Conspecificity of the Peruvian Corallina ferreyrae with C. caespitosa (Corallinaceae, Rhodophyta) inferred from genomic analysis of the type specimen

Abstract

High-throughput sequencing of an isotype specimen of Corallina ferreyrae from Peru resulted in the assembly of its complete mitogenome (GenBank accession number MK408747) and plastid genome (GenBank MK408748). The mitogenome is 25,953 bp in length and contains 48 genes. The plastid genome is 176,889 bp and contains 233 genes. The organellar genomes share a high-level of gene synteny to other Corallinales. Genetic analysis of standard marker sequences of C. ferreyrae reveals it is conspecific with C. caespitosa. Corallina ferreyrae has priority of publication over C. caespitosa, which we hereby propose as a heterotypic synonym of C. ferreyrae. These data show that C. ferreyrae is not endemic to the Peruvian coast, instead, it is widely distributed in the Atlantic and Pacific Oceans.

Keywords:

• Corallina
• Corallina caespitosa
• Corallina ferreyrae
• mitogenome
• plastid genome

The marine red algal genus Corallina is composed of thirty accepted species (Guiry and Guiry 2019). Previous studies emphasized the need for an exhaustive revision of Corallina to determine the extent of its pseudocryptic diversity (Harvey et al. 2002; Walker et al. 2009). In Peru, only two species of Corallina are currently recognized: C. ferreyrae Dawson, Acleto & Foldvik (1964) and C. chilensis Decaisne in Harvey (1849). Corallina ferreyrae was originally described from Pucusana, Peru, and said to differ from other species by its prominent development of flagelliform branchlets. The name C. ferreyrae, however, has been ignored in the literature since. Here, we performed high-throughput sequencing on an isotype specimen of C. ferreyrae to determine its relationship to other species of Corallina.

DNA was extracted from C. ferreyrae (Specimen Voucher- UC1404138) using the Quick-DNA Plant/Seed (Zymo Research, California, USA) following the manufacturer’s instructions. The 150 bp PE Illumina library construction and sequencing was performed using myGenomics, LLC (Alpharetta, Georgia, USA). The genomes were assembled using default de novo settings in MEGAHIT (Li et al. 2015) and CLC Genomics Workbench 12.0 (QIAGEN Bioinformatics, Redwood City, CA, USA). The genes were annotated manually using blastx, NCBI ORFfinder, and tRNAscan-SE 1.21 (Schattner et al. 2005). The C. ferreyrae mitogenome was aligned to other mitogenomes with MAFFT (Katoh and Standley 2013). The phylogenetic analysis was executed using RAxML-NG (Kozlov et al. 2018) with the GTR + gamma model and 100 bootstraps. The tree was visualized with TreeDyn 198.3 at Phylogeny.fr (Dereeper et al. 2008).

The mitogenome of C. ferreyrae is 25,953 bp in length and contains 48 genes. The mitogenome is A + T biased (70.5%) and contains 23 tRNA (trnG, trnL, trnM, trnR, and trnS are duplicated), five ribosomal proteins (rpl16, rpl20, rps3, rps11, and rps12), two rRNA (rrl and rrs), TatC, ymf39, and 17 other genes involved in electron transport and oxidative phosphorylation. The plastid genome of C. ferreyrae is 176,889 bp and contains 233 genes. The genome is AT rich (70.0%) and contains 47 ribosomal proteins, 31 tRNA, 30 photosystem I and II, 28 ycf, 10 phycobiliprotein, eight cytochrome b/f complex, eight ATP synthase, four RNA polymerase, four orfs, three rRNA, and 60 other genes. The mitogenome and plastid genome of C. ferreyrae are similar in length, content, and organization to other coralline algae (Janouškovec et al. 2013; Williamson et al. 2016; Gabrielson et al. 2018; Lee et al. 2018).

Phylogenetic analysis of the C. ferreyrae mitogenome resolves it in a fully supported clade with the generitype C. officinalis, sister to Calliarthrton tuberculosum (Figure 1). A BLAST analysis of cox1, psbA, and rbcL gene markers of C. ferreyrae found exact matches to sequences of C. casepitosa R. H. Walker, J. Brodie, and L. M. Irvine (Walker et al. 2009). Corallina ferreyrae has priority over C. caespitosa and these data, therefore, support placing C. caespitosa in synonymy under C. ferreyrae. Given the hundreds of names classified to Corallina, it has not escaped our notice that there are likely older binomials that have priority over this relatively new name, C. ferreyrae.

Figure 1. Maximum likelihood phylogram of the mitogenome of Corallina ferreyrae and related calcified red algae. Numbers along branches are RaxML bootstrap supports based on 100 replicates. The legend below represents the scale for nucleotide substitutions.

Acknowledgements

We thank Kathy Ann Miller at UC for providing the type material of Corallina ferreyrae.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.

Additional information

Funding

This research was supported by Peruvian Fondecyt Fund (E009-2018-01) with award number 070-2018 to M.S.C. and award number 062-2018 to D.E.B. This study was also supported by Chilean Fondecyt award number 3180539 to M.S.C. and funding from Toribio Rodriguez de Mendoza National University with award number RCU 456-2018-UNTRM/CU to D.E.B.