Genomic and phylogenetic analysis of <i>Ceramium cimbricum</i> (Ceramiales, Rhodophyta) from the Atlantic and Pacific Oceans supports the naming of a new invasive Pacific entity <i>Ceramium sungminbooi</i> sp. nov.

Hughey, Jeffery R.; Boo, Ga Hun

doi:10.1515/bot-2016-0036

Cited by 12 publications

(9 citation statements)

References 26 publications

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“…Sequence alignment and phylogenetic analyses. We assembled a dataset consisting of the 51 newly sequenced chloroplast genomes, an incomplete genome (Polysiphonia teges) for which we recovered 79 genes and the four genomes previously published for the order Ceramiales (Salomaki et al 2015, Verbruggen and Costa 2015, Hughey and Boo 2016. All proteincoding genes were aligned at the amino acid level using MAFFTv7.245 (Katoh and Standley 2013) using default settings and checked visually in Geneious 6.1.7 (Biomatters, Auckland, New Zealand).…”

Section: Methodsmentioning

confidence: 99%

Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta)

Díaz‐Tapia

Maggs

West

et al. 2017

Journal of Phycology

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With over a thousand species, the Rhodomelaceae is the most species-rich family of red algae. While its genera have been assigned to 14 tribes, the high-level classification of the family has never been evaluated with a molecular phylogeny. Here, we reassess its classification by integrating genome-scale phylogenetic analysis with observations of the morphological characters of clades. In order to resolve relationships among the main lineages of the family we constructed a phylogeny with 55 chloroplast genomes (52 newly determined). The majority of branches were resolved with full bootstrap support. We then added 266 rbcL, 125 18S rRNA gene and 143 cox1 sequences to construct a comprehensive phylogeny containing nearly half of all known species in the family (407 species in 89 genera). These analyses suggest the same subdivision into higher-level lineages, but included many branches with moderate or poor support. The circumscription for nine of the 13 previously described tribes was supported, but the Lophothalieae, Polysiphonieae, Pterosiphonieae and Herposiphonieae required revision, and five new tribes and one resurrected tribe were segregated from them. Rhizoid anatomy is highlighted as a key diagnostic character for the morphological delineation of several lineages. This work provides the most extensive phylogenetic analysis of the Rhodomelaceae to date and successfully resolves the relationships among major clades of the family. Our data show that organellar genomes obtained through high-throughput sequencing produce well-resolved phylogenies of difficult groups, and their more general application in algal systematics will likely permit deciphering questions about classification at many taxonomic levels.

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Section: Methodsmentioning

confidence: 99%

Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta)

Díaz‐Tapia

Maggs

West

et al. 2017

Journal of Phycology

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“…The sdhD gene was reported missing from the mitochondria of Ceramium japonicum and Asparagopsis taxiformis (Yang et al 2015) and the gene is also not annotated in the more recently published mitochondrial genome of Ceramium sungminbooi (Hughey and Boo 2016). Upon reanalysis, an ORF was identified between nad4 and nad2 , in the conserved Florideophyceae location of sdhD in the published mitochondrial genomes for all three species (see tables 1 and 3).…”

Section: Resultsmentioning

confidence: 99%

Red Algal Mitochondrial Genomes are More Complete than Previously Reported

Salomaki

Lane²

2016

Genome Biol Evol

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The enslavement of an alpha-proteobacterial endosymbiont by the last common eukaryotic ancestor resulted in large-scale gene transfer of endosymbiont genes to the host nucleus as the endosymbiont transitioned into the mitochondrion. Mitochondrial genomes have experienced widespread gene loss and genome reduction within eukaryotes and DNA sequencing has revealed that most of these gene losses occurred early in eukaryotic lineage diversification. On a broad scale, more recent modifications to organelle genomes appear to be conserved and phylogenetically informative. The first red algal mitochondrial genome was sequenced more than 20 years ago, and an additional 29 Florideophyceae mitochondria have been added over the past decade. A total of 32 genes have been described to have been missing or considered non-functional pseudogenes from these Florideophyceae mitochondria. These losses have been attributed to endosymbiotic gene transfer or the evolution of a parasitic life strategy. Here we sequenced the mitochondrial genomes from the red algal parasite Choreocolax polysiphoniae and its host Vertebrata lanosa and found them to be complete and conserved in structure with other Florideophyceae mitochondria. This result led us to resequence the previously published parasite Gracilariophila oryzoides and its host Gracilariopsis andersonii, as well as reevaluate reported gene losses from published Florideophyceae mitochondria. Multiple independent losses of rpl20 and a single loss of rps11 can be verified. However by reannotating published data and resequencing specimens when possible, we were able to identify the majority of genes that have been reported as lost or pseudogenes from Florideophyceae mitochondria.

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“…Phylogenetic analysis. A data matrix comprising 17 proteincoding genes (accB, acpP, fabH, ilvH, odpA, rne, rpl16, rpl20, rpl3, rps14, rps16, rps19, sufB, trpA, trpG, tsf, and ycf19) and two plastid-encoded rRNAs (rnl and rns) that were shared between the Harveyella mirabilis plastid, the partial Leachiella pacifica plastid, and 55 completely sequenced plastid genomes from the Ceramiales was assembled to investigate the placement of H. mirabilis and L. pacifica, within the Rhodomelaceae (Salomaki et al 2015, Verbruggen and Costa 2015, Hughey and Boo 2016, D ıaz-Tapia et al 2017. Shared plastid genes were extracted into 19 distinct data sets in Geneious Pro v. 9.1.5 (Kearse et al 2012).…”

Section: Methodsmentioning

confidence: 99%

Molecular phylogenetics supports a clade of red algal parasites retaining native plastids: taxonomy and terminology revised

Salomaki

Lane

2019

Journal of Phycology

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Parasitism is a life strategy that has repeatedly evolved within the Florideophyceae. Historically, the terms adelphoparasite and alloparasite have been used to distinguish parasites based on the relative phylogenetic relationship of host and parasite. However, analyses using molecular phylogenetics indicate that nearly all red algal parasites infect within their taxonomic family, and a range of relationships exist between host and parasite. To date, all investigated adelphoparasites have lost their plastid, and instead, incorporate a host‐derived plastid when packaging spores. In contrast, a highly reduced plastid lacking photosynthesis genes was sequenced from the alloparasite Choreocolax polysiphoniae. Here we present the complete Harveyella mirabilis plastid genome, which has also lost genes involved in photosynthesis, and a partial plastid genome from Leachiella pacifica. The H. mirabilis plastid shares more synteny with free‐living red algal plastids than that of C. polysiphoniae. Phylogenetic analysis demonstrates that C. polysiphoniae, H. mirabilis, and L. pacifica form a robustly supported clade of parasites, which retain their own plastid genomes, within the Rhodomelaceae. We therefore transfer all three genera from the exclusively parasitic family, Choreocolacaceae, to the Rhodomelaceae. Additionally, we recommend applying the terms archaeplastic parasites (formerly alloparasites), and neoplastic parasites (formerly adelphoparasites) to distinguish red algal parasites using a biological framework rather than taxonomic affiliation with their hosts.

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Genomic and phylogenetic analysis of Ceramium cimbricum (Ceramiales, Rhodophyta) from the Atlantic and Pacific Oceans supports the naming of a new invasive Pacific entity Ceramium sungminbooi sp. nov.

Cited by 12 publications

References 26 publications

Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta)

Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta)

Red Algal Mitochondrial Genomes are More Complete than Previously Reported

Molecular phylogenetics supports a clade of red algal parasites retaining native plastids: taxonomy and terminology revised

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