The complete mitochondrial and plastid genomes of Corallina chilensis (Corallinaceae, Rhodophyta) from Tomales Bay, California, USA

Abstract

Genomic analysis of the marine alga Corallina chilensis from Tomales Bay, California, USA, resulted in the assembly of its complete mitogenome (GenBank accession number MK598844) and plastid genome (GenBank MK598845). The mitogenome is 25,895 bp in length and contains 50 genes. The plastid genome is 178,350 bp and contains 233 genes. The organellar genomes share a high-level of gene synteny to other Corallinales. Comparison of rbcL and cox1 gene sequences of C. chilensis from Tomales Bay reveals it is identical to three specimens from British Columbia, Canada and very similar to a specimen of C. chilensis from southern California. These genetic data confirm that C. chilensis is distributed in Pacific North America.

Keywords:

• Corallina
• Corallina chilensis
• Corallinaceae
• mitogenome
• plastid genome

Corallina chilensis Decaisne (Harvey 1849) is a calcified, intertidal marine red alga originally collected by Charles Darwin from Valparaíso, Chile. Harvey’s species diagnosis described it as being 2.5–5 cm in height with slender stems below and broader and bipinnate stems above (Harvey 1849). The binomial was long regarded as C. officinalis var. chilensis (Decaisne) Kützing (1858), but was recently elevated to specific status by Williamson et al. (2016). We performed high-throughput sequencing on a specimen of C. chilensis from Tomales Bay, California, to determine its genomic structure and genetic relationship to other species of Corallina.

DNA was extracted from C. chilensis (Specimen Voucher – UC2050474) following the protocol of Lindstrom et al. (2011). 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 Geneious Prime (Biomatters Limited, Auckland, New Zealand) and annotated using Geneious Prime and blastx, NCBI ORFfinder, and tRNAscan-SE 1.21 (Schattner et al. 2005). The C. chilensis 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) and pairwise distances were calculated using default parameters in DIVEIN with the GTR model (Deng et al. 2010).

The mitogenome of C. chilensis is 25,895 bp in length and contains 50 genes. It is A + T rich (70.5%) and contains 23 tRNA (trnG, trnL, trnM, trnR, trnS are duplicated), 5 ribosomal proteins (rpl16, rpl20, rps3, rps11, rps12), 2 rRNA (rrl, rrs), orf158, TatC, ymf39, and 17 other genes involved in electron transport and oxidative phosphorylation. The plastid genome of C. chilensis is 178,350 bp and contains 233 genes. The genome is also A + T biased (70.0%) and contains 47 ribosomal proteins, 31 tRNA, 30 photosystem I and II, 28 ycf, 10 phycobiliprotein, 8 cytochrome b/f complex, 8 ATP synthase, 4 RNA polymerase, 4 orfs, 3 rRNA, and 60 other genes. The mitogenome and plastid genome of C. chilensis are similar in length, content, and organization to other coralline red algae (Janouškovec et al. 2013; Bi et al. 2016; Williamson et al. 2016; Lee et al. 2018; Gabrielson et al. 2018; Bustamante et al. 2019).

Phylogenetic analysis of the C. chilensis mitogenome resolved it in a fully supported clade with C. officinalis L. and C. ferreyrae E.Y. Dawson, Acleto & Foldvik (Figure 1). The mitogenome of C. chilensis differed in pairwise distance from C. officinalis by 9.8% and C. ferreyrae by 10.8%. The plastid genome of C. chilensis differed from C. ferreyrae by 2.9%. A BLAST analysis of cox1 and rbcL sequences of C. chilensis from Tomales Bay identified three identical sequences from British Columbia, Canada (as C. frondescens) (Hind and Saunders 2013) and a nearly identical sequence from a specimen of C. chilensis from Monarch Bay, Orange County, California (Williamson et al. 2015).

Figure 1. Maximum likelihood phylogram of the mitogenome of C. chilensis 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.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This research was supported by National Science Foundation award number [1832446] to Hartnell College.