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Ulvella species are widely distributed in ocean and freshwater habitats and from high latitudes to the tropics. However, no species of this genus have been found in the Qinghai–Tibetan Plateau. In the present study, five rock specimens were collected from the bottom of Qinghai Lake at a depth of about 15–28 m, from which three unialgal strains were isolated. These strains were characterized by prostrate pseudoparenchyma, irregular or radial branch filaments, and mono- or polystromatic discs or rosettes formed by consecutive filaments, with thalli that can grow up to 180 um in length, suggesting that they may be Ulvella species. Phylogenetic analysis based on 18S rDNA and tufA cpDNA sequences revealed that the isolates formed a strong branch among other Ulvella species and were closely related to Ulvella leptochaete and Ulvellawaernii. This result was also confirmed by neighbor-joining tree inference based on ITS2 secondary structure. Unlike other members of Ulvella, the isolated strain was characterized by its unique habitat, field morphology of thallus, size of vegetative cells, and number of pyrenoids. Based on these morphological differences, the phylogenetic analysis, and the comparison of ITS2 secondary structure with relative species, the strain isolated in this study was proposed to be a novel Ulvella sp. The alga was found on the bottom of brackish lakes on the Qinghai–Tibetan Plateau, which meant that our sampling range needed to be expanded further. [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]

Filamentous green algae Chaetophorales present numerous taxonomic problems as many other green algae. Phylogenetic analyses based on nuclear genes have limited solutions. Studies with appropriate chloroplast molecular markers may solve this problems; however, suitable molecular markers for the order Chaetophorales are still unknown. In this study, 50 chloroplast genomes of Chlorophyceae, including 15 of Chaetophorales, were subjected to single protein‐coding gene phylogenetic analyses, and substitution rate and evolutionary rate assays, and PCR amplification verification was conducted to screen the suitable molecular markers. Phylogenetic analyses of three chloroplast representative genes (psaB, tufA, and rbcL) amplified from 124 strains of Chaetophorales showed that phylogenetic relationships were not improved by increasing the number of samples, implying that the genes themselves, rather than limited samples, were the reason for the unsupported Topology I. Seven genes (atpF, atpI, ccsA, cemA, chlB, psbB, and rpl2) with robust support were selected to be the most suitable molecular markers for phylogenetic analyses of Chaetophorales, and the concatenated seven genes could replace the time‐consuming and labor‐intensive phylogenetic analyses based on chloroplast genome to some extent. To further solve the taxonomic problems of Chaetophorales, suitable chloroplast markers combined with more taxon‐rich approach could be helpful and efficient. [ABSTRACT FROM AUTHOR]

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes. [ABSTRACT FROM AUTHOR]

Trentepohliales is an aerial order of Chlorophyta with approximately 80 species distributed mainly in tropical and subtropical regions. The taxonomy of this genus is quite difficult and presents a challenge for many phycologists. Although plentiful molecular data is available, most of the sequences are not identified at the species level. In the present study, we described a new specimen with detailed morphological data and identified it as Trentepohlia odorata. A phylogenetic analysis showed T. odorata as a novel lineage in Trentepohliales. T. odorata has the closest relationship with T. annulata, which is expected since sporangia of both species are without stalk cell and with dorsal pore. Species with such morphological characteristics may represent deep lineages in Trentepohliales. Although an increasing number of chloroplast genomes of Ulvophyceae have been reported in recent years, the whole plastome of Trentepohliales has not yet been reported. Thus, the chloroplast genome of Trentepohlia odorata was reported in the present study. The whole plastome was 399,372 bp in length, with 63 predicted protein-coding genes, 31 tRNAs, and 3 rRNAs. Additionally, we annotated 95 free-standing open reading frames, of which seven were annotated with plastid origins, 16 with eukaryotic genome origins, and 33 with bacterial genome origins. Four rpo genes (rpoA, rpoB, rpoC1, and rpoC2) were annotated within ORF clusters. These four genes were fragmented into several (partial) ORFs by in-frame stop codons. Additionally, we detected a frame shift mutation in the rpoB gene. The phylogenetic analysis supported that Trentepohliales clustered with Dasycladales and nested into the BDT clade (Bryopsidales, Dasycladales and Trentepohliales). Our results present the first whole chloroplast genome of a species of Trentepohliales and provided new data for understanding the evolution of the chloroplast genome in Ulvophyceae. [ABSTRACT FROM AUTHOR]