Abstract Organellar genomes serve as useful models for genome evolution and contain some of the most widely used phylogenetic markers, but they are poorly characterized in many lineages. Here, we report 20 novel mitochondrial genomes and 16 novel plastid genomes from the brown algae. We focused our efforts on the orders Chordales and Laminariales but also provide the first plastid genomes (plastomes) from Desmarestiales and Sphacelariales, the first mitochondrial genome (mitome) from Ralfsiales and a nearly complete mitome from Sphacelariales. We then compared gene content, sequence evolution rates, shifts in genome structural arrangements, and intron distributions across lineages. We confirm that gene content is largely conserved in both organellar genomes across the brown algal tree of life, with few cases of gene gain or loss. We further show that substitution rates are generally lower in plastid than mitochondrial genes, but plastomes are more variable in gene arrangement, as mitomes tend to be colinear even among distantly related lineages (with exceptions). Patterns of intron distribution across organellar genomes are complex. In particular, the mitomes of several laminarialean species possess group II introns that have T7-like ORFs, found previously only in mitochondrial genomes of Pylaiella spp. (Ectocarpales). The distribution of these mitochondrial introns is inconsistent with vertical transmission and likely reflects invasion by horizontal gene transfer between lineages. In the most extreme case, the mitome of Hedophyllum nigripes is ∼40% larger than the mitomes of close relatives because of these introns. Our results provide substantial insight into organellar evolution across the brown algae.
Significance Our work challenges the existing paradigm that marine Arctic ecosystems are depauperate extensions of southerly (temperate) communities established in the wake of recent glaciation, fundamentally changing how these systems should be viewed and interpreted. We forward hypotheses regarding the history of Arctic marine systems, particularly with regards to endemism being an integral feature of Arctic biomes, and present a firm framework for future evolutionary research in this system typically viewed as “ecologically immature.”
Seaweeds are considered a promising source of phytochemical compounds, including polyphenols. The Australian shoreline hosts a diverse array of seaweeds; however, the phenolic profile and the antioxidant potential of most species remain unclear, necessitating further exploration. To this end, ten red seaweeds were collected, identified using molecular testing, and their phenolic compounds were extracted using acidified ethanol and subjected to ten in vitro assays. The Relative Antioxidant Capacity Index (RACI) was calculated for each sample to compare the overall results. The results indicated that Phacelocarpus peperocarpos exhibited the highest overall phenolic and antioxidant potential, followed by Callophyllis sp. and Rhodophyllis sp.. A total of 365 phenolic compounds were screened, comprising 85 phenolic acids, 164 flavonoids, and 118 other polyphenols. Correlation analysis displayed a positive correlation between phenolic content, antioxidant activity, and the identified phenolic compounds. Overall, this study sheds light on the polyphenol content and antioxidant potential of ten red seaweed species from Queenscliff, Victoria, through various in vitro assays and LC-ESI-QTOF-MS/MS characterization. The findings indicate that Australian red seaweeds are a promising source of polyphenols and exhibit considerable antioxidant properties, underscoring their potential in providing substantial health benefits and functional food products.
The genomic era continues to revolutionize our understanding of the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long-standing questions about the evolution of biodiversity largely unexplored. Here, we used whole-genome sequencing (WGS) datasets to survey species diversity in the kelp genus Alaria, compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia, A. praelonga, A. crispa, A. marginata, and A. esculenta), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single-nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high-quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria, which we hypothesize represents the synonymized taxon A. grandifolia. The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A. praelonga, A. crispa, and putative A. grandifolia, and between some lineages of the A. marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and biodiversity beyond amplicon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria. We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.
Provided in this project are vcf files and occurrence data related to phylogenomic analysis of the kelp Alaria. All detailed methods, including filtering parameters, can be found in the article sharing this project title (article currently in review). Alaria_occurence_data_2iv20.csv: occurrence data used for Fig. 1 map, sourced from records from Luning 1990 (Biogeography of Seaweeds), Barcode of Life Data Systems, and Macroalgal Portal.
Alaria_phylogenomics_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).
Alaria_phylogenomics_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).
Alaria_phylogenomics_SNP_final_LD.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).
Alaria_phylogenomics_SNP_final_LD.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).
Alaria_phylogenomics_SNP_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to KU-791D_nuclear_scaffolds.fasta. This file has no SNP filters applied to it.
Alaria_Undaria_final_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to Undaria pinnatifida genome (Shan et al. 2020). This file has no SNP filters applied to it.
Alaria_Undaria_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).
Alaria_Undaria_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).
KU-791D_nuclear_scaffolds.fasta: reference nuclear scaffolds for Alaria esculenta used for mapping reads from various species of Alaria.
Abstract The extent that Pleistocene climate variability promoted speciation has been much debated. Here, we surveyed genetic markers in winged kelp Alaria in the Gulf of Alaska, Northeast Pacific Ocean to understand how paleoclimates may have influenced diversity in this kelp. The study included wide geographic sampling over 2800 km and large sample sizes compared to previous studies of this kelp. Mitochondrial 5′-COI (664 bp), plastid rbcL-3′ (740 bp) and 8 microsatellite markers in 16 populations resolved 5 well-defined lineages. COI-rbcL haplotypes were distributed chaotically among populations around the Gulf of Alaska. Principal Coordinates Analysis of microsatellite genotypes grouped plants largely by organellar lineage instead of geography, indicating reproductive isolation among lineages. However, microsatellite markers detected hybrids at 3 sites where lineages co-occurred. Local adaptation on various time scales may be responsible for some genetic differences between populations located along wave-energy and salinity gradients, but the chaotic pattern of variability over hundreds of kilometers is likely due to isolations in northern refugia during Pleistocene ice ages. The range of divergences between populations indicates that episodic glaciations led to the creation of new lineages, but population turnover (local extinctions and recolonizations) limited the formation of new species in the Northeastern Pacific Ocean.
Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic group, which is very distantly related to animals and land plants, is still poorly characterised at the genome level. Here we analyse 60 new genomes that include species from all the major brown algal orders. Comparative analysis of these genomes indicated the occurrence of several major events coinciding approximately with the emergence of the brown algal lineage. These included marked gain of new orthologous gene families, enhanced protein domain rearrangement, horizontal gene transfer events and the acquisition of novel signaling molecules and metabolic pathways. The latter include enzymes implicated in processes emblematic of the brown algae such as biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. These early genomic innovations enabled the adaptation of brown algae to their intertidal habitats. The subsequent diversification of the brown algal orders tended to involve loss of gene families, and genomic features were identified that correlated with the emergence of differences in life cycle strategy, flagellar structure and halogen metabolism. We show that integration of large viral genomes has had a significant impact on brown algal genome content and propose that this process has persisted throughout the evolutionary history of the lineage. Finally, analysis of microevolutionary patterns within the genus Ectocarpus indicated that deep gene flow between species may be an important factor in genome evolution on more recent timescales.
Chilean species of marine macroalgae with amphitropical distributions oftentimes result from introductions out of the Northern Hemisphere. This possibility was investigated using haplotype data in an amphitropical red macroalgae present in Chile, Callophyllis variegata. Published sequence records from Canada and the United States were supplemented with new collections from Chile (April 2014âNovember 2015). Specimens of C. variegata were amplified for the 5â² end of the cytochrome c oxidase subunit I gene (COI-5P) and the full length nuclear internal transcribed spacer region. Haplotype networks and biogeographic distributions were used to infer whether C. variegata was introduced between hemispheres, and several population parameters were estimated using IMa2 analyses. C. variegata displayed a natural amphitropical distribution, with an isolation time of approximately 938 ka between hemispheres. It is hypothesized that contemporary populations of C. variegata were established from a refugial population during the late Pleistocene, and may have crossed the tropics via rafting on buoyant species of kelp or along deep-water refugia coincident with global cooling, representing a rare case of a non-human mediated amphitropical distribution. Key words: amphitropical; Chile; IMa2; non-native; red algae
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