Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes

- Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes.
- Results: In the present study, seven complete and five fragmentary chloroplast genomes were harvested..
- Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order.
- Conclusions: chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and.
- Full list of author information is available at the end of the article.
- Most of the aforementioned phylogenetic stud- ies are based on one or a few rRNA genes and were per- formed with partial Chaetophoralean taxa, and few studies have focused on chloroplast genes and the chloroplast genome..
- Thus far, only two organelle genomes have been pub- lished in Chaetophorales [25, 26], thus restricting our understanding of the taxonomic status and evolution of this group.
- This study attempted to obtain 12 chloroplast genomes in Chaetophorales.
- This study aimed to phylogenetically reconstruct order Chaetophor- ales and determine the taxonomic scheme and to further the current understanding of the evolution of the order Chaetophorales..
- All complete chloroplast genomes of Chaetophorales (Table 1) consistently contained 67 protein-coding genes and 3 rRNA genes without inverted repeats (IR)..
- Significant differences were observed in genome size, GC content, total number of genes, number of tRNAs, number of introns, and number of protein-coding genes distributed on the posi- tive and negative strands of the genome respectively..
- The chloroplast genome size ranged bp.
- Aphanochaete elegans (HB201732) had the smallest chloroplast genome, and Stigeoclonium helveticum (UTEX 441) had the largest chloroplast genome.
- Furthermore, the distribution of genes on the coding strand was skewed and varied among spe- cies.
- The total length of the coding region accounted for and Aphanochaete elegans (HB201732) accounted for the highest proportion, while Stigeoclonium sp.
- Furthermore, five fragmentary chloroplast genomes were obtained.
- Despite different degrees of deletions in the chloroplast genome, partial genome sequences we generated, including complete sequences of all 58 protein-coding genes shared among the completely.
- Phylogenetic analyses based on the four nuclear concatenated markers (18S + 5.8S + ITS2 + partial 28S rDNA).
- The average content of A, T, C, and G was and 28.70%, respectively, of which the G + C content (50.16%) was greater than that of the A + T content (49.84.
- Phylogenetic analyses based on the chloroplast protein- coding genes.
- Maximum likelihood (ML) phylogenetic trees gener- ated with the concatenated nucleotide (nt) data set treated with three methods (partitioned by gene pos- ition, codon position, and gene position without 3rd codon positions) had low support values at the node of the clade (orders Chaetophorales and Chaetopeltidales Fig.
- this can be visualized on the basis of two aspects: the topologies and the support value, especially in the OCC clade.
- The support values in concatenated datasets of the chloroplast were mark- edly higher than those on rDNA datasets.
- In the OCC clade, Oedogoniales was located at the base of the branch, and Chaetophorales and Chaeto- peltidales were most closely related.
- Chaetophoraceae sensu lato was located Table 1 The complete chloroplast genome features of the Chaetophorales.
- at the top branch of the Chaetophorales, displaying a basal split into the two well-supported clades, represent- ing Fritschiellaceae and Chaetophoraceae sensu stricto, respectively.
- ProgressiveMauve was used to analyze synteny in the chloroplast genome in Chaetophorales and set Schizomeris leibleinii as the reference genome [26].
- Evolution of the Chaetophorales based on the germination type of zoospores.
- 1 ML and Bayesian phylogenetic tree of the Chaetophorales constructed by using a concatenated data set of four markers (18S + 5.8S + ITS2 + partial 28S rDNA).
- The numbers on the nodes represent the posterior probabilities (PP)/bootstrap support values (BP) above 50/0.50.
- Strains for chloroplast genomes investigated in this study are shaded in grey.
- In Chaeto- phoraceae sensu lato, zoospores of the family Chaeto- phoraceae sensu stricto and family Fritschiellaceae were present for erect germination and prostrate ger- mination, respectively [23]..
- Based on the germination type of zoospores, the evolu- tionary hypothesis of Chaetophorales was proposed: the clade including Schizomeriaceae and Aphanochaetaceae including zoospores for erect and prostrate germination, respectively, was most closely related to the original ances- tors of Chaetophorales, wherein the aforementioned two families were clustered together and located at the base of Chaetophorales.
- Unlike most green algae, the chloroplast genome of Chaetophorales does not have a typical quadripartite structure (a large single-copy region, a small single- copy region, and two inverted repeats separated by the single-copy region), and the inverted repeat region (IR) is obliterated.
- 2 ML and Bayesian phylogenetic tree of the Chlorophyceae constructed by using 58 protein-coding genes of the chloroplast genomes.
- The posterior probabilities (PP)/bootstrap support values (BP) above 50/0.50 are only shown on the key nodes.
- The tree was rooted with four species of the Ulvophyceae.
- Strains for chloroplast genomes investigated in this study are in bold.
- In general, the size of the chloroplast genome of Chaetophorales tends to increase among families from Schizomeriaceae to Chaetophoraceae.
- The smallest chloroplast genome belongs to Aphanochaete elegans (family Aphanochaetaceae) and the largest one be- longs to Fritschiella tuberosa (family Fritschiellaceae), despite its fragmentary chloroplast genomes.
- Plant evolution in Chaetophorales has become more complex, consistent with that in the chloroplast genome, which tends to expand from the base to the top..
- Evolution of the chloroplast genome in Chaetophorales tends to cause AT enrichment, consistent with other green algal groups [6].
- In contrast with Chaetophorales plastomes, contiguous genes in the Floydiella chloroplast genome mark- edly tend to be clustered on the same strand [47].
- The distri- bution of protein-coding genes in two chains of the chloroplast genome vary among different species.
- Synteny analyses have accounted for numerous complex rearrange- ments and inversions among the chloroplast genomes of Chaetophorales.
- 3 ML and Bayesian phylogenetic tree of the Chlorophyceae constructed by using concatenated 58 amino acid (aa) data set of the.
- chloroplast genomes.
- Phylogenetic analyses based on nuclear rDNA were in- congruent with chloroplast genes, especially on the.
- 4 Synteny comparison of the Chaetophorales chloroplast genomes using progressiveMauve.
- b, Synteny comparison of the family Schizomeridaceae (Schizomeris leibleinii HQ700713) and Aphanochaetaceae (Aphanochaete confervicola MN659373.
- blocks above the centre line indicate they are on the same strand, and blocks below the centre line indicate they are on the opposite strand.
- Al- though support values of phylogenetic trees based on nt datasets were lower than those based on aa datasets at certain nodes, all of them supported the same unique topologies of the OCC clade and Chaetophorales..
- By in- creasing the sizes of the chloroplast genomes of Chaetophorales, the present results confirmed that Chaetophorales and Chaetopeltidales constituted a clade, in contrast with basal Oedogoniales in the OCC group..
- In conclusion, chloroplast genome structure analyses, syn- teny analyses, and the zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales.
- The polymerase chain reaction (PCR) of the 18S rDNA was amplified according to Medlin et al.
- 5 Chloroplast genomic feature and evolutionary relationship based on the zoospore germination of the Chaetophorales.
- The guide tree inferred from the chloroplast genomes by using progressiveMauve.
- The numbers on the node represent the size/number of gene/GC content of the chloroplast respectively.
- Chloroplast DNA sequencing, assembly, and annotation Twelve species were used to isolate the chloroplast DNA..
- The chloroplast genes were annotated using an online DOGMA tool [66].
- Phylogenetic analyses based on chloroplast genome Total 49 Chlorophyceae (Chlorophyta) taxa were used to generate the analysed nucleotide and amino acid data sets.
- Table 2 Detail information on the species with Chloroplast genome data of the order Chaetophorales.
- An epiphyte on the Oedogonium, freshwater..
- Hubei province, China, on the water grass, freshwater..
- Guizhou province, China, on the Lotus leaf in a pool, freshwater..
- Liu, 2016, Tibet, China, on the stones in a stream, freshwater..
- Liu, 2017, Aershan, Hinggan, Inner mongolia province, China, on the stones in Halaha river, freshwater..
- Wuhan Botanical Garden, Chinese Academy of Sciences, on the stick in a pool, freshwater..
- Sanbar of Yangtze River, on the moist soil..
- Shuangrufeng, on the Lotus leaf in a pool, freshwater..
- MrBayes was ran for 5,000,000 generations, sampling and printing every 500 and bootstrap analyses with 1000 replicates of the ML dataset were performed to estimate the statis- tical reliability.
- Gene map of seven complete chloroplast genomes of the Chaetophorales.
- The grey circle on the inside shows a graph of the GC content.
- The funding agency had no role in the design of the study, collection, analysis, or interpretation of data, or in writing the manuscript..
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