Characterization and organelle genome sequencing of Pyropia species from Myanmar

Abstract

Pyropia is a genus comprising red algae of the Bangiaceae family that is commonly found in intertidal zones worldwide. However, understanding of Pyropia species that are prone to tropical regions remains limited despite recent breakthroughs in genomic research. Within the realm of Pyropia species thriving in tropical regions, P. vietnamensis stands out as a widely recognized species. In this study, we aimed to investigate Pyropia species in the southwest coast of Myanmar using physiological and molecular approaches, culture-based analyses, chloroplast rbcL and nuclear SSU gene sequencing, and whole chloroplast and mitochondrial genome sequencing. Physiological analysis showed that the Myanmar samples were more heat-tolerant than their Japanese counterparts, including those of subtropical origin. Additionally, molecular characterization revealed that the Myanmar samples were closely related to P. vietnamensis from India. This study is the first to sequence the chloroplast and mitochondrial genomes of Pyropia species from tropical regions. A unique deletion event was observed within a ribosomal RNA gene cluster in the chloroplast genome of the studied Pyropia species, which is a deviation from the usual characteristics of most Pyropia species. This study improves current understanding of the physiological and molecular characteristics of this comparatively understudied Pyropia species that grows in tropical regions.

Figure 1

Maximum likelihood phylogram of 111 Bangiales taxa computed from the concatenated nuclear SSU ribosomal RNA (nrSSU) and RuBisCO LSU (rbcL) data from Myanmar specimens, and the dataset described by Sutherland et al. (TreeBASE ID: S11223) using RaxML. The numbers at the nodes represent bootstrap values (% over 500 replicates). The scale bar denotes the number of substitutions per site. Samples from Myanmar are highlighted in orange. The clade names used in the figure are those described by Yang et al.. Bootstrap values less than 50% were not shown. A total of 3260 nucleotide positions (804 parsimony informative sites) were used in this analysis. The alignment data is available in fasta format as Supplementary Dataset 3, and ML tree is available in newick format as Supplementary Dataset 4.

Figure 2

Growth of conchocelis filaments of Pyropia vietnamensis strain Myanmar A, B, C, Pyropia yezoensis strain noma3 gou, and Pyropia tanegashimensis at different temperatures (20, 25 and 30 °C). Formation of conchosporangia is indicated with arrows.

Figure 3

Effects of salinity and temperature (26, 28, and 30 °C) on the growth of natural spore germlings of Pyropia vietnamensis strain Myanmar A, B and C. No spore germling were observed at 26 °C in P. vietnamensis strain Myanmar A at 15 psu. Error bars represent standard deviation of triplicate cultures. Statistical significance was calculated by t-test and asterisk above the histograms indicates significant difference level: *P < 0.05. The data being compared are represented by specific colored asterisk for clarification.

Figure 4

Physical map of the chloroplast genome of Pyropia vietnamensis strain Myanmar A/C created using OrganellarGenomeDraw (OGDRAW; ogdraw.mpimp-golm.mpg.de). Genes are coloured according to their function. Anticlockwise transcribed genes are on the outer side and clockwise transcribed genes are on the inner side of the circle. Dashed area in the inner circle indicates the guanine–cytosine (GC) content of the organelle genomes.

Figure 5

Comparisons of the rRNA repeat regions of (A) Japanese seaweed (P. yezoensis), (B) Myanmar seaweed (P. vietnamensis), and (C) Korean seaweed (P. dentata).

Figure 6

Physical map of the mitochondrial genome of Myanmar seaweed created using OGDRAW (ogdraw.mpimp-golm.mpg.de). Genes are coloured according to their function. Anticlockwise transcribed genes are on the outer side and clockwise transcribed genes are on the inner side of the circle. Dashed area in the inner circle indicates the guanine–cytosine (GC) content of the organelle genomes.

Figure 7

Maximum likelihood (ML) tree of chloroplast genomes of Pyropia species. Protein sequences were extracted from the chloroplast genome dataset of Myanmar seaweed and from available sequence data in the database. Orthologous groups were extracted by using Orthofinder. Bootstrap support values are presented at each node. A total of 28,466 amino acid positions (4072 parsimony informative sites) were used in this analysis. The origin of the samples used in this analysis are described in Supplementary Table 5. The alignment data are available in fasta format as Supplementary Dataset 13, and ML tree is available in Newick format as Supplementary Dataset 14.

Figure 8

Maximum likelihood (ML) tree of mitochondria genomes of Pyropia species. Protein sequences were extracted from the mitochondria genome dataset of Myanmar seaweed and from available sequence data in the database. Orthologous groups were extracted by using Orthofinder. Bootstrap support values are presented at each node. A total of 5455 amino acid positions (1514 parsimony informative sites) were used in this analysis. The origin of the samples used in this analysis is described in Supplementary Table 6. The alignment data are available in fasta format as Supplementary Dataset 15, and ML tree is available in Newick format as Supplementary Dataset 16.