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Epilithic green algae play crucial roles in aquatic ecosystems. While traditional morphological approaches have provided valuable insights into these algae, their limitations in resolving cryptic species and fully capturing the extent of diversity have impeded a comprehensive understanding. The diversity and phylogenetic relationships of these algae largely remain unexplored. In the present study, single molecular real-time (SMRT) sequencing of the full-length 18S rDNA was employed to investigate the molecular diversity and phylogenetic relationships of epilithic green algae in biodiversity conservation hotspots. A total of 79 709 algal reads were generated, yielding 169 amplicon sequence variants (ASVs) from 21 epilithic riverine green algal assemblages classified in the Ulvophyceae, Chlorophyceae and Trebouxiophyceae. The 10 families in which the greatest number of unique ASVs (diversity) were observed were the Ulvellaceae, Protosiphonaceae, Chlorococcaceae, Watanabeaceae, Chlorellaceae, Neochloridaceae, Chaetophoraceae, Hazeniaceae, Tupiellaceae and Scenedesmaceae. Unique clades formed by a substantial number of sequences of green algae were detected within the Ulvales/Ulotrichales (Ulvophyceae) and the Chlorococcaceae/Protosiphonaceae (Chlorophyceae). This study has unveiled hidden diversity within epilithic green algae, expanding our knowledge of their evolutionary relationships and providing fundamental data for taxonomic investigations within this group, as well as contributing to the assessment of algal diversity in biodiversity conservation hotspots. This study suggests that these epilithic green algal assemblages may be significantly more diverse than previously recognized, but we acknowledge the limited ecological and temporal scope of our sampling effort and the resulting effects on which taxa are identified, warranting further research. Molecular analysis shows high hidden diversity of epilithic green algae The families Ulvellaceae and Protosiphonaceae had the greatest number of unique ASVs Many unique clades within the Ulvales/Ulotrichales and Chlorococcaceae/Protosiphonaceae [ABSTRACT FROM AUTHOR]

The order Oedogoniales comprises three genera, Oedogonium, Oedocladium and Bulbochaete, which were classified based on traditional morphological criteria, and includes more than 600 described species. This group is economically important in astaxanthin production and the energy sector. However, only one mitochondrial genome (mitogenome) has been reported so far. This study determined the mitochondrial genomes of seven Oedogoniales species, including six Oedogonium species and Oedocladium prescottii. Comparative analyses between the newly determined mitogenomes and the previously reported Bulbochaete rectangularis var. hiloensis mitogenome showed that all eight mitogenomes comprised 12 protein-coding genes (PCGs) and two rRNAs; however, the mitogenomes differed in their genome sizes, GC content, tRNAs, non-coding regions and introns. Synteny analysis of the eight mitogenomes revealed a high degree of syntenic conservation in general, with some rearrangements and inversions. The average nucleotide identity (ANI) analysis of the eight mitogenomes indicated Oedogonium dentireticulatum showed high similarity with Oedogonium sp3 (ANI of 96.32%). Most of the PCGs of the eight mitogenomes presented the conventional start codon ATG and stop codon TAR (TAA/TAG/TGA), and the synonymous codon preferences were conserved. Phylogenetic results indicated that Oedogonium was polyphyletic, and species of Oedocladium clustered with Oedogonium, while the position of B. rectangularis var. hiloensis was uncertain for the incongruent phylogenetic results. Statistical analyses of substitution rates demonstrated no significant differences among the three genera, and the dN/dS ratios based on branch model showed that cob, cox1 and nad4 of Oedocladium prescottii and B. rectangularis var. hiloensis were putative fast-evolving genes. These findings suggested that the traditional taxonomy of Oedogoniales did not define natural groups, and that species of Oedocladium and Bulbochaete may have undergone rapid evolution. [ABSTRACT FROM AUTHOR]

Chaetophora lobata is the type species of the polyphyletic genus Chaetophora. Clarification of its species identification, phylogenetic relationships, and plastome characteristics is helpful for taxonomic revisions and evolutionary studies of this genus. This study presents detailed information on morphology, culture, phylogenetic analysis, phylogenomics and comparative genomics of C. lobata. The complete morphological description and phylogenetic analyses based on nuclear rDNA and chloroplast protein-coding genes were robust for the identification of C. lobata. Moreover, de novo sequencing was used to determine the 222 213 bp chloroplast genome, which lacked inverted repeats as in all other members of the Chaetophorales. The chloroplast DNA (cpDNA) of C. lobata was found to be AT-rich (68.2%), consisting of 67 protein-coding genes, among which 62 genes were encoded on the plus strand and five genes were encoded on the minus strand with significant imbalance in distribution. Additionally, 28 tRNA genes, three rRNA genes, 16 introns and 18 putative open reading frames (ORFs) were annotated. Eight ORFs arranged in a row occupied about 18 kbp between psaA and atpI genes, and 16 introns (14 group I introns and 2 group II introns) were annotated in nine genes. Six genes contained nine intronic ORFs. Synteny and rearrangements analysis clearly showed the closest relationships between Chaetophora sp. and C. lobata. Substitution rate estimation indicated that the cpDNA of Chaetophorales was under purifying selection and most species were under similar evolutionary pressure. These findings can help advance research on the taxonomy and phylogeny of the order Chaetophorales. [ABSTRACT FROM AUTHOR]

The Oedogoniales comprises the genera Oedogonium, Oedocladium and Bulbochaete which include more than 600 described species. However, only two chloroplast genome sequences have been reported to date, and little is known about the evolutionary relationships between these genera or their infrageneric classification. This group is economically important in astaxanthin production and the energy sector. We examined four Oedocladium strains from different locations in China. One was identified as O. prescottii, and the morphology and molecular data for the other three strains suggested that they were O. carolinianum. Our chloroplast (cp) genome sequences of O. prescottii (FACHB-2452) and O. carolinianum (FACHB-2453) were compared with previously reported Oedogoniales cp genomes. The cp genome of O. carolinianum FACHB-2453 was of similar size, structure and composition to that of O. carolinianum UTEX LB 1686, apart from two missing group I introns in the genes psbA and psbD. O. prescottii showed more differences with regard to genome size, structure, number of genes and introns, and repeats than the other Oedogoniales cp genomes. The inverted repeats (IRs) region of the O. prescottii cp genome had a 10-kb contraction. Synteny analysis of the four cp genomes showed a high degree of syntenic conservation in general; however, some structural variation at genus level was observed in Oedocladium. In phylogenetic analyses of Oedocladium using sequences of 18S rDNA, ITS and 59 cp protein-coding genes, species were placed on two separate branches within the Oedogonium clade, indicating that Oedocladium is a paraphyletic group. [ABSTRACT FROM AUTHOR]

This study is the first to determine the transcriptomes of eight colonial volvocine algae: Pandorina morum, P. colemaniae, Volvulina compacta, Eudorina elegans, E. cylindrica, Yamagishiella unicocca, Colemanosphaera charkowiensis and C. angeleri. By analysing these data together with the whole-genome data of Chlamydomonas reinhardtii and other colonial volvocine algae, we determined 26 979 gene families and 105 single-copy orthogroups. Using the single-copy orthogroups, we adopted a supermatrix and coalescent-based approach to perform phylotranscriptomic analysis of colonial volvocine algae. The phylogenetic relationships of most species were consistent with those of a previous study, and the results showed paraphyly of the genus Pandorina. Then, we analysed gene family expansion and contraction in colonial volvocine algae and found that they exhibited a large number of expanded and contracted gene families. In particular, the common ancestor of the Volvocaceae had the largest number of expanded gene families, which may be associated with the increased volume of extracellular matrix. Finally, using the ML method to analyse the substitution rates among colonial volvocine algae based on single-copy orthogroups, we showed a significantly higher non-synonymous substitution (dN) rate in Tetrabaena socialis. By analysing the differences in the dN/dS ratio, we found that more orthogroups exhibited a significantly higher dN/dS in T. socialis; we speculate that the higher dN/dS could indicate relaxed selection pressure and that this lower constraint allows the accumulation of more non-synonymous mutations in T. socialis. [ABSTRACT FROM AUTHOR]

Many species belonging to the coccoid green algae genus Coelastrella are considered potential candidates for the large-scale production of natural pigments and biofuels. However, little is known about the structural, functional and molecular aspects of the chloroplast genomes (cpDNAs) of this genus. In the present study, the complete sequence of the cpDNA of strain FACHB-2138, which was further identified as Coelastrella saipanensis Hanagata based on morphological and molecular analyses, was elucidated. The 196 140 bp cpDNA sequence that was assembled as a circular map was found to possess the typical quadripartite structure. The two identical copies of 11 897 bp inverted repeat (IR) sequences were separated from one another by single copy regions. The large single copy region (LSC) was 104 949 bp, whereas the small single copy region (SSC) was 67 397 bp. The cpDNA encoded a total of 96 unique genes, which included 67 protein-coding genes, three rRNA genes and 26 tRNA genes. A total of 19 group I introns were annotated in this genome. Comparative analyses with three species from the family Scenedesmaceae showed C. saipanensis had a slightly expanded genome, higher GC content and less skewed distribution of its genes between the two DNA strands than that of the other three species. The cpDNA data deduced from the present study helps to expand our present understanding of plant systematics and phylogenetic reconstruction, and identify the possible biotechnological applications of the species belonging to the studied taxa. [ABSTRACT FROM AUTHOR]