Organellar genomes of giant kelp from the southern hemisphere

Figures & data

Figure 1. Macrocystis pyrifera mitochondrial genome map.

Figure 2. Macrocystis pyrifera chloroplast genome map.

Figure 3. (a) Maximum likelihood phylogeny combining concatenated coding sequences from mitochondria and chloroplasts. Ultrafast bootstrapping is shown in the support values, only above 90%. (b) Haplotype network for cox1 from Macrocystis pyrifera. Haplotypes were obtained from Macaya et al. (2010) and Durrant, Barrett, Edgar, Coleman, & Burridge (2015), in which each haplotype represented only one sequence. Mutations are shown as hatch marks in connecting lines. Haplotypes are shaded according to geographic origin. (c) Whole-genome alignment built with MAUVE. Locally Collinear Blocks (LCBs; light red) show high similarities between genomes from southern and northern hemisphere individuals. Below LCB, gene synteny of each genome is shown: ribosomal RNA genes in red, coding genes in white and transfer RNA genes in green. Orange blocks in chloroplast genomes indicate repeat regions.

Figure 4. Genetic variation distribution of chloroplast and mitochondrial coding proteins. (a) uncorrected pairwise divergence, (b) synonymous substitution rate and (c) nonsynonymous substitution rate.

Table 1. The top 10 protein genes with the highest nonsynonymous substitution rates in chloroplast and mitochondrial genomes. dN, nonsynonymous substitution rates; dS, synonymous substitution rates.

Gene	Sequence Length	Pairwise Divergence	dN	dS
Chloroplast
ycf34	285	1.06%	0.0119	1.00E^–04
rpl32	237	0.85%	0.0105	1.00E^–04
orf147	441	0.45%	0.0073	1.00E^–04
rpl5	561	0.36%	0.0043	0
rpl4	645	0.31%	0.0038	0
ycf19	357	0.28%	0.0037	0
rpl1	690	0.29%	0.0036	0
ycf54	372	0.27%	0.0031	0
atpG	468	0.43%	0.0029	0.0092
rpl9	465	0.43%	0.0029	0.0115
Mitochondrion
orf377	1131	4.07%	0.0357	0.1047
rpl31	204	2.46%	0.0179	0.0628
rps11	495	2.23%	0.0119	0.1181
rps7	495	1.42%	0.0097	0.0486
rps12	390	2.09%	0.0096	0.0821
rps2	648	1.08%	0.0093	0.0224
cox2	3852	1.33%	0.0079	0.048
rps4	795	0.88%	0.0072	0.026
rps8	369	1.63%	0.0067	0.0719
tatC	750	1.60%	0.0052	0.0683

Durrant, H. M. S., Barrett, N. S., Edgar, G. J., Coleman, M. A., & Burridge, C. P. (2015). Shallow phylogeographic histories of key species in a biodiversity hotspot. Phycologia, 54, 556–565. doi:10.2216/15-24.1

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Data availability statement

The data that support the findings of this study are openly available in GenBank (https://www.ncbi.nlm.nih.gov/genbank), accession number ON227496 for mitochondrion and ON227495 for chloroplast.