Macrocystis pyrifera (Linnaeus) C. Agardh 1820 belongs to the class Phaeophyceae, order Laminariales, and family Laminariaceae [1]. This species exhibits remarkable adaptability to intricate intertidal habitats and has the capability to sustain its basal metabolism even in exceedingly harsh environmental conditions (Fig. 1). The biological characteristics and distribution patterns of M. pyrifera are distinctly unique, rendering it an exemplary subject for phylogeographic investigations [2]. It is frequently utilized as a primary resource for microbial fermentation and the conversion of carbohydrates into environmentally sustainable bioactive compounds. This practice not only yields substantial economic benefits but also contributes positively to ecological preservation [3]. In recent years, M. pyrifera has garnered extensive attention from scientific researchers engaged in marine ecosystem development and the exploration of bioactive substances.

Fig. 1.
figure 1

Plant image of M. pyrifera. This photo was taken by Shaoxin Liang.

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The fresh specimens were collected from the intertidal rocky shores of Playa Rosada, located along the coast of Valdivia in southern Chile (39°39′ S, 73°13′ W). These specimens have been meticulously preserved under voucher number FIO2023031201 at the First Institute of Oceanography, Ministry of Natural Resources (https://www.fio.org.cn/, Jinlai Miao, miaojinlai@fio.org.cn).

The construction of the whole genome library of the M. pyrifera mitochondrion was carried out by Shanghai Biozeron Biological Technology Co. Ltd. Genomic DNA extraction was performed using a modified cetyltrimethylammonium bromide (CTAB) method. Subsequently, the extracted DNA was utilized for the construction of a 500-bp paired-end library using the NEBNext Ultra DNA Library Prep Kit, designed for Illumina sequencing [4]. Then, we employed the Illumina NovaSeq 6000 platform for paired-end sequencing. The mitochondrial genes were meticulously annotated through the utilization of the GeSeq online tool, employing default parameters for the prediction of protein-coding genes, tRNA, and rRNA. The precise positioning of each coding gene was ascertained through thorough BLAST searches against reference mitochondrial genes. NOVOPlasty v4.2 software was utilized to assemble the mitochondrial genome of M. pyrifera. By enhancing the quality of the original data through quality filtering, we achieved a more accurate assembly, which enabled the prediction of functional genes [5, 6]. The depth of coverage was determined by aligning the reads to the mitochondrial genome sequence with bowtie2 v2.3.4.3, facilitating the evaluation of assembly accuracy [7]. The mitochondrial genome map of M. pyrifera was drawn using the OGDRAW tool [8]. Functional annotations were performed using sequence-similarity Blast searches with a typical cut-off E-value of 10–5 against several publicly available protein database of Kyoto Encyclopedi of Genes and Genomes (KEGG).

We employed MEGA 7.0 for the construction of multiple sequence alignments, aimed at elucidating the phylogenetic relationship of M. pyrifera. Subsequently, a maximum-likelihood (ML) phylogenetic tree was generated using the mitochondrial genomes of 26 species selected from the NCBI-GenBank database. In this analysis, the nucleotide substitution model utilized was the General Time Reversible (GTR, nst = 6) model [9].

The mitochondrial genome was 37 289 base pairs, with coding genes totaling 28 956 bp, constituting approximately 77.65% of the total length (Fig. 2). The mitochondrial genome sequence has 100% total coverage with an average of 181.42× base coverage, ranging from 3× to 353× (Fig. A1). The composition of the mitochondrial genome was as follows: 29.74% A, 38.47% T, 19.10% G, and 12.69% C, resulting in a G+C content of 31.80%. Within the coding genes, there were 25 tRNA genes, three rRNA genes and 38 protein-coding genes. Among the protein-coding genes, tatC and cob exhibit functions in environmental information processing, whereas atp9, nad1, nad5, nad7, cox1, cox3, and cob are associated with environmental adaptation (Table A1).

Fig. 2.
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Schematic map of overall features of the M. pyrifera mitochondrial genome (The inner circle indicates the GC content, and the external circle indicates the genes having different colors based on their functions. The different colored legends in the bottom left corner represent genes with different functions).

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The phylogenetic tree is divided into Laminariaceae, Alariaceae, Lessoniaceae, Acinetosporaceae, Chordariaceae, Scytosiphonaceae, Desmarestiaceae, Sargassaceae and Fucaceae at the family level (Fig. 3). Dictyota dichotoma was generatedas an outgroup. It is observed that M. pyrifera formed a monophyletic clade together with Macrocystis integrifolia. M. pyrifera and M. integrifoli have the closest genetic relationship and both of them belong to Laminariaceae.

Fig. 3.
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Phylogenetic tree of M. pyrifera and 26 species constructed using the ML method based on mitochondrial genome sequences.

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In this study, we successfully assembled and analyzed the complete mitochondrial genome of M. pyrifera. The mitochondrial genome of M. pyrifera spans a length of 37 289 bp, with a notably high AT content. Additionally, phylogenetic analysis was conducted. The phylogenetic analysis confirmed that M. pyrifera exhibited the closest relationship with Macrocystis integrifolia. The complete mitochondrial genome of M. pyrifera contributed to an enhanced understanding of its phylogenetic position within phaeophyceae and the evolutionary dynamics of organellar genomes in brown algae, promotingnovel references for the genetic and phylogenetic research of M. pyrifera through the provision of these data. Genes with functions of environmental information processing and environmental adaptation play a pivotal role in M. pyrifera’s ability to adapt and response to external environmental changes. This contributes to our ongoing exploration of the intricacies of plant growth, development, and genes linked to environmental adaptation.

While the family Laminariaceae boasts a diverse array of species, the available plant sequences within the Laminariaceae remain relatively limited on NCBI. The revelation of the mitochondrial genome sequence of M. pyrifera will offer valuable insights into the phylogeny and gene functions within the family Laminariaceae. It is beneficial for enhancing the efficient utilization of natural resources and contributing to environmental conservation.