Comparative Chloroplast Genome Analyses of Ilex (Aquifoliaceae): Insights Into Evolutionary Dynamics and Phylogenetic Relationships

Abstract BackgroundDespite many species of Ilex (Aquifoliaceae) are of horticultural importance and are widely grown in parks and gardens throughout the world for their foliage and decorative berries, limited genetic information has greatly hampered our understanding of the chloroplast genome evolution and phylogenetic relationships within the genus. This study attempted to address these problems by comparing the chloroplast genomes and analyzing phylogenetic relationships within the genus.ResultsIn this study, analyses of chloroplast genome structure, codon usage, GC content, gene rearrangement, nucleotide diversity, inverted repeats (IR) boundary, repeat sequence, and SSR component were conducted by comparing 41 chloroplast genomes of Ilex. The results showed that these Ilex chloroplast genomes were evolutionary conserved at the genome level and no rearrangement of the complete cp genome in the 41 Ilex genomes was recorded. On the contrary, there were still a few mutational hotspots identified from these chloroplast genomes, which were considered as hypervariable regions useful for future phylogenetic studies and DNA barcoding. Using the complete chloroplast genome sequences, we reconstructed a highly supported phylogeny of Ilex and well-resolved the complicated relationships among the different lineages within Ilex.ConclusionThe present study increased our understanding of the chloroplast genome evolution and phylogenetic relationships within Ilex. The availability of these genetic resources will be helpful for the future studies in DNA barcoding, species delimitation, phylogenetic reconstruction as well as the hybridization and introgression events between distantly related lineages within Ilex.

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Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.)

Forests ◽

10.3390/f11030309 ◽

2020 ◽

Vol 11 (3) ◽

pp. 309

Author(s):

Konrad Celiński ◽

Hanna Kijak ◽

Justyna Wiland-Szymańska

Keyword(s):

Chloroplast Genome ◽

Canary Islands ◽

Genome Structure ◽

Gc Content ◽

Phylogenetic Inference ◽

Single Copy ◽

Genetic Identification ◽

Chloroplast Genomes ◽

Mutational Hotspots ◽

Dracaena Draco

Dracaena draco, which belongs to the genus Dracaena, is an endemic succulent of the Canary Islands. Although it is one of the most popular and widely grown ornamental plants in the world, little is known about its genomic variability. Next generation sequencing, especially in combination with advanced bioinformatics analysis, is a new standard in taxonomic and phylogenetic research. Therefore, in this study, the complete D. draco chloroplast genome (cp) was sequenced and analyzed in order to provide new genomic information and to elucidate phylogenetic relationships, particularly within the genus Dracaena. The D. draco chloroplast genome is 155,422 bp, total guanine-cytosine (GC) content is 37.6%, and it has a typical quadripartite plastid genome structure with four separate regions, including one large single copy region of 83,942 bp length and one small single copy region of 18,472 bp length, separated by two inverted repeat regions, each 26,504 bp in length. One hundred and thirty-two genes were identified, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Seventy-seven simple sequence repeats were also detected. Comparative analysis of the sequence data of various members of Asparagales revealed mutational hotspots potentially useful for their genetic identification. Phylogenetic inference based on 16 complete chloroplast genomes of Asparagales strongly suggested that Dracaena species form one monophyletic group, and that close relationships exist between D. draco, D. cochinchinensis and D. cambodiana. This study provides new and valuable data for further taxonomic, evolutionary and phylogenetic studies within the Dracaena genus.

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Comparative analyses of 3654 chloroplast genomes unraveled new insights into the evolutionary mechanism of green plants

10.1101/655241 ◽

2019 ◽

Cited By ~ 1

Author(s):

Ting Yang ◽

Xuezhu Liao ◽

Lingxiao Yang ◽

Yang Liu ◽

Weixue Mu ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Strong Support ◽

Gc Content ◽

Taxon Sampling ◽

Data Sets ◽

Green Plants ◽

Comparative Analyses ◽

Chloroplast Genomes ◽

The Matrix

AbstractBackgroundChloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. It is possible to compare the chloroplast genome structure to elucidate the evolutionary history of the green plants.ResultsWe compared the 3654 chloroplast genomes of the green plants and found extreme conservation of gene orders and gene blocks in the green plant such as ATP synthase cluster, Phytosystem, Cytochrome cluster, and Ribosomal cluster. For the chloroplast-based phylogenomics, we used three different data sets to recover the relationships within green plants which accounted for biased GC content and could mitigate the bias in molecular data sets by increasing taxon sampling. The main topology results include: I) Chlorokybales + Mesostigmatales as the earliest-branching lineage and a clade comprising Zygnematales+ Desmidiales formed a grade as the sister group to the land plants, II) Based on matrix AA data, Bryophytes was strongly supported as monophyletic but for matrix nt123 data, hornworts, mosses and liverworts were placed as successive sister lineages of Tracheophytes with strong support, III) Magnoliids were placed in the outside of Monocots using the matrix nt123 data and the matrix AA data, IV) Ceratophyllales + Chloranthales as sister to the Eudicots using matrix nt123 data, but when using matrix nt12 data and AA data, only Ceratophyllales sister to the Eudicots.ConclusionWe present the first of its kind large scale comparative analyses of the chloroplast coding gene constitution for 3654 green plants. Some important genes likely showed co-occurrence and formed gene cluster and gene blocks in Streptophyta. We found a clear expansion of IRs (Inverted Repeats) among seed plants. The comprehensive taxon sampling and different data sets recovered a strong relationship for green plants.

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

10.21203/rs.2.21773/v1 ◽

2020 ◽

Author(s):

Benwen Liu ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, 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 Chaetopeltidales.

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Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

Frontiers in Genetics ◽

10.3389/fgene.2021.687844 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jin Xu ◽

Chen Liu ◽

Yun Song ◽

Mingfu Li

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Future Research ◽

Trna Genes ◽

Evolutionary Analysis ◽

Chloroplast Genomes

The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.

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

10.21203/rs.2.21773/v2 ◽

2020 ◽

Author(s):

Benwen Liu(Former Corresponding Author) ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu(New Corresponding Author)

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background: Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily through phylogenetic analysis based on rDNA sequences. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). The phylogenetic relationships among families in order Chaetophorales remain unclear. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales . Results: In the present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales. Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. 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 Chaetopeltidales.

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Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications

BMC Genomics ◽

10.1186/s12864-021-07807-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Chao Luo ◽

Wulue Huang ◽

Huayu Sun ◽

Huseyin Yer ◽

Xinyi Li ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Genome Structure ◽

Sequence Divergence ◽

Rrna Genes ◽

Karst Area ◽

Ancestral State ◽

Genomic Resources ◽

Repeat Sequences ◽

Chloroplast Genomes

Abstract Background Impatiens L. is a genus of complex taxonomy that belongs to the family Balsaminaceae (Ericales) and contains approximately 1000 species. The genus is well known for its economic, medicinal, ornamental, and horticultural value. However, knowledge about its germplasm identification, molecular phylogeny, and chloroplast genomics is limited, and taxonomic uncertainties still exist due to overlapping morphological features and insufficient genomic resources. Results We sequenced the chloroplast genomes of six different species (Impatiens chlorosepala, Impatiens fanjingshanica, Impatiens guizhouensis, Impatiens linearisepala, Impatiens loulanensis, and Impatiens stenosepala) in the karst area of China and compared them with those of six previously published Balsaminaceae species. We contrasted genomic features and repeat sequences, assessed sequence divergence and constructed phylogenetic relationships. Except for those of I. alpicola, I. pritzelii and I. glandulifera, the complete chloroplast genomes ranging in size from 151,366 bp (I. alpicola) to 154,189 bp (Hydrocera triflora) encoded 115 distinct genes [81 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) genes]. Moreover, the characteristics of the long repeat sequences and simple sequence repeats (SSRs) were determined. psbK-psbI, trnT-GGU-psbD, rpl36-rps8, rpoB-trnC-GCA, trnK-UUU-rps16, trnQ-UUG, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, and ycf4-cemA were identified as divergence hotspot regions and thus might be suitable for species identification and phylogenetic studies. Additionally, the phylogenetic relationships based on Maximum likelihood (ML) and Bayesian inference (BI) of the whole chloroplast genomes showed that the chloroplast genome structure of I. guizhouensis represents the ancestral state of the Balsaminaceae family. Conclusion Our study provided detailed information about nucleotide diversity hotspots and the types of repeats, which can be used to develop molecular markers applicable to Balsaminaceae species. We also reconstructed and analyzed the relationships of some Impatiens species and assessed their taxonomic statuses based on the complete chloroplast genomes. Together, the findings of the current study might provide valuable genomic resources for systematic evolution of the Balsaminaceae species.

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Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes

PeerJ ◽

10.7717/peerj.7480 ◽

2019 ◽

Vol 7 ◽

pp. e7480 ◽

Cited By ~ 5

Author(s):

Qi Chen ◽

Xiaobo Wu ◽

Dequan Zhang

Keyword(s):

Chloroplast Genome ◽

Related Species ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Gc Content ◽

Closely Related Species ◽

Complete Chloroplast Genome ◽

Plastid Genomes ◽

Chloroplast Genomes ◽

Fritillaria Cirrhosa

Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.

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Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

Forests ◽

10.3390/f12101303 ◽

2021 ◽

Vol 12 (10) ◽

pp. 1303

Author(s):

Xiaojin Liu ◽

Daping Xu ◽

Zhou Hong ◽

Ningnan Zhang ◽

Zhiyi Cui

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Evolutionary Dynamics ◽

Divergence Time ◽

Purifying Selection ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes ◽

Branch Model ◽

Extant Species ◽

Ndh Genes

Santalum (Santalaceae, sandalwood) is a hemiparasitic genus that includes approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of phylogenetic relationships will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. The Santalum chloroplast genome contains typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 110 unique genes. The whole set of ndh genes and the infA gene were found to lose their functions. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Branch-model-based selection analyses showed that the Santalum species were under widespread purifying selection. Our phylogenomic assessment provides an improved resolution to the phylogenetic relationships of Santalum compared to the past analyses. Our divergence time analysis showed that the crown age of Santalum was 8.46 Mya (million years ago), the first divergence occurred around 6.97 Mya, and diversification was completed approximately 1 Mya. By sequencing the 11 Santalum species chloroplast genomes, we identified the variations in the Santalum chloroplast genomes. Using the chloroplast genome sequences, phylogeny and divergence time analyses discovered that the Santalum species were likely to originate due to radiation evolution, and most speciation events occurred less than 1 Mya.

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Comparative analysis of chloroplast genome structure and molecular dating in Myrtales

BMC Plant Biology ◽

10.1186/s12870-021-02985-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xiao-Feng Zhang ◽

Jacob B. Landis ◽

Hong-Xin Wang ◽

Zhi-Xin Zhu ◽

Hua-Feng Wang

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Divergence Time ◽

Gc Content ◽

Single Copy ◽

Molecular Dating ◽

Rrna Genes ◽

Chloroplast Structure ◽

Chloroplast Genomes ◽

Part Structure

Abstract Background Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point. Results A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214–171,315 bp and exhibit a typical four part structure. The IR region is between 23,901–36,747 bp, with the large single copy region spanning 83,691–91,249 bp and the small single copy region spanning 11,150–19,703 bp. In total, 123–133 genes are present in the chloroplasts including 77–81 protein coding genes, four rRNA genes and 30–31 tRNA genes. The GC content was 36.9–38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7–37.3%, 30.6–36.8% and 39.7–43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88–114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50–118.62 Ma). Conclusions The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.

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

10.21203/rs.2.21773/v3 ◽

2020 ◽

Author(s):

Benwen Liu ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade ◽

Genomic Analyses

Abstract Background: Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily based on short and less informative rDNA sequences. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales.Results: In the present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales. Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships.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 Chaetopeltidales.

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