Analysis of the complete organellar genomes of Palmaria decipiens (Palmariaceae, Rhodophyta) from Antarctica confirms its taxonomic placement in the genus Palmaria

Abstract

Palmaria decipiens (Reinsch) R.W.Ricker is a ecologically important red seaweed restricted to high latitudes of the southern hemisphere. Here, we contribute to the bioinformatics and evolutionary systematics of the Palmariales by performing high throughput sequencing analysis on a specimen of P. decipiens from the western Antarctic Peninsula. The P. decipiens mitogenome is 26,645 base pairs (bp) in length and contains 49 genes (GenBank accession MN967053) and the plastid genome is 193,007 bp and contains 245 genes (GenBank accession MN967052). The mitogenome and plastid genome of P. decipiens are similar to P. palmata from Japan in pairwise genetic distances (93.71% and 98.14%, respectively), and P. palmata from the Maine, USA (87.45% and 94.57%, respectively). The genomes of P. decipiens showed high gene synteny with P. palmata, however several tRNA differences are documented. Organellar genome content and phylogenetic analyses of P. decipiens supports its placement in the genus Palmaria.

Keywords:

• Antarctica
• macroalgae
• mitogenome
• palmariales
• plastid genome

Palmaria decipiens is a dominant marine red algal ecosystem species that occurs in the intertidal and subtidal, where it provides habitat, nourishment and shelter for many marine organisms (Becker et al. 2011). It is characterized as having reddish to purple, unbranched blades, that extend up to 70 cm long and have a lubricous glossy surface (Ricker 1987; Becker et al. 2011). To better understand the taxonomy of Palmaria and P. decipiens, the complete mitogenome and plastid genome of P. decipiens from Yelcho Chilean station, Doumer Island, Antarctic Peninsula (64°52′41″S, 63°35′51″W) were characterized.

DNA was extracted from P. decipiens (Specimen Voucher- LMS000004 in HIP, see Thiers 2016) using the NucleoSpin Plant II Kit (Macherey-Nagel, Düren, Germany) following the manufacturer’s instructions. The 150 bp PE Illumina library construction and sequencing was performed by myGenomics, LLC (Alpharetta, Georgia, USA). The genomes were assembled using default de novo settings in MEGAHIT (Li et al. 2016) and Geneious Prime to close the gaps (Biomatters, Ltd, Auckland, New Zealand). The genes were annotated manually using blastx, NCBI ORFfinder, tRNAscan-SE 1.21 (Schattner et al. 2005), and RNammer (Lagesen et al. 2007). The P. decipiens plastid genome was aligned to other plastomes using MAFFT (Katoh and Standley 2013). The phylogenetic analysis was executed with RAxML-NG (Kozlov et al. 2019) using the GTR + gamma model and 1000 bootstraps. The tree was visualized with TreeDyn 198.3 at Phylogeny.fr (Dereeper et al. 2008).

The mitogenome of P. decipiens is 26,645 bp in length and contains 49 genes. It is A + T-rich (67.0%) and includes 23 tRNA, 5 ribosomal proteins, 2 rRNA (rrl, rrs), and 19 other genes involved in mitochondrial function. The plastid genome of P. decipiens is 193,007 bp and contains 245 genes. It is also A + T biased (65.2%) and includes 45 ribosomal proteins, 33 tRNA, 32 photosystem I and II, 30 ycf, 12 cytochrome b/f complex, 8 ATP synthase, 4 RNA polymerase, 6 rRNA, and 75 other genes. The mitogenome of P. decipiens lacks the trnI gene, but like P. palmata from Japan contains trnD and trnH (Kumagai et al. 2019). The plastid genome of P. decipiens differs from P. palmata from Japan and Maine, USA, by the addition of the trnE gene (Costa et al. 2016; Kumagai et al. 2019). Pairwise genetic distances of the mitogenome and plastid genome of P. decipiens and P. palmata from Japan are more similar in mitogenome (93.71%) and plastid genome (98.14%) sequence than P. decipiens is to P. palmata from the Maine, USA (87.45% and 94.57%, respectively). These organellar data support the existence of three distinct entities: P. palmata from the Atlantic; P. ‘palmata’ from Japan; and P. decipiens from Antarctica.

Phylogenetic analysis of the plastid genome of P. decipiens positions it in a clade with P. palmata from Japan and the USA (Figure 1). This evolutionary relationship is similar to the most recent analyses in which the Palmariales is closely allied with the Acrochaetiales, Balbianiales, and Nemaliales (Costa et al. 2016; Yang et al. 2016; Saunders et al. 2018).

Figure 1. Maximum likelihood phylogram of Palmaria decipiens (MN967052) and related Nemaliophycidae plastid genomes. Numbers along branches are RaxML bootstrap supports based on 1000 nreps. The legend below represents the scale for nucleotide substitutions.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This study was supported by FONDECYT [3180539] to M.S.C. and by FONDECYT [1180433] and Proyecto Conicyt PIA Apoyo CCTE [AFB170008] Instituto de Ecología y Biodiversidad (IEB) to A.M.