An evaluation of methodology to determine algal genome completeness

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

The hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina and long-read Pacific Biosciences (PacBio) sequencing platforms combined with chromatin conformation capture data from the Chicago and Hi-C platforms. The genome was 55.87 Mb in length and assembled to a high contiguity (N50: 304.34 kb) of 12 chromosomes built from 112 scaffolds, with a total of only 4.34 Mb (~ 7.77%) remaining unplaced. The final assemblies were evaluated for completeness of the genome by using Benchmarking Universal Single Copy Orthologs (BUSCO) v4.1.4, and based on 4464 total BUSCO polyporales group searches, the assemblies yielded 4264 (95.52%) of the conserved orthologs as complete and only a few fragmented BUSCO of 42 (0.94%) as well as a missing BUSCO of 158 (3.53%). Genome annotation predicted a total of 21,074 coding genes, with a GC content ratio of 59.2%. The genome features were analyzed with different databases, which revealed 2471 Gene Ontology/GO (11.72%), 5418 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthologous/KO (25.71%), 13,913 Cluster of Orthologous Groups of proteins/COG (66.02%), 60 ABC transporter (0.28%), 1049 Carbohydrate-Active Enzymes/CAZy (4.98%), 4005 pathogen-host interactions/PHI (19%), and 515 fungal transcription factor/FTFD (2.44%) genes. The results obtained in this study provide deep insight for further studies in the future.

Identification of Incomplete Annotations of Biosynthesis Pathways in Rhodophytes Using a Multi-Omics Approach

Rhodophytes (red algae) are an important source of natural products and are, therefore, a current research focus in terms of metabolite production. The recent increase in publicly available Rhodophyte whole genome and transcriptome assemblies provides the resources needed for in silico metabolic pathway analysis. Thus, this study aimed to create a Rhodophyte multi-omics resource, utilising both genomes and transcriptome assemblies with functional annotations to explore Rhodophyte metabolism. The genomes and transcriptomes of 72 Rhodophytes were functionally annotated and integrated with metabolic reconstruction and phylogenetic inference, orthology prediction, and gene duplication analysis to analyse their metabolic pathways. This resource was utilised via two main investigations: the identification of bioactive sterol biosynthesis pathways and the evolutionary analysis of gene duplications for known enzymes. We report that sterol pathways, including campesterol, β-sitosterol, ergocalciferol and cholesterol biosynthesis pathways, all showed incomplete annotated pathways across all Rhodophytes despite prior in vivo studies showing otherwise. Gene duplication analysis revealed high rates of duplication of halide-associated haem peroxidases in Florideophyte algae, which are involved in the biosynthesis of drug-related halogenated secondary metabolites. In summary, this research revealed trends in Rhodophyte metabolic pathways that have been under-researched and require further functional analysis. Furthermore, the high duplication of haem peroxidases and other peroxidase enzymes offers insight into the potential drug development of Rhodophyte halogenated secondary metabolites.

A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp's economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.

Addressing the pervasive scarcity of structural annotation in eukaryotic algae

Despite a continuous increase in algal genome sequencing, structural annotations of most algal genome assemblies remain unavailable. This pervasive scarcity of genome annotation has restricted rigorous investigation of these genomic resources and may have precipitated misleading biological interpretations. However, the annotation process for eukaryotic algal species is often challenging as genomic resources and transcriptomic evidence are not always available. To address this challenge, we benchmark the cutting-edge gene prediction methods that can be generalized for a broad range of non-model eukaryotes. Using the most accurate methods selected based on high-quality algal genomes, we predict structural annotations for 135 unannotated algal genomes. Using previously available genomic data pooled together with new data obtained in this study, we identified the core orthologous genes and the multi-gene phylogeny of eukaryotic algae, including of previously unexplored algal species. This study not only provides a benchmark for the use of structural annotation methods on a variety of non-model eukaryotes, but also compensates for missing data in the current spectrum of algal genomic resources. These results bring us one step closer to the full potential of eukaryotic algal genomics.

Metabolic plasticity of mixotrophic algae is key for their persistence in browning environments

Light availability is the main regulator of primary production, shaping photosynthetic communities and their production of ecologically important biomolecules. In freshwater ecosystems, increasing dissolved organic carbon (DOC) concentrations, commonly known as browning, leads to lower light availability and the proliferation of mixotrophic phytoplankton. Here, a mixotrophic algal species (Cryptomonas sp.) was grown under five increasing DOC concentrations to uncover the plastic responses behind the success of mixotrophs in browning environments and their effect in the availability of nutritionally important biomolecules. In addition to the browning treatments, phototrophic, heterotrophic and mixotrophic growth conditions were used as controls. Despite reduced light availability, browning did not impair algal growth compared to phototrophic conditions. Comparative transcriptomics showed that genes related to photosynthesis were down‐regulated, whereas phagotrophy gene categories (phagosome, lysosome and endocytosis) were up‐regulated along the browning gradient. Stable isotope analysis of phospholipid fractions validated these results, highlighting that the studied mixotroph increases its reliance on heterotrophic processes with browning. Metabolic pathway reconstruction using transcriptomic data suggests that organic carbon is acquired through phagotrophy and used to provide energy in conjunction with photosynthesis. Although metabolic responses to browning were observed, essential fatty acid content was similar between treatments while sterol content was slightly higher upon browning. Together, our results provide a mechanistic model of how a mixotrophic alga responds to browning and how such responses affect the availability of nutritionally essential biomolecules for higher trophic levels.

Annotated Genome Sequence of the High-Biomass-Producing Yellow-Green Alga Tribonema minus

Here, we report the annotated genome sequence for a heterokont alga from the class Xanthophyceae. This high-biomass-producing strain, Tribonema minus UTEX B 3156, was isolated from a wastewater treatment plant in California. It is stable in outdoor raceway ponds and is a promising industrial feedstock for biofuels and bioproducts.

Application of omics research in seaweeds with a focus on red seaweeds

Targeted 'omics' research for seaweeds, utilizing various computational and informatics frameworks, has the potential to rapidly develop our understanding of biological processes at the molecular level and contribute to solutions for the most pressing environmental and social issues of our time. Here, a systematic review into the current status of seaweed omics research was undertaken to evaluate the biological diversity of seaweed species investigated (red, green and brown phyla), the levels to which the work was undertaken (from full genome to transcripts, proteins or metabolites) and the field of research to which it has contributed. We report that from 1994 to 2021 the majority of seaweed omics research has been performed on the red seaweeds (45% of total studies), with more than half of these studies based upon two genera Pyropia and Gracilaria. A smaller number of studies examined brown seaweed (key genera Saccharina and Sargassum) and green seaweed (primarily Ulva). Overall, seaweed omics research is most highly associated with the field of evolution (46% of total studies), followed by the fields of ecology, natural products and their biosynthesis, omics methodology and seaweed-microbe interactions. Synthesis and specific outcomes derived from omics studies in the red seaweeds are provided. Together, these studies have provided a broad-scale interrogation of seaweeds, facilitating our ability to answer fundamental queries and develop applied outcomes. Crucial to the next steps will be establishing analytical tools and databases that can be more broadly utilized by practitioners and researchers across the globe because of their shared interest in the key seaweed genera.