Characterization of the Complete Mitochondrial Genome of the Red Alga Ahnfeltiopsis flabelliformis (Rhodophyta, Gigartinales, Phyllophoraceae) and Its Phylogenetic Analysis
by
, , and
Maheshkumar Prakash Patil
1,2,†
,
Jong-Oh Kim
2,3,†, 
Young-Ryun Kim
4,
Nilesh Nirmal
5
,
Gun-Do Kim
2,3,* and
Kyunghoi Kim
6,* 1
Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
2
Department of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
3
School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
4
Marine Eco-Technology Institute, Busan 48520, Republic of Korea
5
Department of Food Science, Institute of Nutrition, Mahidol University, Salaya 73170, Thailand
6
Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Biology 2025, 14(6), 638; https://doi.org/10.3390/biology14060638
Submission received: 24 March 2025
/
Revised: 21 May 2025
/
Accepted: 22 May 2025
/
Published: 30 May 2025
Simple Summary
Red algae, particularly those in the order Gigartinales, are valuable for their bioactive compounds and hold significant economic and ecological importance. Mitochondrial genomes serve as crucial markers for species identification and phylogenetic studies. However, limited mitochondrial genome data exist for Gigartinales species. This study presents the first complete mitochondrial genome sequence of Ahnfeltiopsis flabelliformis, a species in the Phyllophoraceae family. The mitochondrial genome features are in line with the red algal species and phylogenetic study positions A. flabelliformis within a well-supported Phyllophoraceae clade. The findings of this study enhance our understanding of red algal evolutionary history and offer valuable genetic markers for future research on phylogenetics and species classification within this family.
Abstract
Red algae are recognized for their health-promoting bioactive substances and dietary fibers, making them important as functional food. In order to identify species and determine phylogenetic relationships, mitochondrial genes serve as important markers. Thus, this study sequenced the complete mitochondrial genome of Ahnfeltiopsis flabelliformis, compared with Phyllophoraceae species, and performs phylogenetic analysis to reveal its evolutionary position. The genome is 25,992 bp long, has 71.3% of biased AT content, and comprises 24 protein-coding genes (PCGs), 22 tRNA, and three rRNA genes. The overall base composition of its mitochondrial genome was 37.4% for A, 33.9% for T, 14.7% for G, 14.0% for C and 28.7% for GC. The gene content, annotation, and genetic makeup are identical to those of Phyllophoraceae species. Phylogenetic study based on the complete mitochondrial genome and shared mitochondrial genes revealed that the six Phyllophoraceae species form a well-supported clade. Within this clade, A. flabelliformis groups with Gymnogongrus griffithsiae, and together they form a distinct subclade including four species of the Mastocarpus. The results indicate that A. flabelliformis shares a closer evolutionary relationship with G. griffithsiae than with Mastocarpus species. Future research on Ahnfeltiopsis is necessary to comprehend the evolutionary history and phylogenetic relationships among species in this genus.
1. Introduction
Rhodophyta comprises a monophyletic group of multicellular photosynthetic eukaryotes. Under the phylum Rhodophyta (comprising about 1094 genera, and 7708 species), some of the common classes of algae include Bangiophyceae (185 species), Compsopogonophyceae (70 species), Cyanidiophyceae (11 species), Florideophyceae (7155 species), Porphyridiophyceae (9 species), Rhodellophyceae (8 species), Stylonematophyceae (48 species), and Classis incertae (68 species) [1]. Of these, 968 species are placed in the order Gigartinales of the Class Florideophyceae, which is predominantly marine, containing multicellular algae. In fact, red algae are most often found in marine environments and are uncommon in freshwaters [2]. Currently, there are only a limited number of Gigartinales species (approximately 50) for which complete mitochondrial genome data is available in GenBank (https://www.ncbi.nlm.nih.gov/nuccore, accessed on 1 December 2024). So, analysis of the complete mitochondrial genome of red algae is important, which will be helpful in tracing the proper evolutionary history of red algae, comparative genomics through characteristic features, and gene transfer; it enhances phylogenetic classification and identification of species.
Red algae, particularly members of the order Gigartinales within the class Rhodophyta, are economically important and serve as rich sources of bioactive compounds with diverse biotechnological applications [3,4,5]. These include polysaccharides such as carrageenan and agar, which are used in a wide range of applications related to food, cosmetics, and medicine [6,7,8]. In recent studies, Ahnfeltiopsis flabelliformis has been reported for the richness of carrageenan and their biomedical applications [9,10].
Ahnfeltiopsis flabelliformis (Harvey) Masuda 1993 [11] is a species of red macroalgae within the family Phyllophoraceae (Phylum—Rhodophyta, Class—Florideophyceae, Order—Gigartinales), predominantly found in marine environments [1,2,12]. Three species of Ahnfeltiopsis (A. catenata, A. flabelliformis, A. paradoxa) have been reported in Korea, with A. flabelliformis being a conspicuous and common species [13,14]. Previously documented occurrences in the Far Eastern seas have been re-evaluated, with many of them being assigned to different species based on phylogenetic and morphological analysis [15]. Recent taxonomic findings highlight the significance of combining classic morphological studies with modern molecular approaches to appropriately classify as well as understand the diversity of red algae [15,16]. However, to date, there has been no complete nucleotide sequence of the mitochondrial genome of Ahnfeltiopsis species reported. Therefore, it is important that we perform research on complete mitochondrial genome analysis and the species’ phylogenetic position based on molecular genetics.
The objective of the present study was to analyze and annotate the complete nucleotide sequence of the mitochondrial genome of the Ahnfeltiopsis flabelliformis. Additionally, this research explored the phylogenetic relationship among Gigartinales species by using PCG sequences, thereby establishing a foundation for future investigations into red algae phylogenetics. Additionally, getting the full mitochondrial genomes of A. flabelliformis is important for finding new genetic markers that will help genetics, genetic diversity, and evolution research in the Phyllophoraceae family. This study presents the first complete annotated sequence of the mitochondrial genome for the genus Ahnfeltiopsis.
2. Materials and Methods
2.1. Sample Collection, Genomic DNA Extraction and Sequencing
A specimen of the red macroalga Ahnfeltiopsis flabelliformis (Figure S1) was captured from the shoreline of Busan, Republic of Korea (35°28′ N, 129°25′ E) in June 2023. The specimen was submitted to the Ecological Restoration Group at the Marine Eco-Technology Institute in Busan, Republic of Korea (contact: Dr. Young-Ryun Kim, yykim@marineeco.co.kr) under the voucher number PU-T01-S-MA-07. Total genomic DNA was extracted with a DNeasy Plant Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions. DNA concentration was determined by a NanoDrop spectrophotometer (Thermo Fisher Scientific D1000, Waltham, MA, USA). The genomic DNA was stored at −20 °C prior to further analyses. The A. flabelliformis library was prepared and sequenced by Macrogen (Daejeon, Republic of Korea; https://www.macrogen.com/ko/). The whole mitochondrial genome sequence was generated using high-throughput sequencing (Illumina HiSeq 2500 platform with insert size 350 bp and sequencing mode paired ends 2 × 150 bp).
2.2. Sequence Assembly, Annotation, and Analysis
Trimmomatic v0.36 was used to remove adapter sequences and low-quality reads (Q < 20) to ensure the accuracy of the analysis [17]. The mitochondrial genome was assembled by randomly sampling the cleaned reads, and only the sampled reads were used for de novo assembly. The quality of sequencing data was checked by FastQC v0.11.5 [18]. The high-quality reads were assembled into the mitochondrial genome using NOVOPlasty v4.2.1 [19]. The assembled contigs were compared with the known mitochondrial genome sequences in the NCBI database by BLAST analysis. Mitochondrial genetic code: Translation Table 4 (Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma) was used to annotate the mitochondrial genome using MFannot [20]. Open reading frames (ORF) finder and BLAST searches against the NCBI protein database were performed for the identification of PCGs [21]. Transfer RNAs (tRNAs) were identified using tRNAscan-SE 2.0 [22]. RNAweasel was used to confirm the location of RNAs, and to detect introns [23]. Tandem Repeats Finder program V4.09 was used for repeat sequences identification and analysis [24]. The mitochondrial genome map was produced using OGDRAW v1.3.1 [25]. The nucleotide compositions and the relative synonymous codon usage (RSCU) were determined using MEGA11 v11.2.8 [26]. Strand asymmetry was calculated in terms of formulae: GC-skew = [G − C]/[G + C], and AT-skew = [A − T]/[A + T] [27].
2.3. Phylogenetic Analysis
To determine the evolutionary relationship of A. flabelliformis within the Gigartinales species. The mitochondrial genome sequences of all available 45 red algal species were downloaded from GenBank, out of which 44 species were in-group and Porphyra umbilicalis (NC_018544) was selected as the outgroup (Table S1). The maximum likelihood (ML) phylogenetic analyses were performed based on complete mitochondrial genome sequences. The multiple sequences were aligned using MAFFT v7.0 online platform [28]. We used IQ-TREE’s Modelfinder to identify and select suitable models based on the Bayesian information criterion (BIC) [29] The phylogenetic tree using the maximum likelihood (ML) method was constructed in IQ-TREE, using the GTR + F + I + G4 model [30]. The generated phylogenetic trees were visualized using the iTOL v.7 web server [31].
3. Results and Discussion
3.1. Mitochondrial Genome Structure and Nucleotide Composition
The A. flabelliformis library was made, adapter sequences were cut down, and low-quality reads were removed, and then filtered reads were subjected to de novo assembly, resulting in a contig consisting of 25,992 bp with a GC contents of 28.6% (Supplementary Table S2). Figure 1 illustrates the gene map, and Table 1 shows the characteristics of the mitochondrial genome of A. flabelliformis. The complete mitochondrial genome length was 25,992 bp and available in GenBank with accession number PQ685980. The mitochondrial genome of A. flabelliformis has 49 genes, which are made up of 24 PCGs, 22 tRNAs, and 3 rRNAs. These genes code for RNAs, respiratory chain subunits, ATP synthase subunits, ribosomal protein subunits, and independent protein translocase (Supplementary Table S3). Among the genes, 11 PCGs, 11 tRNAs, and two rRNA genes were located in the heavy (H) strand. The light (L) strand contained 13 PCGs, 11 tRNAs, and one rRNA gene (Table 1). The intergenic nucleotide analysis revealed that the junction between the rps12 and trnE genes was overlapping by 16 bp, and the interval between adjacent genes was 2515 bp, which accounts for 9.67% of the complete mitochondrial genome. The complete mitochondrial genome of A. flabelliformis base composition was 37.4% adenine (A), 33.9% thymine (T), 14.7 guanine (G), and 14.0% cytosine (C), with a biased AT content of 71.3%. The AT content was slightly higher, and the GC content was slightly lower than the other Phyllophoraceae species (Table 2). The whole genome exhibited positive AT- and GC-skewness, suggesting a preference for using A’s over T’s and G’s over C’s. A comparison of A. flabelliformis with other species in the Phyllophoraceae family showed some similarities in the way their genomes were organized and the genes they contained, but there were also clear differences. The mitochondrial genomes of Phyllophoraceae species are usually 25 to 26 kb long and have 23 to 25 PCGs, 22 to 23 tRNAs, and 3 rRNAs with a biased AT composition. On the other hand, A. flabelliformis and G. griffithsiae (OP537223) share many mitochondrial genome characteristics, including nucleotide composition, biased AT composition, number of genes, and skewness (Table 2). The mitochondrial genome of A. flabelliformis is remarkably similar to other Florideophyceae species in terms of gene content, gene sequences, gene organization, and AT composition [32,33,34,35,36,37,38].
Overall comparisons revealed that A. flabelliformis shares greater sequence similarity with G. griffithsiae than with Mastocarpus species, reflecting a closer evolutionary relationship within the Phyllophoraceae family. The presence of conserved synteny and shared gene content among these species indicates a high level of mitochondrial genome conservation, particularly in genes associated with core metabolic functions. The identified PCGs primarily encode components of the oxidative phosphorylation pathway—such as subunits of NADH dehydrogenase, cytochrome oxidase, and ATP synthase—highlighting their essential roles in mitochondrial energy production and strong functional constraints across lineages. Additionally, the presence of a complete set of tRNAs supports efficient mitochondrial translation. Despite these conserved features, differences observed in intergenic regions and specific ORFs suggest lineage-specific divergence, which may reflect adaptive responses to distinct ecological niches or environmental stressors encountered by A. flabelliformis.
3.2. Protein-Coding Gene Features
The A. flabelliformis mitochondrial genome consists of 24 PCGs (17,733 bp) comprised 68.22% of the total mitochondrial genome. nad5 and atp9 are the longest and shortest gene with 2004 bp and 231 bp in length, respectively (Table 1). The nucleotide composition and base skews value of PCGs are given in Table 3. The 24 PCGs in A. flabelliformis had an AT content of 71.8%; the values ranged from 66.4% for cox1 to 78.4% for tatC. Additionally, there were five PCGs with positive AT-skew and fourteen PCGs with positive GC-skew, indicating base skews. Base skews result from strand-specific mutation rates, and replication-transcription biases which cause nucleotide composition variation [39]. The number of PCGs in the mitochondrial genomes of Phyllophoraceae species ranges from 23 to 25. Notably, M. cristatus, M. latissimus, and M. papillatus possess an additional hypothetical PCG, while M. cristatus and M. stellatus show a loss of the rpl20 gene in their mitochondrial genome (Table 2 and Table 4). All PCGs of A. flabelliformis are identical; however, 14 PCGs vary in length among four Mastocarpus species and the G. griffithsiae (Table 4). The variation in PCGs lengths and base skews in red algal mitochondrial genomes is influenced by strand asymmetry, environmental adaptation, and evolutionary streamlining [40,41,42]. Genome reduction and selective pressure for compact mitochondrial genomes also resulted in differences in PCG lengths across red algal species [40,43,44]. The start codon for all PCGs in the A. flabelliformis mitochondrial genome was identified as ATG (Table 4). However, comparisons within the Phyllophoraceae family revealed variations, with GTG serving as the start codon for the sdh4 gene in M. cristatus. Additionally, the tatC gene utilized both ATA and GTG, while the atp6 gene initiated with ATT, ATC, and ATA start codons. In all PCGs, the stop codon TAA was utilized, with the exception of the TAG codon identified in the cox1 gene of A. flabelliformis. Comparison with other species in the family Phyllophoraceae reveals the use of distinct stop codons in eight genes: TAA in the cox1 gene and TAG in atp4, cob, nad6, sdh2, rps11, nad4, and rpl20. The overall sequencing, genomic structure, and organization of the A. flabelliformis mitochondrial genome were to be highly similar to other mitochondrial genomes from the order Gigartinales of class Florideophyceae. Comparative analysis has revealed that the mitochondrial genomes of other evolutionarily distant red algae, such as those from the classes Cyanidiophyceae and Bangiophyceae, higher sequence dissimilarities and genome rearrangements than those of the class Florideophyceae [40].
The codon usage and RSCU analysis results of A. flabelliformis mitochondrial PCGs are shown in Table S4. The total length of 24 PCGs in A. flabelliformis is 17,733 bp, containing total of 5887 codons (excluding stop codons). The number of encoded codons varies from 1 to 556, with a total of 62 codons encoding 20 amino acids, excluding the stop codons (UAA, UAG). The UUA codon for leucine had a high frequency of occurrence (N = 472) and the highest RSCU value (3.74 In this study, unbiased leucine (CUU) and methionine (AUG) codons were observed, and 28 codons among 62 codons showed a preference with an RSCU value more than 1, indicating a higher priority for these codons [45]. Out of the studied codons, 32 had a low bias, shown by their RSCU scores being less than 1. These findings are consistent with the preponderance of codons in the Phyllophoraceae species (G. griffithsiae, M. cristatus, M. latissimus, M. papillatus, and M. stellatus) (Table S4). These variations in codon use patterns across mitochondrial PCGs among species represent the complex linkage of evolutionary events including natural selection, genomic restrictions, and mutation pressure, which over time shapes the genetic composition of organisms [40,41,42,43,44]. More research is required to better understand the codon use bias of mitochondrial genes in red algae.
3.3. Ribosomal and Transfer RNA Genes
The mitochondrial genome of A. flabelliformis has an RNA genes composition that is both common and unusual among Phyllophoraceae species. Three rRNA genes (rnl, rns, and rrn5) were identified in the mitochondrial genome of A. flabelliformis, aligning with the characteristics observed in Phyllophoraceae species (Table S5). The rnl and rns were identified on the H strand, while rrn5 was located on the L strand. Notably, the sizes of the rnl and rns genes in A. flabelliformis are larger compared to those in other species (G. griffithsiae and Mastocarpus species). The variations in genes composition are due to evolutionary changes [46].
The mitochondrial genome of A. flabelliformis comprises 22 tRNA genes, totaling 1665 bp, which accounts for 6.41% of the whole genome, with individual tRNA sizes ranging from 72 to 88 bp (Table 1), reflecting the structural diversity of RNA molecules. The number of tRNA genes in Phyllophoraceae species mitochondrial genomes ranges from 22 to 23 (Table S6). Notably, A. flabelliformis mitochondrial genome lacks the trnI gene-a feature also observed in other Phyllophoraceae species-suggesting a shared evolutionary loss or functional compensation mechanism within the family. In addition, A. flabelliformis shares the absence of trnS (GCT) with M. stellatus and G. griffithsiae. Although these species do not form a monophyletic clade, their shared gene absence implies independent gene loss events, supporting the idea of convergent evolution affecting mitochondrial tRNA content within Phyllophoraceae. In spite of these absences, the mitochondrial genome of A. flabelliformis retains characteristics typical of Phyllophoraceae, such as two codons for both the trnL and trnR genes and two copies of trnM (CAT). These patterns of gene presence, absence, and duplication highlight the dynamic evolutionary processes shaping mitochondrial genomes in red algae. While gene content among Florideophyceae species tends to be conserved, lineage-specific evolutionary pressures contribute to observed differences [44,46,47,48]. Functionally, the loss of certain mitochondrial tRNAs may not hinder translation, as nuclear-encoded tRNAs can be imported into the mitochondria-a compensatory mechanism previously reported in red algae [49,50].
3.4. Phylogenetic Relationship Within Gigartinales
The ML phylogenetic tree based on complete mitochondrial genome sequences of species within order Gigartinales shows the A. flabelliformis placed with G. griffithsiae and is closely related to Mastocarpus species within the Phyllophoraceae family (Figure 2). Strong bootstrap support values strengthen this grouping, indicating a well-supported evolutionary connection. The phylogenetic tree based on complete mitochondrial genome sequences of species within Phyllophoraceae also supports the placement of A. flabelliformis within the family Phyllophoraceae and closely related to G. griffithsiae and Mastocarpus species (Figure S2). The distinct separation of A. flabelliformis from Gigartinaceae species, suggests significant genetic divergence within the order Gigartinales. These findings are consistent with prior work that highlighted mitochondrial genome data as a reliable tool for determining evolutionary connections among red algae [40,44]. These results are consistent with previous studies and contribute to a better understanding of the evolutionary relationships within the Phyllophoraceae family. The newly sequenced mitochondrial genome of A. flabelliformis provides valuable phylogenetic relationships among Phyllophoraceae species, supporting taxonomic classifications. Moreover, comparative analysis reveals conserved and divergent regions that may reflect lineage-specific evolutionary pressures, contributing to a better understanding of mitochondrial genome evolution in Rhodophyta. Future studies incorporating additional Ahnfeltiopsis taxa could enhance our understanding of the genus’s evolutionary history and refine phylogenetic relationships within Phyllophoraceae.
4. Conclusions
This study determined the complete nucleotide sequence of the mitochondrial genome of A. flabelliformis. The comparative study revealed a high degree of similarity in the structure, organization, and gene content of the mitochondrial genome of A. flabelliformis compared to that of G. griffithsiae, its closest evolutionary relative with a fully sequenced mitochondrial genome. This similarity extends to other organisms within the family Phyllophoraceae, including M. latissimus, M. papillatus, M. stellatus, and M. cristatus. The phylogenetic relationship also indicates that A. flabelliformis is placed within the Phyllophoraceae family and closely related with G. griffithsiae. Further research into the molecular phylogeny of all species of the genus, as well as morphology and molecular biology, will be required to test and refine the above research.
Supplementary Materials
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/biology14060638/s1, Figure S1: A specimen image of Ahnfeltiopsis flabelliformis (family Phyllophoraceae) collected from the coast of Busan, South Korea. This marine macroalga is 5 to 8 cm long, cartilaginous, and flat-thallus, with dichotomous or irregular branching, fan-shaped (flabelliform) with deep red to reddish-brown color and lighter-colored tips or shoots; Figure S2: Maximum Likelihood (ML) topology constructed using the complete mitochondrial genome sequences of A. flabelliformis (in this study) and other five species belongs to the family Phyllophoraceae and Porphyra umblicalis as an outgroup member. ML bootstrap support values are annotated at each node, indicating the statistical support for individual branches in the topology; Table S1: List of the species from Gigartinales order used in this study; Table S2: Summary of Ahnfeltiopsis flabelliformis mitochondrial genome data produced/stats during de novo assembly analysis in Illumina platform using NOVOPlasty v4.2.1 assembly method; Table S3: Annotation of mitochondrial functional genes of Ahnfeltiopsis flabelliformis; Table S4: Relative Synonymous Codon Usage (RSCU) values of complete protein-coding genes in the mitochondrial genome of Phyllophoraceae species; Table S5: Mitochondrial rRNA in Phyllophoraceae species; Table S6: Mitochondrial tRNA in Phyllophoraceae species.
Author Contributions
M.P.P., J.-O.K., G.-D.K., and K.K. conceptualized and designed the study and contributed to manuscript writing. M.P.P., J.-O.K., Y.-R.K., G.-D.K., and K.K. were responsible for conducting the experiments and analyzing the data. M.P.P. managed visualization, software development, data curation, and preparation of the original draft. Y.-R.K. handled sample collection, identification, and deposition. N.N. analyzing data, validation, visualization, and critical revision of the manuscript. G.-D.K., and K.K. oversaw the interpretation of experimental data, critical revisions of the manuscript, funding acquisition, and final approval of the version for publication. All authors have read and agreed to the published version of the manuscript.
Funding
This research was financially supported by the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea (20220537). A part of this research was supported by Learning & Academic research institution for Master’s PhD students and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education (No. RS-2023-00301702). This work was also supported by the Global Joint Research Program funded by the Pukyong National University (202411550001).
Institutional Review Board Statement
Not applicable.
Informed Consent Statement
Not applicable.
Data Availability Statement
Data associated with this study has been deposited at NCBI under the accession number PQ685980 (https://www.ncbi.nlm.nih.gov/nuccore/PQ685980). All data generated or analyzed during this study are included in this article and its Supplementary Information Files.
Conflicts of Interest
The authors declare no conflicts of interest.
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Figure 1.
The circular mitochondrial genome of Ahnfeltiopsis flabelliformis (GenBank accession number: PQ685980). The arrow directions show gene orientation, the different colors reflect the groupings of functional genes together with their acronyms, and the inner circle indicates the GC content.
Figure 1.
The circular mitochondrial genome of Ahnfeltiopsis flabelliformis (GenBank accession number: PQ685980). The arrow directions show gene orientation, the different colors reflect the groupings of functional genes together with their acronyms, and the inner circle indicates the GC content.
Figure 2.
Maximum likelihood (ML) tree constructed using the complete mitochondrial genome sequences, effectively distinguishing Ahnfeltiopsis flabelliformis from other species of the Gigartinales order. The cladogram also offers perceptions into the evolutionary relations across diverse taxonomic levels within the Gigartinales order. ML bootstrap support values are annotated at each node, indicating the statistical support for individual branches in the topology.
Figure 2.
Maximum likelihood (ML) tree constructed using the complete mitochondrial genome sequences, effectively distinguishing Ahnfeltiopsis flabelliformis from other species of the Gigartinales order. The cladogram also offers perceptions into the evolutionary relations across diverse taxonomic levels within the Gigartinales order. ML bootstrap support values are annotated at each node, indicating the statistical support for individual branches in the topology.
Table 1.
List of annotated genes, including their boundaries, sizes, and intergenic nucleotides (IN), start and stop codons, anticodons and number of amino acids for Ahnfeltiopsis flabelliformis.
Table 1.
List of annotated genes, including their boundaries, sizes, and intergenic nucleotides (IN), start and stop codons, anticodons and number of amino acids for Ahnfeltiopsis flabelliformis.
| Gene | Position | Size (bp) | Coding Strand | IN | Codon | Anti-Codon | Amino Acids | ||
|---|---|---|---|---|---|---|---|---|---|
| Start | End | Start | Stop | ||||||
| rnl | 1 | 2613 | 2613 | H | 0 | - | - | - | - |
| rps3 | 2640 | 3332 | 693 | H | 26 | ATG | TAA | - | 230 |
| rpl16 | 3344 | 3760 | 417 | H | 11 | ATG | TAA | - | 138 |
| trnD | 3765 | 3836 | 72 | H | 4 | - | - | GTC | - |
| cox1 | 3879 | 5471 | 1593 | H | 42 | ATG | TAA | - | 530 |
| cox2 | 5489 | 6250 | 762 | H | 17 | ATG | TAA | - | 253 |
| cox3 | 6421 | 7239 | 819 | H | 170 | ATG | TAA | - | 272 |
| atp4 | 7250 | 7798 | 549 | H | 10 | ATG | TAA | - | 182 |
| trnG | 7808 | 7881 | 74 | H | 9 | - | - | TCC | - |
| trnQ | 7884 | 7955 | 72 | H | 2 | - | - | TTG | - |
| trnL | 8062 | 8145 | 84 | H | 106 | - | - | TAA | - |
| cob | 8192 | 9334 | 1143 | H | 46 | ATG | TAA | - | 380 |
| trnL | 9394 | 9476 | 83 | L | 59 | - | - | TAG | - |
| nad6 | 9481 | 10,098 | 618 | L | 4 | ATG | TAA | - | 205 |
| trnG | 10,123 | 10,195 | 73 | L | 24 | - | - | GCC | - |
| trnH | 10,208 | 10,282 | 75 | H | 12 | - | - | GTG | - |
| sdh2 | 10,283 | 11,041 | 759 | L | 0 | ATG | TAA | - | 252 |
| sdh3 | 11,046 | 11,447 | 402 | L | 4 | ATG | TAA | - | 133 |
| trnF | 11,470 | 11,541 | 72 | L | 22 | - | - | GAA | - |
| trnS | 11,561 | 11,644 | 84 | L | 19 | - | - | TGA | - |
| trnP | 11,655 | 11,727 | 73 | L | 10 | - | - | TGG | - |
| atp9 | 11,753 | 11,983 | 231 | L | 25 | ATG | TAA | - | 76 |
| trnC | 12,027 | 12,098 | 72 | L | 43 | - | - | GCA | - |
| trnM | 12,105 | 12,187 | 83 | L | 6 | - | - | CAT | - |
| rps11 | 12,190 | 12,546 | 357 | L | 2 | ATG | TAA | - | 118 |
| rrn5 | 12,568 | 12,675 | 108 | L | 21 | - | - | - | - |
| nad3 | 12,688 | 13,053 | 366 | L | 12 | ATG | TAA | - | 121 |
| nad1 | 13,075 | 14,055 | 981 | L | 21 | ATG | TAA | - | 326 |
| nad2 | 14,082 | 15,575 | 1494 | L | 26 | ATG | TAA | - | 497 |
| sdh4 | 15,592 | 15,831 | 240 | L | 16 | ATG | TAA | - | 79 |
| nad4 | 15,848 | 17,329 | 1482 | L | 16 | ATG | TAA | - | 493 |
| nad5 | 17,910 | 19,913 | 2004 | L | 580 | ATG | TAA | - | 667 |
| atp8 | 19,925 | 20,335 | 411 | L | 11 | ATG | TAA | - | 136 |
| atp6 | 20,348 | 21,109 | 762 | L | 12 | ATG | TAA | - | 253 |
| trnW | 21,147 | 21,218 | 72 | L | 37 | - | - | TCA | - |
| trnA | 21,739 | 21,812 | 74 | L | 520 | - | - | TGC | - |
| trnR | 21,846 | 21,919 | 74 | L | 33 | - | - | TCT | - |
| trnY | 21,931 | 22,018 | 88 | L | 11 | - | - | GTA | - |
| trnN | 22,330 | 22,402 | 73 | H | 311 | - | - | GTT | - |
| trnV | 22,410 | 22,482 | 73 | H | 7 | - | - | TAC | - |
| trnR | 22,530 | 22,604 | 75 | H | 47 | - | - | ACG | - |
| trnK | 22,632 | 22,705 | 74 | H | 27 | - | - | TTT | - |
| tatC | 22,753 | 23,460 | 708 | H | 47 | ATG | TAA | - | 235 |
| rps12 | 23,461 | 23,844 | 384 | H | 0 | ATG | TAA | - | 127 |
| trnE | 23,830 | 23,901 | 72 | H | −16 | - | - | TTC | - |
| trnM | 23,908 | 23,980 | 73 | H | 6 | - | - | CAT | - |
| rpl20 | 23,992 | 24,243 | 252 | H | 11 | ATG | TAA | - | 83 |
| rns | 24,276 | 25,648 | 1373 | H | 32 | - | - | - | - |
| nad4L | 25,687 | 25,992 | 306 | H | 38 | ATG | TAA | - | 101 |
Table 2.
General features of the complete mitochondrial genome of Phyllophoraceae species (ORF* indicates unidentified reading frame).
Table 2.
General features of the complete mitochondrial genome of Phyllophoraceae species (ORF* indicates unidentified reading frame).
| Species (Accession No.) | Size (bp) | Nucleotide Composition (%) | AT-Skew | GC-Skew | Number of Genes | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | T | G | C | A + T | G + C | PCG | tRNA | rRNA | ORF* | ||||
| Ahnfeltiopsis flabelliformis (PQ685980) | 25,992 | 37.4 | 33.9 | 14.7 | 14.0 | 71.3 | 28.7 | 0.049 | 0.023 | 24 | 22 | 3 | 0 |
| Gymnogongrus griffithsiae (OP537223) | 25,812 | 37.0 | 33.6 | 15.2 | 14.2 | 70.6 | 29.4 | 0.048 | 0.035 | 24 | 22 | 3 | 0 |
| Mastocarpus cristatus (OP537224) | 25,838 | 35.5 | 31.8 | 16.7 | 16.0 | 67.3 | 32.7 | 0.054 | 0.023 | 24 | 23 | 3 | 1 |
| Mastocarpus latissimus (OP451857) | 26,208 | 36.2 | 32.2 | 16.2 | 15.5 | 68.4 | 31.6 | 0.059 | 0.023 | 25 | 23 | 3 | 1 |
| Mastocarpus papillatus (OP451852) | 26,132 | 34.3 | 30.6 | 18.1 | 17.0 | 64.9 | 35.1 | 0.058 | 0.023 | 25 | 23 | 3 | 1 |
| Mastocarpus stellatus (OP537222) | 25,826 | 36.4 | 32.5 | 15.9 | 15.2 | 68.9 | 31.1 | 0.057 | 0.022 | 23 | 22 | 3 | 0 |
Table 3.
Nucleotide composition and skewness of PCGs in the mitochondrial genome of Ahnfeltiopsis flabelliformis.
Table 3.
Nucleotide composition and skewness of PCGs in the mitochondrial genome of Ahnfeltiopsis flabelliformis.
| PCG | Length (bp) | Nucleotide Composition (%) | AT-Skewness | GC-Skewness | |||||
|---|---|---|---|---|---|---|---|---|---|
| A | T | G | C | A + T | G + C | ||||
| rps3 | 693 | 37.2 | 36.9 | 12.3 | 13.6 | 74.2 | 25.8 | 0.004 | −0.050 |
| rpl16 | 417 | 41.2 | 31.4 | 13.9 | 13.4 | 72.7 | 27.3 | 0.135 | 0.018 |
| cox1 | 1593 | 26.9 | 39.5 | 17.0 | 16.6 | 66.4 | 33.6 | −0.189 | 0.013 |
| cox2 | 762 | 31.1 | 36.5 | 17.5 | 15.0 | 67.6 | 32.4 | −0.080 | 0.077 |
| cox3 | 819 | 25.8 | 42.9 | 17.2 | 14.2 | 68.6 | 31.4 | −0.249 | 0.097 |
| atp4 | 549 | 37.5 | 39.2 | 9.3 | 14.0 | 76.7 | 23.3 | −0.021 | −0.203 |
| cob | 1143 | 27.0 | 42.6 | 16.1 | 14.3 | 69.6 | 30.4 | −0.224 | 0.061 |
| nad6 | 618 | 29.1 | 42.9 | 15.0 | 12.9 | 72.0 | 28.0 | −0.191 | 0.075 |
| sdh2 | 759 | 35.7 | 36.2 | 13.7 | 14.4 | 71.9 | 28.1 | −0.007 | −0.023 |
| sdh3 | 402 | 28.6 | 47.5 | 8.2 | 15.7 | 76.1 | 23.9 | −0.248 | −0.313 |
| atp9 | 231 | 26.0 | 40.7 | 20.3 | 13.0 | 66.7 | 33.3 | −0.221 | 0.221 |
| rps11 | 357 | 42.6 | 32.8 | 12.0 | 12.6 | 75.4 | 24.6 | 0.130 | −0.023 |
| nad3 | 366 | 30.3 | 45.9 | 13.7 | 10.1 | 76.2 | 23.8 | −0.204 | 0.149 |
| nad1 | 981 | 28.7 | 40.8 | 16.5 | 14.0 | 69.5 | 30.5 | −0.173 | 0.084 |
| nad2 | 1494 | 28.1 | 46.0 | 13.3 | 12.6 | 74.1 | 25.9 | −0.241 | 0.028 |
| sdh4 | 240 | 35.0 | 43.3 | 10.4 | 11.3 | 78.3 | 21.7 | −0.106 | −0.038 |
| nad4 | 1482 | 27.6 | 44.5 | 14.0 | 13.9 | 72.1 | 27.9 | −0.234 | 0.005 |
| nad5 | 2004 | 26.4 | 44.0 | 16.1 | 13.5 | 70.5 | 29.5 | −0.249 | 0.088 |
| atp8 | 411 | 38.4 | 38.7 | 8.5 | 14.4 | 77.1 | 22.9 | −0.003 | −0.255 |
| atp6 | 762 | 28.7 | 43.8 | 13.0 | 14.4 | 72.6 | 27.4 | −0.208 | −0.053 |
| tatC | 708 | 28.4 | 50.0 | 9.3 | 12.3 | 78.4 | 21.6 | −0.276 | −0.137 |
| rps12 | 384 | 38.3 | 29.9 | 17.2 | 14.6 | 68.2 | 31.8 | 0.122 | 0.082 |
| rpl20 | 252 | 42.9 | 35.3 | 9.9 | 11.9 | 78.2 | 21.8 | 0.096 | −0.091 |
| nad4L | 306 | 32.7 | 41.2 | 14.4 | 11.8 | 73.9 | 26.1 | −0.115 | 0.100 |
| Total | 17,733 | 30.3 | 41.5 | 14.3 | 13.08 | 71.8 | 28.2 | - | - |
Table 4.
Characteristics of the mitochondrial PCGs in six Phyllophoraceae species.
| Genes | Length (bp) | Amino Acids | Start Codon | Stop Codon | Coding Strand |
|---|---|---|---|---|---|
| rps3 | 693 | 230 | ATG | TAA | H |
| rpl16 | 417 a,d/435 b/414 c/411 e/420 f | 138 a,d/144 b/137 c/136 e/139 f | ATG | TAA | H |
| cox1 | 1593 a/1596 b/1608 c,d,e,f | 530 a/531 b/535 c,d,e,f | ATG | TAG a,b/TAA c,d,e,f | H |
| cox2 | 762 a/771 b,c,d,e,f | 253 a/256 b,c,d,e,f | ATG | TAA | H |
| cox3 | 819 | 272 | ATG | TAA | H |
| atp4 | 549 a,b/552 c,d,e,f | 182 a,b/183 c,d,e,f | ATG | TAA a,b,c,e,f/TAG d | H |
| cob | 1143 a,b/1146 c,d,e/1152 f | 380 a,b/381 c,d,e/383 f | ATG | TAA a,b,c,e,f/TAG d | H |
| nad6 | 618 a,c,e/609 b/615 d,f | 205 a,c,e/202 b/204 d,f | ATG | TAA a,c,d,e,f/TAG b | L |
| sdh2 | 759 a/762 b/753 c,d,e,f | 252 a/253 b/250 c,d,e,f | ATG | TAA a,b,c/TAG d,e,f | L |
| sdh3 | 402 a,b,d,f/447 c/396 e | 133 a,b,d,f/148 c/131 e | ATG | TAA | L |
| atp9 | 231 | 76 | ATG | TAA | L |
| rps11 | 357 a,b/360 c,d,e,f | 118 a,b/119 c,d,e,f | ATG | TAA a,b,c,d,f/TAG e | L |
| nad3 | 366 | 121 | ATG | TAA | L |
| nad1 | 981 | 326 | ATG | TAA | L |
| nad2 | 1494 | 497 | ATG | TAA | L |
| sdh4 | 240 | 79 | ATG a,b,d,e,f/GTG c | TAA | L |
| nad4 | 1482 a,c/1479 b/1473 d,e,f | 493 a,c/492 b/490 d,e,f | ATG | TAA a,b,c,f/TAG d,e | L |
| nad5 | 2004 | 667 | ATG | TAA | L |
| atp8 | 411 a/414 b,c,d,e,f | 136 a/137 b,c,d,e,f | ATG | TAA | L |
| atp6 | 762 a/771 b,c,d,e,f | 253 a/256 b,c,d,e,f | ATG a/ATT b/ATC c,d,e/ATA f | TAA | L |
| tatC | 708 a/783 b/738 c,d,f/543 e | 235 a/260 b/245 c,d,f/180 e | ATG a/ATA b,c,d,f/GTG e | TAA | H |
| rps12 | 384 | 127 | ATG | TAA | H |
| rpl20 * | 252 a,b,d/264 e | 83 a,b,d/87 e | ATG a,b,d,e | TAA a,b,d/TAG e | H |
| nad4L | 306 | 101 | ATG | TAA | H |
a A. flabelliformis (PQ685980); b G. griffithsiae (OP537223); c M. cristatus (OP537224); d M. latissimus (OP451857); e M. papillatus (OP451852); f M. stellatus (OP537222); * gene rpl20 absent in M. cristatus, and M. stellatus.
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Patil, M.P.; Kim, J.-O.; Kim, Y.-R.; Nirmal, N.; Kim, G.-D.; Kim, K. Characterization of the Complete Mitochondrial Genome of the Red Alga Ahnfeltiopsis flabelliformis (Rhodophyta, Gigartinales, Phyllophoraceae) and Its Phylogenetic Analysis. Biology 2025, 14, 638. https://doi.org/10.3390/biology14060638
AMA Style
Patil MP, Kim J-O, Kim Y-R, Nirmal N, Kim G-D, Kim K. Characterization of the Complete Mitochondrial Genome of the Red Alga Ahnfeltiopsis flabelliformis (Rhodophyta, Gigartinales, Phyllophoraceae) and Its Phylogenetic Analysis. Biology. 2025; 14(6):638. https://doi.org/10.3390/biology14060638
Chicago/Turabian StylePatil, Maheshkumar Prakash, Jong-Oh Kim, Young-Ryun Kim, Nilesh Nirmal, Gun-Do Kim, and Kyunghoi Kim. 2025. "Characterization of the Complete Mitochondrial Genome of the Red Alga Ahnfeltiopsis flabelliformis (Rhodophyta, Gigartinales, Phyllophoraceae) and Its Phylogenetic Analysis" Biology 14, no. 6: 638. https://doi.org/10.3390/biology14060638
APA StylePatil, M. P., Kim, J.-O., Kim, Y.-R., Nirmal, N., Kim, G.-D., & Kim, K. (2025). Characterization of the Complete Mitochondrial Genome of the Red Alga Ahnfeltiopsis flabelliformis (Rhodophyta, Gigartinales, Phyllophoraceae) and Its Phylogenetic Analysis. Biology, 14(6), 638. https://doi.org/10.3390/biology14060638
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