Hidden genetic diversity in the green alga Spirogyra (Zygnematophyceae, Streptophyta)

Abstract

Background: The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae) is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate.

Results: We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclear ribosomal DNA (SSU rDNA) strands of different origin. The resulting SSU rDNA sequences were used for phylogenetic analyses using complex evolutionary models (posterior probability, maximum likelihood, neighbor joining, and maximum parsimony methods). The sequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53 individual clones, but our results still support monophyly of the genus. Our data set did not contain a single slow-evolving taxon that would have been placed on a shorter branch compared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a secondary loss of the 1506 group I intron, which formed a long-branched group within the genus. The phylogenetic relationship to the genus Spirotaenia was not resolved satisfactorily. The genetic distance within the genus Spirogyra exceeded the distances measured within any other genus of the remaining Zygnemataceae included in this study.

Conclusion: Overall, we define eight distinct clades of Spirogyra, one of them including the genus Sirogonium. A large number of non-homoplasious synapomorphies (NHS; 114 NHS in total) was found for Spirogyra (41 NHS) and for each clade (totaling 73 NHS). This emphasizes the high genetic diversity of this genus and the distance to the remaining Zygnematophyceae.

Figure 1

Combined Zygnematophyceae and Spirogyra SSU rRNA phylogeny: Molecular phylogeny of Desmidiaceae, Peniaceae, Closteriaceae, Mesotaeniaceae and Zygnemataceae based on SSU alignment. The phylogenetic tree was inferred by maximum likelihood analyses of 1720 aligned positions of 33 taxa using PAUP* 4.0b10. TrN+G+I was chosen as best evolutionary model (base frequencies: A 0.25, C 0.23, G 0.27, T 0.25; rate matrix: A-C 1.0000, A-G 1.8721, A-T 1.0000, C-G 1.0000, C-T 4.5252, G-T 1.0000) with the proportion of invariable sites (I= 0.4608) and gamma distribution parameter (G= 0.6376). Posterior Probabilities (>95%; bold; calculated by MrBayes 3.1.2 using the covariation settings (3 million generations, trees from 4100 – 30000)) as well as bootstrap values (>50%) of the maximum likelihood (100 replicates; bold italic), neighbor-joining (1000 replicates; italic), and maximum parsimony (1000 replicates; not bold) are given in the tree (PP/ML/NJ/MP). No outgroup was used. ATT4, 5, 7 and 8 refer to alternative tree topologies tested with consel – please refer to Table 1 for details. Figure  1a: upper right corner: Combined Zygnematophyceae and Spirogyra SSU rRNA phylogeny (same as Figure  1) using 2 taxa as outgroup; numbers in brackets indicate number of taxa included in groups.

Figure 2

Spirogyra SSU rRNA phylogeny: Unrooted molecular phylogeny of Spirogyra based on SSU alignment. Individual clades are highlighted in white boxes; group with secondary loss of group I IC1 intron highlighted by light green-box. The phylogenetic tree was inferred by maximum likelihood analyses of 1645 aligned positions of 55 taxa using PAUP* 4.0b10. GTR+G+I was chosen as best evolutionary model (base frequencies: A 0.23, C 0.24, G 0.29, T 0.24; rate matrix: A-C 1.4341, A-G 2.6641, A-T 1.2357, C-G 1.6993, C-T 5.2526, G-T 1.0000) with the proportion of invariable sites (I= 0.6009) and gamma distribution parameter (G= 0.6856). Posterior Probabilities (>95%; bold; calculated by MrBayes 3.1.2 using the covariation settings (2 million generations, trees from 11070 – 20000)) as well as bootstrap values (>50%) of the maximum likelihood (100 replicates; bold italic), neighbor-joining (1000 replicates; italic), and maximum parsimony (1000 replicates; not bold) are given in the tree (PP/ML/NJ/MP). No outgroup was used, tree was rooted using clade A.

Figure 3

Putative secondary structure model of the nuclear encoded SSU rRNA of Spirogyra sp.; Strain WRH5 (Acc.No. JQ 239088) from Clade B was chosen as representative sequence; 100% consensus bases for the genus Spirogyra are given in upper case letters, variable positions in lower case letters; NHS for Spirogyra are marked with blue circles, NHS for one of the clades are marked by green circles, the assigned number indicates the number in the table; see Additional file 4: Table S4 for details.