Expansion of photoreception-related gene families may drive ecological adaptation of the dominant diatom species Skeletonema marinoi

Genome-wide characterization and expression analysis of WRKY family genes in the biosynthesis of triptolide in Tripterygium wilfordii

BACKGROUND

WRKY transcription factors play a vital role in regulating plant growth, development, and secondary metabolism. Tripterygium wilfordii is a medicinal plant that has been widely utilized in rheumatoid arthritis therapy; it contains triptolide, a prominent bioactive constituent exhibiting potent anti-inflammatory and anti-tumor properties. However, the mechanism underlying the regulatory effects of WRKY on triptolide biosynthesis is poorly understood.

RESULTS

In this study, 95 TwWRKY genes were identified in the T. wilfordii genome, which were divided into three groups. Phylogenetic analysis indicated that the TwWRKY were conservative relative to other plants. Collinearity analysis revealed that gene duplications played a crucial role in the evolution of this gene family. Transcriptome data from various plant tissues were integrated by correlation analysis, and a gene-to-metabolite network was successfully mapped; consequently, 32 TwWRKY genes were selected as potential regulators of triptolide biosynthesis. Furthermore, the expression changes in the 32 TwWRKY genes were analyzed following methyl jasmonate (MeJA) induction, and the key candidates likely to regulate the biosynthesis of triptolide were screened. Finally, we performed subcellular localization on the key candidate gene TW23G00056.1 and found that it plays its biological role in the nucleus.

CONCLUSION

Our study provides a valuable resource for further research on TwWRKY in T. wilfordii. The candidate genes reported here lay the foundation for elucidating the regulatory mechanism of triptolide.

Three reference genomes for freshwater diatom ecology and evolution

Diatoms are an important component of marine and freshwater ecosystems. Although the majority of described diatom species live in freshwater systems, genome sequencing efforts have focused primarily on marine species. Genomic resources for freshwater species have the potential to improve our understanding of diatom ecology and evolution, particularly in the context of major environmental shifts. We used long- and short-read sequencing platforms to assemble reference genomes for three freshwater diatom species, all in the order Thalalassiosirales, which are abundant in the plankton of oceans, lakes, reservoirs, and rivers worldwide. We targeted three species that cover the breadth of phylogenetic diversity in the cyclostephanoid clade of Thalassiosirales: Cyclostephanos tholiformis (JALLPB020000000), Discostella pseudostelligera (JALLBG020000000), and Praestephanos triporus (JALLAZ020000000). The reference genome for D. pseudostelligera was considerably smaller (39 Mb) than those of both P. triporus (73 Mb) and C. tholiformis (177 Mb). Long-read sequencing allowed for the assembly of scaffold-level genomes, including regions rich in repetitive DNA. Compared to short-read assemblies, long-read assemblies increased the contig N50 length as much as 37-fold and reduced the number of contigs by more than 88%. Transcriptome-guided annotation of the protein-coding genes identified between 10,000 and 12,000 genes. This work provides further demonstration of the value of long-read sequencing and provides novel genomic resources for understanding the ecology and evolution of freshwater diatoms.

High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida)

Diatoms are unicellular eukaryotic microorganisms thriving in most aquatic environments thanks to the expression of biosynthetic pathways for secondary metabolites involved in defence and adaptation to environmental changes. The sequencing of the transcriptome of the cosmopolitan diatom Thalassiosira rotula Meunier 1910 (synonym of Thalassiosira gravida Cleve 1896) and of the metagenome of its associated microbiome revealed the presence of biosynthetic pathways synthesising molecules and compounds useful for the algae survival and with potential biotechnological applications. Here we present the genome of a Neapolitan T. rotula strain, which is 672 Mbp in size due to a high proportion of repetitive elements (63.59%) and segmental duplications (14%), while the number of predicted genes resulted to be comparable to that of smaller diatom genomes. DNA methylation was predominantly located in transposable elements.

Harmonized coexistence of intragenomic variations in diatom Skeletonema strains

Metabarcoding analysis has been demonstrated to be an effective technology for monitoring diversity and dynamics of phytoplankton including Skeletonema species. Although molecular diversity uncovered in metabarcoding projects has generally been interpreted as sum of interspecies diversity and intraspecies diversity, accumulating evidence suggests that it also harbors unprecedentedly high levels of intra-genomic variations (IGVs). As up to thousands of amplicon sequence variants (ASVs) identified in a typical metabarcoding project can be annotated to be Skeletonema species, we hypothesize that substantial portions of these ASVs are contributed by IGVs. Here, the nature of IGVs in Skeletonema species was quantitatively analyzed by carrying out single-strain metabarcoding analysis of 18S rDNA V4 in 49 strains belonging to seven Skeletonema species. Results showed that each Skeletonema strain harbored a high level of IGVs as expected. While many Skeletonema strains each contained one dominant ASV and a substantial number of ASVs displaying much lower relative abundance, other Skeletonema strains each contained multiple ASVs with comparable or nearly equally abundances. Thus the co-existence of multiple dominant ASVs in a single cell indicated a tug-of-war of these variants in evolution, which may eventually result in harmonized coexistence of multiple dominant ASVs. A total of nine dominant ASVs and 652 non-dominant ASVs were found in 49 strains of seven Skeletonema species, indicating rich interspecies and intraspecies variations, and complex evolution of IGVs in genus of Skeletonema. The results confirmed that the extensive degree of IGVs was the main contributor to the high molecular diversity revealed by metabarcoding analysis. This study highlights the importance of quantitative characterization of IGVs in Skeletonema species for accurate interpretation of species diversity in metabarcoding analysis.

A high-quality genome of the early diverging tychoplanktonic diatom Paralia guyana

The diatom Paralia guyana is a tychoplanktonic microalgal species that represents one of the early diverging diatoms. P. guyana can thrive in both planktonic and benthic habitats, making a significant contribution to the occurrence of red tide events. Although a dozen diatom genomes have been sequenced, the identity of the early diverging diatoms remains elusive. The understanding of the evolutionary clades and mechanisms of ecological adaptation in P. guyana is limited by the absence of a high-quality genome assembly. In this study, the first high-quality genome assembly for the early diverging diatom P. guyana was established using PacBio single molecular sequencing. The assembled genome has a size of 558.85 Mb, making it the largest diatom genome on record, with a contig N50 size of 26.06 Mb. A total of 27,121 protein-coding genes were predicted in the P. guyana genome, of which 22,904 predicted genes (84.45%) were functionally annotated. This data and analysis provide innovative genomic resources for tychoplanktonic microalgal species and shed light on the evolutionary origins of diatoms.

Acquisition and evolution of the neurotoxin domoic acid biosynthesis gene cluster in Pseudo-nitzschia species

Of the hitherto over 60 taxonomically identified species in the genus of Pseudo-nitzschia, 26 have been confirmed to be toxigenic. Nevertheless, the acquisition and evolution of the toxin biosynthesis (dab) genes by this extensive group of Pseudo-nitzschia species remains unclear. Through constructing chromosome-level genomes of three Pseudo-nitzschia species and draft genomes of ten additional Pseudo-nitzschia species, putative genomic integration sites for the dab genes in Pseudo-nitzschia species were explored. A putative breakpoint was observed in syntenic regions in the dab gene cluster-lacking Pseudo-nitzschia species, suggesting potential independent losses of dab genes. The breakpoints between this pair of conserved genes were also identified in some dab genes-possessing Pseudo-nitzschia species, suggesting that the dab gene clusters transposed to other loci after the initial integration. A "single acquisition, multiple independent losses (SAMIL)" model is proposed to explain the acquisition and evolution of the dab gene cluster in Pseudo-nitzschia species.

Chromosome-level genome assembly of marine diatom Skeletonema tropicum

Skeletonema tropicum is a marine diatom of the genus Skeletonema that also includes many well-known species including S. marinoi. S. tropicum is a high temperature preferring species thriving in tropical ocean regions or temperate ocean regions during summer-autumn. However, mechanisms of ecological adaptation of S. tropicum remain poorly understood due partially to the lack of a high-quality whole genome assembly. Here, we report the first high-quality chromosome-scale genome assembly for S. tropicum, using cutting-edge technologies including PacBio single molecular sequencing and high-throughput chromatin conformation capture. The assembled genome has a size of 78.78 Mb with a scaffold N50 of 3.17 Mb, anchored to 23 pseudo-chromosomes. In total, 20,613 protein-coding genes were predicted, of which 17,757 (86.14%) genes were functionally annotated. Collinearity analysis of the genomes of S. tropicum and S. marinoi revealed that these two genomes were highly homologous. This chromosome-level genome assembly of S. tropicum provides a valuable genomic platform for comparative analysis of mechanisms of ecological adaption.