uncertain despite its fundamental importance to understanding plant evolution. Previous studies have demonstrated that land plants evolved from streptophyte algae, but different lineages of streptophytes have been suggested to be the sister group of land plants. To better understand the evolutionary history of land plants and to determine the potential effects of "long-branch attraction" in phylogenetic reconstruction, we analyzed a chloroplast genome data set including three new chloroplast genomes from streptophyte algae: Coleochaetae orbicularis (Coleochaetales), Nitella hookeri (Charales), and Spirogyra communis (Zygnematales). We further applied a site pattern sorting method together with site- and time-heterogeneous models to investigate the branching order among streptophytes and land plants. Our chloroplast phylogenomic analyses support previous hypotheses based on nuclear data in placing Zygnematales alone, or a clade consisting of Coleochaetales plus Zygnematales, as the closest living relatives of land plants.
authors.affiliation: Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: Bojian
authors.initials: B
authors.lastname: Zhong
authors.forename: Zhenxiang
authors.initials: Z
authors.lastname: Xi
authors.forename: Vadim V
authors.initials: VV
authors.lastname: Goremykin
authors.forename: Richard
authors.initials: R
authors.lastname: Fong
authors.forename: Patricia A
authors.initials: PA
authors.lastname: McLenachan
authors.forename: Philip M
authors.initials: PM
authors.lastname: Novis
authors.forename: Charles C
authors.initials: CC
authors.lastname: Davis
authors.forename: David
authors.initials: D
authors.lastname: Penny
mesh_terms: D005075:Biological Evolution; D000460:Chlorophyta / Q000145:classification / Q000235:genetics*; D048028:DNA, Algal / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D019669:Embryophyta / Q000145:classification / Q000235:genetics*; D054628:Genome, Chloroplast; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D048028:DNA, Algal; D018742:DNA, Chloroplast
keywords: chloroplast genomes; heterogeneous models; land plants; phylogenomics; streptophyte algae