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Background: The MinION Access Program (MAP, 2014-2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries. In 2014, faced with a fragmented Illumina assembly for the chloroplast genome of the green algal holobiont Caulerpa ashmeadii, we applied to the MAP to test the prospects of nanopore reads to investigate such intricacies, as well as further explore the hologenome of this species with native and hybrid approaches., Results: The chloroplast genome could only be resolved as a circular molecule in nanopore assemblies, which also revealed structural variants (i.e. chloroplast polymorphism or heteroplasmy). Signal and Illumina polishing of nanopore-assembled organelle genomes (chloroplast and mitochondrion) reflected the importance of coverage on final quality and current limitations. In hybrid assembly, our modest nanopore data sets showed encouraging results to improve assembly length, contiguity, repeat content, and binning of the larger nuclear and bacterial genomes. Profiling of the holobiont with nanopore or Illumina data unveiled a dominant Rhodospirillaceae (Alphaproteobacteria) species among six putative endosymbionts. While very fragmented, the cumulative hybrid assembly length of C. ashmeadii's nuclear genome reached 24.4 Mbp, including 2.1 Mbp in repeat, ranging closely with GenomeScope's estimate (> 26.3 Mbp, including 4.8 Mbp in repeat)., Conclusion: Our findings relying on a very modest number of nanopore R9 reads as compared to current output with newer chemistries demonstrate the promising prospects of the technology for the assembly and profiling of an algal hologenome and resolution of structural variation. The discovery of polymorphic 'chlorotypes' in C. ashmeadii, most likely mediated by homing endonucleases and/or retrohoming by reverse transcriptases, represents the first report of chloroplast heteroplasmy in the siphonous green algae. Improving contiguity of C. ashmeadii's nuclear and bacterial genomes will require deeper nanopore sequencing to greatly increase the coverage of these larger genomic compartments.

Caulerpa J.V. Lamouroux is a genus of green macroalgae belonging to the family Caulerpaceae in the order Bryopsidales. The genus comprises 104 currently accepted species, of which 51 have been recorded from Pacific Islands. Among these islands, French Polynesia is found in the middle of the South Pacific Ocean and includes five archipelagos (i.e., the Austral, Gambier, Marquesas, Society, and Tuamotu Islands) where seaweed inventories have reported a total of 16 Caulerpa species so far based on morphology. Here, based on a sampling covering the five archipelagos of French Polynesia, we attempt to (i) verify the taxonomy of Caulerpa species present in these regions based on phylogeny, (ii) describe in more detail the specific diversity between the five archipelagos, and (iii) provide a morphological identification tool for these species. We successfully obtained 134 new tufA sequences for phylogenetic analyses, which corresponded to 13 species. We propose to resurrect C. pickeringii Harvey & Bailey for representatives of C. webbiana var. pickeringii and classify it in the Caulerpa subgenus Araucarioideae. We also transfer C. seuratii to C. pickeringii based on genetic results. A new morphological identification key is provided as well as an updated distribution of Caulerpa species across French Polynesia. [ABSTRACT FROM AUTHOR]

Routine DNA barcoding with the chloroplast gene tufA identified novel records of an unknown and denuded (i.e. lacking branchlets) Caulerpa species previously reported from the Florida Middle Grounds. tufA barcoding not only confirmed the matching molecular identity of this taxon with several newly collected denuded specimens from shallow habitats of the Yucatán shelf, but also with a set of plumose specimens previously collected from mesophotic depths of the West Florida shelf and recorded as Caulerpa sertularioides. Sequencing of two additional, faster-evolving DNA markers, i.e. nuclear ITS and the newly tested chloroplast-encoded rpoA, each confirmed conspecificity of the above morphotypes and the molecular separation of the new taxon from C. sertularioides and filiform species found in the region, namely C. cupressoides f. denudata and C. fastigiata. In light of our sequencing results and review of the early taxonomic history of filiform Caulerpa, we propose the description of Caulerpa wysorii sp. nov. for this new species that exhibits two distinct morphotypes in currently available collections, i.e. filiform or plumose assimilators. We also subsume C. tongaensis within the broadly distributed C. fastigiata, whose lectotype is also designated herein. In addition to Caulerpa wysorii sp. nov., we discovered yet another unknown denuded species from the Campeche Banks represented by a single specimen thus far. [ABSTRACT FROM AUTHOR]

The siphonous green algal family Caulerpaceae includes the monotypic genus Caulerpella and the species-rich genus Caulerpa. A molecular phylogeny was inferred from chloroplast tufA and rbcL DNA sequences analyzed together with a five marker dataset of non-caulerpacean siphonous green algae. Six Caulerpaceae lineages were revealed, but relationships between them remained largely unresolved. A Caulerpella clade representing multiple cryptic species was nested within the genus Caulerpa. Therefore, that genus is subsumed and Caulerpa ambigua Okamura is reinstated. Caulerpa subgenus status is proposed for the six lineages substantiated by morphological characters, viz., three monotypic subgenera Cliftonii, Hedleyi, and Caulerpella, subgenus Araucarioideae exhibiting stolons covered with scale-like appendages, subgenus Charoideae characterized by a verticillate branching mode, and subgenus Caulerpa for a clade regarded as the Caulerpa core clade. The latter subgenus is subdivided in two sections, i.e., Sedoideae for species with pyrenoids and a species-rich section Caulerpa. A single section with the same name is proposed for each of the other five subgenera. In addition, species status is proposed for Caulerpa filicoides var. andamanensis (W.R. Taylor). All Caulerpa species without sequence data were examined (or data were taken from species descriptions) and classified in the new classification scheme. A temporal framework of Caulerpa diversification is provided by calibrating the phylogeny in geological time. The chronogram suggests that Caulerpa diversified into subgenera and sections after the Triassic- Jurassic mass extinction and that infra-section species radiation happened after the Cretaceous- Tertiary mass extinction. [ABSTRACT FROM AUTHOR]

Morphological and molecular evidence is provided to further document the status of the enigmatic taxon known asCaulerpa floridanaW.R. Taylor from White Shoal, Dry Tortugas, Florida. DNA sequencing of three historical herbarium specimens (WRT329, WRT345 and WRT349) housed at the University of Michigan Herbarium (MICH) demonstrated the molecular separation of this species based on the reconstruction of 931 nucleotides of the chloroplast genetufA.Caulerpa floridanais sister to the western Atlantic endemicC. ashmeadiiHarvey and an unknownCaulerpataxon from the Florida Middle Grounds.Caulerpa floridanamost reliably differs fromC. ashmeadiiby the presence of a sharp, unequivocal apiculus at the tip of each pinnule. A morphological review of southwestern Atlantic records ofC. floridanafrom Brazil excludes these reports as representative of the species. [ABSTRACT FROM AUTHOR]

Molecular characterization (plastid-encoded tufA gene) of New Caledonian members of the Caulerpa racemosa-Caulerpa peltata complex identified five lineages, each possibly harboring multiple species-level entities. On a global scale, the complex encompassed six lineages, two of which were pantropical and the remainder seemingly were restricted to the Indo-Pacific basin. Caulerpa racemosa var. cylindracea, a fast-spreading introduced taxon in the Mediterranean Sea and the Canary Islands, was previously thought to be restricted to southwestern Australia; it was newly reported here for New Caledonia and several northern Australian locations, including the Great Barrier Reef. [ABSTRACT FROM AUTHOR]