Analysis of the complete organellar genomes of the rockweed Fucus spiralis (Fucaceae, Phaeophyceae) supports its infraspecific recognition as Fucus vesiculosus var. spiralis

Abstract

Fucus spiralis L. is a broadly distributed monoecious intertidal seaweed. The specific status of F. spiralis however is debatable. Here, we contribute to the bioinformatics and systematics of F. spiralis by analysing the complete mitochondrial and plastid genomes of a specimen from California, U.S.A. The F. spiralis mitogenome is 36,396 base pairs (bp) in length and contains 67 genes, and the plastid genome is 125,066 bp in length and contains 171 genes. The F. spiralis genomes are 99.7% and 99.8% similar in nucleotide sequence to F. vesiculosus, and support the revised classification of F. spiralis to Fucus vesiculosus var. spiralis.

Keywords:

• California
• Fucus spiralis
• Fucus vesiculosus
• mitogenome
• plastid genome

Fucus spiralis is a common intertidal rockweed that occurs in the Atlantic and northeastern Pacific Oceans, and the Mediterranean Sea (Guiry and Guiry 2018). Hybridization studies demonstrate that F. spiralis forms reproductively successful hybrids with the closely related species F. vesiculosus, which exhibit no significant decrease in hybrid fertility (Kniep 1925; Burrows and Lodge 1951; Billard et al. 2005). Molecular phylogenetic analyses of the two species yield polytomies, and DNA sequences of accepted species markers find that F. spiralis differs from F. vesiculosus by as little as 0 bp for both cox1 and the internal transcribed spacer regions (Serrão et al. 1999; Coyer et al. 2006, 2011; Kucera and Saunders 2008; Laughinghouse et al. 2015). The only diagnostic feature appears to be highly polymorphic microsatellite markers (Engel et al. 2003; Wallace et al. 2004; Billard et al. 2005). In this study, we characterize the organellar genomes of F. spiralis to further understand its relationship to F. vesiculosus.

Fucus spiralis (Voucher Specimen – UC2050586) was collected from Pacific Grove, California (36°38′02.0″N, 121°56′19.7″W); its DNA was isolated following Lindstrom et al. (2011). The 150 bp paired-end library construction and sequencing was performed by myGenomics, LLC (Alpharetta, GA). The genomes were assembled by mapping the reads against F. vesiculosus (GenBank – FM957154, AY494079) with the Low Sensitivity/Fast setting in Geneious R11 (Biomatters Limited, Auckland, New Zealand) and annotated using Sequin software. The mitogenome was aligned with other Phaeophyceae using MAFFT (Katoh and Standley 2013). The RaxML analysis was executed using complete mitogenome sequences at Trex-online (Boc and Makarenkov 2012) with the GTR + gamma model and 1000 fast bootstraps, then visualized with TreeDyn 198.3 at Phylogeny.fr (Dereeper et al. 2008).

The F. spiralis mitogenome (GenBank – MG922856) is 36,396 bp in length and contains 3 rRNA, 26 tRNA, and 28 other protein-coding genes. Its gene content and organization are the same as F. vesiculosus (Oudot-Le Secq et al. 2006). Fucus spiralis differs in sequence from F. vesiculosus by only 114 nucleotide SNPs and 10 gaps (99.7% similar). Comparison of all 9,367 protein coding amino acids finds 18 amino acid substitutions between the two species, of which only nine are radical (=the physiochemical properties are altered). Phylogenetic analysis of F. spiralis positions it in a fully supported clade with F. vesiculosus (Figure 1). The plastid genome (GenBank – MG922855) is 125,066 bp in length and contains duplicate copies of 16S, 23S and 5S rRNAs, 26 tRNAs, and 139 protein-coding genes. It is also highly similar to F. vesiculosus in chromosomal content and structure (Le Corguillé et al. 2009). Fucus spiralis differs in sequence from F. vesiculosus by 234 nucleotide SNPs and 67 gaps (99.8% similar), and shows 168 amino acid substitutions out of 31,893 total amino acids, of which only 32 were radical.

Figure 1. Maximum-likelihood phylogram of Fucus vesiculosus var. spiralis (MG922856) and related Phaeophyceae mitogenomes. Numbers along branches are RaxML bootstrap supports based on 1000 nreps. The legend below represents the scale for nucleotide substitutions.

On the basis of this genomic data and evidence from the biological, marker, and phylogenetic species concepts, we conclude that the name F. spiralis should be reduced to varietal status under F. vesiculosus, F. vesiculosus var. spiralis (Linnaeus) Roth.

Acknowledgements

We wish to thank Long Nguyen for technical support with the Geneious software. This work was partly funded by a 2017–2018 Innovation Grant from Hartnell College to Jeffery R. Hughey.

Disclosure statement

No potential conflict of interest was reported by the authors.