The Bryopsis hypnoides Plastid Genome: Multimeric Forms and Complete Nucleotide Sequence

Abstract

Background Bryopsis hypnoides Lamouroux is a siphonous green alga, and its extruded protoplasm can aggregate spontaneously in seawater and develop into mature individuals. The chloroplast of B. hypnoides is the biggest organelle in the cell and shows strong autonomy. To better understand this organelle, we sequenced and analyzed the chloroplast genome of this green alga.Principal FindingsA total of 111 functional genes, including 69 potential protein-coding genes, 5 ribosomal RNA genes, and 37 tRNA genes were identified. The genome size (153,429 bp), arrangement, and inverted-repeat (IR)-lacking structure of the B. hypnoides chloroplast DNA (cpDNA) closely resembles that of Chlorella vulgaris. Furthermore, our cytogenomic investigations using pulsed-field gel electrophoresis (PFGE) and southern blotting methods showed that the B. hypnoides cpDNA had multimeric forms, including monomer, dimer, trimer, tetramer, and even higher multimers, which is similar to the higher order organization observed previously for higher plant cpDNA. The relative amounts of the four multimeric cpDNA forms were estimated to be about 1, 1/2, 1/4, and 1/8 based on molecular hybridization analysis. Phylogenetic analyses based on a concatenated alignment of chloroplast protein sequences suggested that B. hypnoides is sister to all Chlorophyceae and this placement received moderate support.ConclusionAll of the results suggest that the autonomy of the chloroplasts of B. hypnoides has little to do with the size and gene content of the cpDNA, and the IR-lacking structure of the chloroplasts indirectly demonstrated that the multimeric molecules might result from the random cleavage and fusion of replication intermediates instead of recombinational events.

Photoprotective Non-photochemical Quenching Does Not Prevent Kleptoplasts From Net Photoinactivation

“…The hypothesis was based on the observation that kleptoplasts of Bryopsis hypnoides did not encode ftsH in the chloroplast (cp) genome but are degrading at a faster rate than kleptoplasts of A. acetabulum, in which cp genome ftsH is encoded. Unfortunately, the original publication of the Bryopsis hypnoides genome (Lü et al, 2011) lacked the annotation of ftsH, which was re-annotated later (Leliaert and Lopez-Bautista, 2015). Here, we determined that the ftsH gene in all previously sequenced and annotated cp genomes of Ulvophyceae (see Supplementary Table 1) lack the M41 domain.…”

Phylogeny and Molecular Evolution of the Green Algae

“…All of the available ptDNA sequences for green algae assemble as genome-sized circular molecules, but, like the mitochondrial and plastid DNAs from land plants, they probably exist in vivo as multigenome-sized branched linear forms, which can (as a byproduct of recombination-dependent replication) recombine to generate unit-sized circular molecules (Simpson & Stern, 2002;Bendich, 2004;. Recent data from the ptDNA of the ulvophyte Bryopsis hypnoides support this hypothesis (Lü et al, 2011).…”

“…Thus, it is significant that there are examples from each of the major green algal groups of species that have lost (or almost lost) their ptDNA inverted repeats. Examples include the charophyte green algae Staurastrum punctulatum and Zygnema circumcarinatum , the chlorophyceans F. terrestris and S. helveticum (Bélanger et al, 2006;Brouard et al, 2010), the prasinophytes P. provasolii and Monomastix (Turmel et al, 2009a), the ulvophyte B. hypnoides (Lü et al, 2011), and the trebouxiophytes L. terrestris and Helicosporidium sp. (de Koning & Keeling, 2006;de Cambiaire et al, 2007).…”

New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data

“…Most single and multigene phylogenies have provided weak or no support for monophyly of the class, but have instead supported two clades: one containing Oltmannsiellopsidales, Ulvales and Ulotrichales, the other consisting of Trentepohliales, Bryopsidales, Dasycladales and Cladophorales (e.g., Watanabe and Nakayama, 2007;Cocquyt et al, 2009;Lü et al, 2011). The earliest study providing stronger support for a monophyletic Ulvophyceae was based on phylogenetic analysis of eight nuclear and two plastid genes (Cocquyt et al, 2010).…”

“…Phylogenetic support for the Chlorophyceae clade is high in most single-and multi-gene molecular phylogenetic studies, but the monophyly of Ulvophyceae and Trebouxiophyceae is generally poorly supported (e.g., Lü et al, 2011;Novis et al, 2013) (Supplement S1). Nevertheless, the three classes have been treated as monophyletic so far, and as their respective relationships were explored, all three possible relationships among the classes have been proposed, depending on gene and taxon sampling and phylogenetic methods used (Supplement S1).…”