Complete organellar genomes of Cystophora brownii: Insights into mitochondrial and plastid structure and evolution in brown algae

Abstract

Cystophora (order Fucales) is one of the most diverse genera of habitat‐forming brown algae and is endemic to temperate reefs of Australia and New Zealand. Species in this genus form complex habitat structures that support diverse marine communities and contribute to coastal productivity. However, Cystophora spp. are highly sensitive to environmental stress, and recent declines across parts of their historical range highlight their vulnerability to ocean warming. Despite their ecological importance, genomic resources for Cystophora remain scarce, limiting insight into their evolutionary history, adaptive capacity, and resilience to environmental change. Here, we sequenced, assembled, and annotated the complete plastid and mitochondrial genomes of the widespread species Cystophora brownii using PacBio HiFi long‐read sequencing. We characterized organellar genome architecture and gene content, conducted comparative analyses with other Fucalean taxa, and reconstructed phylogenetic relationships within the Fucales. The mitochondrial genome is 36,047 bp and contains 66 conserved genes (GenBank accession PZ196221). The plastid genome is 124,536 bp and contains 171 conserved genes, including two inverted repeat regions (GenBank accession PX975689). Comparative analyses indicate conserved gene content, order, and structure relative to other Fucalean organellar genomes. Maximum likelihood phylogenetic analyses robustly place C. brownii within the Fucales with strong support, resolving it as sister to the remaining Sargassaceae, suggesting an early divergence within the family that may date to the Miocene. These genomic resources provide a foundation for resolving the evolutionary placement of Cystophora and advancing studies of organellar genome evolution in brown algae.

Abbreviations

bp

base pair

Gbp

giga base pairs

GC

guanine–cytosine content

IR

inverted repeat

mya

million years ago

NCBI

National Center for Biotechnology Information

ORF

open reading frame

INTRODUCTION

Brown algae (Phaeophyceae) are a diverse and ecologically dominant group of marine macroalgae that play key roles in structuring temperate and polar coastal ecosystems (Bringloe et al., 2020; Wernberg & Filbee‐Dexter, 2019). They contribute substantially to primary productivity, nutrient cycling, and the formation of underwater forests that support diverse marine communities (Coleman & Wernberg, 2017; Eger et al., 2023; Pessarrodona et al., 2022; Steneck et al., 2002; Teagle et al., 2017). Within this group, the order Fucales represents one of the most ecological and functionally significant lineages (Coleman & Wernberg, 2017; Thomsen et al., 2024), encompassing over 550 species from 51 genera and nine families (Bringloe et al., 2020; Thomsen et al., 2024). Members of the Fucales group exhibit remarkable morphological and ecological diversity, occupying a wide range of habitats from intertidal zones to subtidal reefs. Fucoids occupy an estimated 2.57 million km² (Fragkopoulou et al., 2022), coverage which surpasses that of other major marine foundation species, including Laminarian kelps (~1.70 million km²), seagrasses (~1.65 million km²), coral reefs (~0.28 million km²), mangroves (~0.15 million km²), and salt marshes (~0.06 million km²; Bunting et al., 2022; Davidson et al., 2019; Fragkopoulou et al., 2022; Jayathilake & Costello, 2021; McKenzie et al., 2020). Moreover, Fucales are also cultivated in some areas (i.e., Japan) for commercial use (Cunningham et al., 2024; Loy & Jeffs, 2025). Despite their ecological and evolutionary significance, genomic resources for many Fucalean taxa remain limited (but see, e.g., Alvarez et al., 2018; Denoeud et al., 2024; Edgeloe et al., 2025; Graf et al., 2017), restricting our ability to investigate their evolutionary history and adaptive potential at the molecular level. In this context, organellar genomes provide compact and highly informative markers that enable robust insights into phylogenetic relationships, genome architecture, and broader patterns of diversification.

Organellar genomes provide powerful resources for understanding algal evolution and systematics (e.g., Denoeud et al., 2024; Lee et al., 2022; Starko et al., 2021; Wheeler et al., 2022). They have been used to distinguish species (i.e., Lee et al., 2022) and reconstruct evolutionary relationships (e.g., Liu et al., 2024; Starko et al., 2019). The mitochondrial and plastid genomes of brown algae are particularly informative because they are relatively conserved and often exist in high copy numbers, making them efficient targets for sequencing and comparative analyses (Reyes‐Prieto et al., 2007). Their gene content, arrangement, and structural features provide valuable insight into genome architecture and the evolutionary processes that shape it (Smith, 2015; Smith & Patrick, 2015). Recent comparative analyses have revealed extensive variation in organellar genome organization across brown algal lineages, including differences in genome size, gene order, and the presence or absence of specific coding regions (e.g., Iha et al., 2023; Liu et al., 2024; Starko et al., 2021; Wheeler et al., 2022). There is evidence of gene loss and gain, rearrangements, and evolutionary transitions in inverted repeat structure, underscoring the dynamic nature of organellar evolution within the Phaeophyceae (see Bringloe et al., 2020) and other taxa including terrestrial land plants (see Wicke et al., 2011). Collectively, organellar genomes represent a critical comparative framework for investigating genome evolution, functional divergence, and the evolutionary history of one of the most ecologically significant lineages of marine macroalgae.

Cystophora (order Fucales) is the second most speciose genus of fucoids globally (Guiry & Guiry, 2025). Members of this genus are endemic to the southern hemisphere, occurring across Australia and New Zealand, with 23 species currently recognized in the region (Guiry & Guiry, 2025). Cystophora species are widely distributed on temperate reefs (Womersley, 1964), where they play important ecological roles by providing habitat structure and resources for diverse marine communities (Pessarrodona & Grimaldi, 2022). Among these, our study species, C. brownii, is particularly noteworthy, representing a key component of temperate reef ecosystems, but like related species, C. brownii is highly sensitive to climatic stressors, especially rising ocean temperatures (Pessarrodona, 2022). Focusing on C. brownii therefore allowed us to investigate both the ecological significance and the climate vulnerability of this important genus. Despite its ecological importance, there remains a striking lack of genomic resources for Cystophora spp. (but see Buchanan & Zuccarello, 2018; Edgeloe et al., 2025), constraining our understanding of the evolutionary relationships between species, the adaptive potential of populations, and the environmental resilience of the extensive underwater forests formed by these taxa. Cystophora is currently placed within the Sargassaceae (Phillips et al., 2001; Silberfeld et al., 2010), and morphological and limited molecular evidence support its position as a distinct and diverse lineage within the family. However, it has not been included in any of the more recent, broad‐scale Fucoid phylogenies that have incorporated high‐throughput sequencing data or expanded taxon sampling (i.e., Starko et al., 2021). Furthermore, the phylogenetic placement of Cystophora within the Fucoid lineage remains unresolved, as current molecular data are insufficient to clarify its evolutionary history relative to other Fucales. Developing genomic resources for species within Cystophora is therefore critical for resolving its phylogenetic position and for better understanding the mechanisms underpinning its ecological success and vulnerability.

Here, we sequenced, assembled, and annotated the complete phaeoplast and mitochondrial genomes of Cystophora brownii (Fucales, Phaeophyceae) using the PacBio HiFi long‐read sequencing platform. Based on the genome architecture and gene composition of both organelles, we conducted comparative analyses with other brown algal taxa and reconstructed their phylogenetic relationships within the Fucales. This species is relatively widespread and is located from Port Denison/Geraldton (29°S 115° E) to Northern Tasmania (40°S 147° E) in Australia (Womersley, 1964). In recent decades, it has retreated down the west coast of Australia as ocean warming pushes it further south (Pessarrodona, 2022). This study provides valuable genomic resources for advancing phylogenetic and evolutionary studies of Cystophora and contributes to the broader understanding of organellar genome evolution in brown algae.

MATERIALS AND METHODS

Genomic DNA extraction and sequencing

A thallus fragment of Cystophora brownii (Fucales, Phaeophyceae) was collected from Rottnest Island, Western Australia (32.002234° S, 115.561207° E) at low tide when individuals were submerged under approximately 1 m of water (Figure 1). Tissue was rinsed thoroughly in sterile seawater to remove epiphytes and debris, blotted dry, rapidly frozen in liquid nitrogen, and stored at −80°C prior to extraction. Total genomic DNA was isolated using a modified cetyltrimethylammonium bromide (CTAB) extraction protocol, incorporating two initial sorbitol washes to remove polysaccharides and secondary metabolites. DNA quality and concentration were assessed using agarose gel electrophoresis, NanoDrop spectrophotometry, and Qubit fluorometry. A high‐quality, high‐molecular‐weight DNA library was prepared and sequenced using the PacBio Revio platform to generate HiFi long reads. DNA extraction and sequencing were performed by DoveTail Genomics (Scotts Valley, California, United States). We obtained 5,945,939 HiFi reads containing 56.9 Gbp of genomic sequencing data from C. brownii using the PacBio Revio HiFi sequencing platform. The sequencing data was high quality, with 98.1% of mitochondrial reads and 98.2% of plastid reads having ≥Q20.

FIGURE 1.

Cystophora brownii (Fucales, Phaeophyceae) specimen from Rottnest Island, Western Australia (32.002234° S, 115.561207° E). Credit: Ebba Wahlberg.

Mitochondrial and plastid genome assembly

Plastid genome assembly was conducted in ptGAUL (Zhou et al., 2023) using default parameters for plastid genome assembly. This software subsamples the data to assemble a plastid genome with only ~50× coverage. Thus, to determine the actual plastid coverage of our sequencing data, we mapped the reads back to plastid assembly in Geneious Prime (Kearse et al., 2012). The mitochondrial genome was recovered from an assembly made using Hifiasm v0.15.4‐r347 (Cheng et al., 2021) with default parameters using MitoFinder (Allio et al., 2020). Like the plastid assembly, we mapped the raw Hifi reads to the mitochondrial assembly to determine mean coverage. In both cases, Pacbio HiFi reads were used as input, and the software packages produced complete circular contigs corresponding to both plastid and mitochondrial genomes, respectively. Genome annotation was conducted using the GeSeq pipeline (Tillich et al., 2017) through the CHLOROBOX web interface, using Sargassum fusiforme (National Center for Biotechnology Information [NCBI] accessions: NC_048511.1; NC_024655.1) organellar genomes as reference sequences for gene prediction and annotation. Transfer RNAs (tRNAs) were annotated using tRNAscan‐SE v2.0.7 (Chan et al., 2021). Open reading frames (ORFs, including non‐conserved orf and ycf genes) were initially predicted using BLAST‐based searches in GeSeq, supplemented by ORF prediction using ORF finder (NCBI), and labeled according to their inferred amino acid length. All annotations were manually checked and corrected using Geneious Prime (Kearse et al., 2012). During annotation of the mitochondrial genome, the cob gene contained a frameshift relative to homologous sequences from closely related Sargassaceae (e.g., Coccophora langsdorfii). Alignment showed that this shift was associated with a run of five T residues, a motif prone to indel errors in long‐read assemblies (e.g., Lorv & McConkey, 2025; Sacristán‐Horcajada et al., 2021). Removing one T at position 223 restored the reading frame and conserved amino acid sequence; thus, this correction was retained in the final annotation. Circular genome maps were generated with OGDRAW integrated within GeSeq (Greiner et al., 2019).

Phylogenetic and comparative genomes analyses

DNA sequences of protein‐coding genes for mitochondrial and plastid genes were downloaded from NCBI GenBank (see Tables S1 and S2 for accession numbers). A total of 19 mitochondrial and 86 plastid protein‐coding genes shared among the 12 taxa were used for the respective phylogenetic analyses (Table S3). Protein sequences for each gene were aligned using MUSCLE v3.8.3 (Edgar, 2004) using default parameters and then checked by eye in Geneious Prime (Kearse et al., 2012). Concatenated protein alignments were generated for each organelle, comprising 14,090 characters for the mitochondrial dataset and 53,529 characters for the plastid dataset. We then performed phylogenetic reconstruction of the protein sequences in RAxML v.4.0 (Stamatakis, 2006) under a GTRGAMMA model of sequence evolution, with branch support estimated from 1000 bootstrap replicates.

In order to compare a subset of annotated mitochondrial and plastid genomes, additional phylogenetic trees were generated on whole genome sequences using the tree builder implemented in Geneious. Pairwise sequence alignments used to construct the distance matrix were performed under a global alignment framework with free end gaps. Alignment parameters were defined using a 65% similarity cost matrix (5.0/4.0). Genetic distances among sequences were calculated using the Tamura–Nei substitution model. Phylogenetic relationships were inferred using the neighbor‐joining algorithm. All trees used Saccharina latissima as the outgroup.

To allow for direct comparisons across genomes of gene order and arrangement (synteny), linearized genomes were produced in Geneious using an arbitrary but consistent starting point across all genomes (the rnl gene for the mitochondrial genomes and the acsF gene for the chloroplast genomes) and exported as a pdf. Annotation categories were then colored to match the ones used for Cystophora brownii genomes (Figures S1 and S2) on Affinity Designer 2 (v 2.6.5). Mauve analyses were run using ProgressiveMauve (Darling et al., 2010) using default settings implemented in Geneious. For the plastid genomes, the outgroup species Saccharina latissima was compared to C. brownii separately as driving major changes in synteny across all Fucales.

RESULTS AND DISCUSSION

Cystophora brownii mitochondrial genome assembly

The complete mitochondrial genome of Cystophora brownii was recovered at mean coverage of 12,247×. The mitogenome was a circular 36,047 bp molecule with 34.4% GC content, similar in size and GC composition to other Fucalean species such as Sargassum polycystum (34,862 bp; GC% = 35.7: Zhang et al., 2022), Fucus spiralis (36,396 bp; GC% = 34.4: Alvarez et al., 2018), and Silvetia siliquosa (36,036 bp; GC% = 33.7: Liang et al., 2022). It contained 66 conserved genes (38 protein‐coding, 25 tRNAs, and three rRNAs), with gene content highly conserved across Fucales (Figure S1; Table 1; Table S4). All coding genes used ATG as the start codon, and most terminated with TAA (64.9%), followed by TAG (21.6%) and TGA (13.5%). We identified three non‐conserved ORFs within the mitogenome. The first, orf 129, is located between the trnG and rpl16 genes, corresponding to the position of orf 129 in S. polycystum (Zhang et al., 2022), orf 132 in F. spiralis (Alvarez et al., 2018), and orf 131 in Si. siliquosa (Liang et al., 2022), suggesting this feature is widespread among Fucales. A second large non‐conserved ORF, orf 338, was identified between the cox3 and atp6 genes, corresponding to the position of orf 379 in F. vesiculosus (Outdot‐Le Secq et al., 2006) and orf 331 in Si. siliquosa (Liang et al., 2022). A third ORF, orf 41, was located between the trnW and trnM genes, corresponding to the position of orf 39 in Coccophora langsdorfii (Graf et al., 2017) orf 43 in F. spiralis (Alvarez et al., 2018), orf 41 in S. polycystum (Zhang et al., 2022) and orf 41 in Turbinaria ornata (Liu & Pang, 2015). A single duplicated tRNA gene (trnM) was identified, a feature also shared with S. polycystum (Table 1). The trnM gene is involved in protein synthesis and plays a crucial role in energy production via the oxidative phosphorylation system (Salinas‐Giege et al., 2015). The presence of this duplicated trnM gene, along with the overall conserved gene architecture (Figure 2, Figure S3), further reinforces the high structural stability observed across other Fucalean mitogenomes (e.g., Starko et al., 2021) and suggests that Cystophora has retained a gene complement typical of the order despite its long independent evolutionary history. Notably, no introns were detected in the mitogenome, which is consistent with mitogenomes of brown algae for which introns have only been documented in a few species, including Pylaiella littoralis (Ectocarpales), and reported sporadically in taxa such as F. vesiculosus (Fucales), some Laminariales, and some Desmarestiales (Ikuta et al., 2008; Kuhsel et al., 1990; Le Corguillé et al., 2009; Starko et al., 2021), indicating patch distribution of introns across the Phaeophyceae. A lack of introns in Cystophora suggests a structurally stable mitogenome, reflecting strong evolutionary conservation of gene architecture within the Fucales. This genomic stability may also align with the relatively long‐term environmental stability of the southern Australian coastline, where Cystophora diversified (Phillips, 2001). The region's persistent geological and oceanographic stability has been proposed as a key driver of both high species richness and the evolution of endemics in the southern Australian macroalgal flora (Phillips, 2001).

TABLE 1.

Number of genes annotated by GeSeq for Cystophora brownii and Sargassum polycystum mitochondrial and plastid genomes. Duplicated genes listed.

Annotation	Cystophora brownii	Sargassum polycystum
Mitochondrial genome
CDS	38	37
tRNA	25	25
rRNA	3	3
Total genes	66	65
Duplicates	trnM	trnM
Plastid genome
CDS	139	139
tRNA	26	26
rRNA	3	3
Total genes	171	171
Duplicates	trnl, trnA, trnM	trnl, trnA, trnM

FIGURE 2.

Linearized organellar genomes (A, mitochondrial; B, plastid) of the newly sequenced Cystophora brownii compared to fucoid species (Coccophora langsdorfii, Sargassum polycystum, Fucus spiralis, and Silvetia siliquosa for both genomes and Turbinaria ornata for the mitochondrial genome only) and the outgroup Saccharina latissima. Genomes were ordered according to whole‐genome neighbor‐joining phylogenetic trees. Gray boxes with a dashed outline indicate inverted repeat (IR) regions separating large and small single‐copy regions (LSC, SSC). Genes are colored according to major annotation categories (see circularized genomes of C. brownii in Figures S1 and S2).

Cystophora brownii plastid genome assembly

The plastid genome of Cystophora brownii was recovered at a mean coverage of 9707x (52x coverage used for assembly). The plastome was a circular 124,536 bp molecule with 30.2% GC content, closely matching the size and composition of other Fucalean plastomes (Figure 2), such as Sargassum polycystum (124,493 bp; GC% = 30.4: Zhang et al., 2022), Fucus spiralis (125,066 bp; GC% = 28.9: Alvarez et al., 2018), and Silvetia siliquosa (124,991 bp; GC% = 28.8: Liang et al., 2022). As with the mitochondrion, ATG was universally used as the start codon, and most genes ended with TAA (79.0%); the remaining ended with TAG (16.67%) and TGA (3.62%). The genome contained 171 genes (139 protein‐coding, 26 tRNAs, and three rRNAs; Table S5), with conserved gene content including duplicated tRNAs (trnI, trnA, trnM) shared with S. polycystum (Table 1). Among these, we identified a large non‐conserved ORF (orf470) located between the psaJ and petA genes, corresponding to the position of orf501 in F. spiralis (Alvarez et al., 2018) and S. polycystum (Zhang et al., 2022), and orf483 in Si. siliquosa (Liang et al., 2022), reflecting a feature that appears relatively common among Fucales. This retention of a stable plastid gene set, including retention of all LIPOR genes (chlI, chlB, chlL and chlN), together with the duplicated tRNAs, reflects the broader pattern of structural conservation seen across Fucalean plastomes (e.g., Alvarez et al., 2018; Le Corguillé et al., 2009; Starko et al., 2021).

The Cystophora brownii plastid genome contained an inverted repeat (IR) region (5437 bp), which is comparable to the size of the IR in other Fucalean plastids (Sargassum serratifolium, 5437 bp: Lee et al., 2022; S. hemiphylum, 5446 bp: Jia et al., 2024; and Coccophora langsdorfii, 5241 bp: Graf et al., 2017). The IR contains the cbbx, rns, trnL, trnA, rnl, rrn5, and rpl21 genes (Figures 2 and S2). For comparative purposes, we applied the same annotation pipeline to the plastid genomes of previously published Fucalean species (S. serratifolium, S. hemiphyllum, and Co. langsdorfii), as well as the kelp brown algae outgroup (S. latissima), to contextualize the structural features observed in C. brownii. The cbbX gene occurred as a full‐length gene in one copy of the IR, with only a partial cbbX fragment incorporated into the opposite IR. This partial fragment was present only in S. serratifolium, S. hemiphyllum, and Co. langsdorfii and was absent from the outgroup S. latissima. This pattern indicates that the duplication of only a portion of the cbbX gene in the second IR is a feature specific to these Fucalean species rather than a complete gene duplication across both IRs. Similarly, the rpl21 gene fragment was not detected in S. latissima or Co. langsdorfii, indicating possible secondary loss or divergence of this region within certain Fucalean taxa. Synteny analysis indicated high conservation of plastid genome architecture within Fucales, whereas comparisons with S. latissima revealed extensive rearrangements, including numerous locally collinear block (LCB) translocations and inversions (Figure S4). This supports greater structural divergence in plastid than mitochondrial genomes in brown algae (Fucales and Laminariales; Starko et al., 2021).

Phylogenetic placement of Cystophora within the Fucales

A maximum likelihood (ML) phylogenetic analysis based on a concatenated alignment of 19 shared mitochondrial and 86 plastid protein‐coding genes from 12 brown algal taxa robustly placed Cystophora brownii within the Fucales with high confidence, resolving it as a sister to the rest of the Sargassaceae rather than as nested among the derived taxa (Figure 3). Brown algae (Phaeophyceae) originated around 450 million years ago (mya) during the Great Ordovician Biodiversification Event (Choi et al., 2024), and the deep evolutionary history and distinctive morphology of Cystophora are consistent with it representing an early‐diverging branch within the Sargassaceae. In contrast to Sargassum, which originated only ~6–7 mya in the Central Indo‐Pacific and subsequently radiated widely (Yip et al., 2020), Cystophora appears to have a much older and more geographically constrained evolutionary history, one closely tied to the long‐term environmental stability of temperate southern Australia (Phillips, 2001). Our organellar genome analyses also provide clarity on the evolutionary placement of Cystophora within the Fucales. Although the genus has long been recognized as morphologically distinct (Womersley, 1964), its phylogenetic position has remained uncertain due to limited genomic data (but see Buchanan & Zuccarello, 2018; Edgeloe et al., 2025) and the sparse representation of southern hemisphere taxa in earlier studies. By leveraging a large, concatenated dataset of mitochondrial and plastid protein‐coding genes, our results robustly placed C. brownii within the Fucales clade and confirmed its affiliation with the Sargassaceae, while also indicating that it occupies a basal position relative to other members of the family. This improved phylogenetic resolution offers insight into the evolutionary history of Cystophora, suggesting an early divergence within the Sargassaceae that may date back to key periods of brown algal diversification in the Miocene (Denoeud et al., 2024; Yip et al., 2020).

FIGURE 3.

Phylogenetic reconstructions derived from proteins encoded by (A) mitochondrial and (B) plastid genes shared by 12 brown algal species. The outgroup “Saccharina latissima” is denoted with a dotted black circle and the focus group “Cystophora brownii” is denoted with a solid black circle. Support values are shown for both ML bootstrapping and posterior probability. The complete gene lists used to generate the concatenated protein alignments are shown in Table S3. The NCBI accession numbers of the genomes used to obtain these sequences are listed in (a) Table S1 and (b) Table S2.

CONCLUSIONS

Here we have reported complete mitochondrial and plastid genomes of the Fucalean genus Cystophora, specifically the species C. brownii. The gene content and organization are consistent with those of other Fucalean species, suggesting that the full organellar genomes have been successfully captured. These new genomic resources provide a foundational tool for a range of future studies. From a conservation perspective, the availability of full mitochondrial and plastid sequences will allow for more detailed assessments of population structure, genetic diversity, and connectivity in Cystophora species, which is particularly critical given their documented sensitivity to ocean warming, the presence of small‐range endemics and recent declines in parts of their historical range. Beyond conservation, these genomes offer a platform for investigating the evolutionary history and phylogenetic placement of Cystophora within the Fucales, as well as comparative analyses of organellar genome evolution across brown algae. Furthermore, these resources can facilitate studies into the adaptive capacity and resilience of Cystophora to changing climatic conditions, including the identification of genes and pathways that may contribute to stress tolerance. Overall, the organellar genomes reported here represent a valuable genetic toolkit that not only strengthens our understanding of Cystophora evolution and biology but also enhances the broader capacity to study and protect Fucalean algae in the face of ongoing environmental change.

AUTHOR CONTRIBUTIONS

Jane M. Edgeloe: Conceptualization (equal); data curation (equal); formal analysis (lead); investigation (lead); methodology (lead); project administration (equal); resources (equal); software (equal); validation (lead); visualization (lead); writing – original draft (lead); writing – review and editing (lead). Samuel Starko: Conceptualization (equal); data curation (equal); formal analysis (supporting); funding acquisition (equal); investigation (supporting); methodology (supporting); project administration (supporting); resources (supporting); software (supporting); supervision (supporting); writing – original draft (supporting); writing – review and editing (supporting). Georgina V. Wood: Conceptualization (equal); data curation (supporting); funding acquisition (equal); methodology (supporting); writing – review and editing (supporting). Albert Pessarrodona: Conceptualization (equal); data curation (supporting); funding acquisition (equal); methodology (supporting); writing – review and editing (supporting). Antoine J. P. Minne: Formal analysis (supporting); methodology (supporting); software (supporting); visualization (supporting); writing – original draft (supporting); writing – review and editing (supporting). Thomas Wernberg: Funding acquisition (supporting); resources (supporting); writing – review and editing (supporting).

Supporting information

Figure S1. Circos plot of the Cystophora brownii mitochondrial assembly. Genes are colored by annotation category as shown in the key. Genes drawn on the inside of the circle are transcribed clockwise and genes on the outside of the circle counterclockwise. The bar graph in the center circle denotes GC content, with the light gray line representing 50% GC.

Figure S2. Circos plot of the Cystophora brownii plastid assembly. Genes are colored by annotation category as shown in the key. Genes drawn on the inside of the circle are transcribed clockwise and genes on the outside of the circle counterclockwise. The bar graph in the center circle denotes GC content, with the light gray line representing 50% GC. The inverted repeats (IRA and IRB) and large (LSC) and small (SSC) single‐copy regions are labeled on the inner circle.

Figure S3. Genome synteny analysis based on multiple mitochondrial genomes alignment using progressiveMauve (2010Darling et al.). The analysis was performed using six Fucalean species (Cystophora brownii, Coccophora langsdorfii, Turbinaria ornata, Sargassum polycystum, Fucus spiralis, and Silvetia siliquosa) and a Laminarian species as the outgroup (Saccharina latissima). Each organellar genome is represented by one locally collinear block (LCB) under which is represented a linearized genome, all starting with the rnl gene. For each LCB, the line inside each colored panel represents the level of nucleotide similarity across genomes. All LCBs are located above the x‐axis (thick black line), showing no inversion of the genome fragment in comparison to the reference genome (C. brownii). Units at the top are in base pairs (bp). Each linearized genome shows protein‐coding genes (white boxes), rRNA genes (red boxes), and tRNA genes (green boxes). See Table S5 for NCBI plastid genomes accession numbers. See Table S4 for NCBI mitochondrial genomes accession numbers.

Figure S4. Genome synteny analysis based on multiple plastid genomes alignment using progressiveMauve (Darling et al., 2010). In panel (A), the analysis was performed using five Fucalean species (Cystophora brownii, Coccophora langsdorfii, Turbinaria ornata, Sargassum polycystum, Fucus spiralis, and Silvetia siliquosa). In panel (B), the analysis was performed to compare Cystophora brownii with Saccharina latissima (Laminarian species used as outgroup). Each organellar genome is represented by one or several locally collinear blocks (LCBs) under which is represented a linearized genome, all starting with the gene acsF. For each LCB, the line inside each colored panel represents the level of nucleotide similarity across genomes. LCBs located beneath the x‐axis (thick black line) show inversion of the genome fragment in comparison to the reference genome (C. brownii). Units at the top are in base pairs (bp). Each linearized genome shows protein‐coding genes (white boxes), rRNA genes (red boxes), and tRNA genes (green boxes). See Table S5 for NCBI plastid genomes accession numbers.

Table S1. NCBI accession numbers for the mitochondrial genomes used to obtain the mitochondrial gene sequences.

Table S2. NCBI accession numbers for the plastid genomes used to obtain the plastid gene sequences.

Table S3. List of protein‐coding genes used in the mitochondria and plastid phylogenetic analyses.

Table S4. GeSeq annotations of the Cystophora brownii mitochondria assembly.

Table S5. GeSeq annotations of the Cystophora brownii plastid assembly.

File S1. Supplemental information for “Complete organellar genomes of Cystophora brownii: Insights into mitochondrial and plastid structure and evolution in brown algae.”

Edgeloe, J. M. , Starko, S. , Wood, G. V. , Pessarrodona, A. , Minne, A. J. P. , & Wernberg, T. (2026). Complete organellar genomes of Cystophora brownii: Insights into mitochondrial and plastid structure and evolution in brown algae. Journal of Phycology, 62, 1193–1203. 10.1111/jpy.70187

DATA AVAILABILITY STATEMENT

The genomic assemblies generated as part of this study can be found at the NCBI database under reference numbers PZ196221 and PX975689. The Cystophora brownii raw PacBio sequence data is deposited under NCBI BioProject ID PRJNA1475903, sample ID SAMN60680340.