Isochrysis galbana is considered an ideal bait for functional foods and nutraceuticals of humans because of its high fucoxanthin (Fx) content. However, multi-omics analysis of the regulatory networks for Fx biosynthesis in I. galbana has not been reported. In this study, we report a high-quality genome assembly of I. galbana LG007, which has a genome size of 92.73 Mb, with a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenetic analysis confirmed the monophyly of Haptophyta, with I. galbana sister to Emiliania huxleyi and Chrysochromulina tobinii. Evolutionary analysis revealed an estimated divergence time between I. galbana and E. huxleyi of ∼ 133 million years ago. Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion, including IgPLMT, IgOAR1, and IgDEGS1. Metabolome analysis showed that the content of carotenoids in I. galbana cultured under green light for 7 days was higher than that under white light, and β-carotene was the main carotenoid, accounting for 79.09% of the total carotenoids. Comprehensive multi-omics analysis revealed that the content of β-carotene, antheraxanthin, zeaxanthin, and Fx was increased by green light induction, which was significantly correlated with the expression of IgMYB98, IgZDS, IgPDS, IgLHCX2, IgZEP, IgLCYb, and IgNSY. These findings contribute to the understanding of Fx biosynthesis and its regulation, providing a valuable reference for food and pharmaceutical applications.

Background: Jasmine (Jasminum), renowned for its ornamental value and captivating fragrance, has given rise to numerous species and accessions. However, limited knowledge exists regarding the evolutionary relationships among various Jasminum species. Results: In the present study, we sequenced seven distinct Jasminum species, resulting in the assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that the size of the 12 cp genomes ranged from 159 to 165 kb and encoded 134–135 genes, including 86–88 protein-coding genes, 38–40 tRNA genes, and 8 rRNA genes. J. nudiflorum exhibited a larger genome size compared to other species, mainly attributed to the elevated number of forward repeats (FRs). Despite the typically conservative nature of chloroplasts, variations in the presence or absence of accD have been observed within J. sambac. The calculation of nucleotide diversity (Pi) values for 19 cp genomes indicated that potential mutation hotspots were more likely to be located in LSC regions than in other regions, particularly in genes ycf2, rbcL, atpE, ndhK, and ndhC (Pi > 0.2). Ka/Ks values revealed strong selection pressure on the genes rps2, atpA, rpoA, rpoC1, and rpl33 when comparing J. sambac with the three most closely related species (J. auriculatum, J. multiflorum, and J. dichotomum). Additionally, SNP identification, along with the results of Structure, PCA, and phylogenetic tree analyses, divided the Jasminum cp genomes into six groups. Notably, J. polyanthum showed gene flow signals from both the G5 group (J. nudiflorum) and the G3 group (J. tortuosum and J. fluminense). Phylogenetic tree analysis reflected that most species from the same genus clustered together with robust support in Oleaceae, strongly supporting the monophyletic nature of cp genomes within the genus Jasminum. Conclusion: Overall, this study provides comprehensive insights into the genomic composition, variation, and phylogenetic relationships among various Jasminum species. These findings enhance our understanding of the genetic diversity and evolutionary history of Jasminum.

The multi-petal “Hutou” jasmine (Jasminum sambac var. Trifoliatum) is highly valued for bonsai cultivation and landscape design, however, the aroma profile and mechanisms underlying floral scent formation remain elusive. In this study, we generate a nearly complete telomere-to-telomere (T2T) genome assembly of “Hutou” jasmine (487.45 Mb with contig N50 of 38.93 Mb). Metabolomic profiling unveils that 16 significantly differential volatiles (SDVs) may play a crucial role in the formation of flower aroma. Among them, five scented SDVs, particularly α-farnesene and pentanoic acid 1-ethenyl-1,5-dimethyl-4-hexenyl ester, contribute to the characteristic aroma profile of “Hutou” jasmine flowers. Weighted gene co-expression network analysis (WGCNA) identifies HTWRKY41, HTWRKY53, and HTHSP90 as the hub genes potentially regulating the production of these 16 metabolites. The expression of selected genes and duplication events drive the increased relative content of major sesquiterpenoids in terpenoid biosynthetic pathway. Four structural genes (BEAT3, BSMT1, BPBT2, and BPBT3) are potentially implicated in the emission of downstream key volatile esters (benzyl acetate, methyl benzoate, and benzyl benzoate) in the phenylpropanoids synthesis. Our integrated dataset of genomics, transcriptomics, and metabolomics present here provides a theoretical basis for the practical utilization of fragrance and genetic improvement in horticultural applications of “Hutou” jasmine.

Jasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal (“SP”), double-petal (“DP”), and multi-petal (“MP”). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions. Here, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, “SP”, “DP”, and “MP-hutou” (“HT”), with PacBio reads and the “HT” chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in “HT”. We identified a 14.3 kb “HT”-specific insertion on Chr7 of the “HT” nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that “DP” and “HT” evolved from “SP”, with “HT” being the most recent derivative of “DP”. The comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.

Tandem repeats in eukaryotic genomes exhibit intrinsic instability that drives rapid evolutionary diversification. However, their evolutionary dynamics in allopolyploid species such as the water hyacinth (Pontederia crassipes or Eichhornia crassipes) remain largely unexplored. Our study used integrated genomic and cytogenetic analyses of this allotetraploid species to characterize five representative tandem repeats, revealing distinct genomic distribution patterns and copy number polymorphisms. The highly abundant centromeric tandem repeat, putative CentEc, was co-localized with the centromeric retrotransposon CREc, indicating conserved centromeric architecture. Remarkably, putative CentEc sequences showed high sequence conservation (91–100%) despite subgenome divergence, indicative of active concerted evolution. Fluorescence in situ hybridization (FISH) analysis showed ubiquitous telomeric repeats across all chromosomes, while an interstitial chromosome region tandem repeat (ICREc) displayed chromosome-specific localization, both exhibiting copy number variation. Furthermore, differential rDNA organization was observed. 5S rDNA was detected on a single chromosome pair, whereas 35S rDNA exhibited multichromosomal distribution with varying intensities. A comparative analysis of subgenome-specific rDNA sequences revealed substantial heterogeneity in both 5S and 35S rDNA units, suggesting subgenome-biased evolutionary trajectories. Collectively, these findings elucidate the structural and evolutionary significance of tandem repeats in shaping the water hyacinth genome, highlighting mechanisms of concerted evolution and subgenome-biased adaptation in invasive polyploids.

In eukaryotes, tandem repeats are often unstable, leading to rapid evolutionary changes. However, the evolutionary dynamics of these repeats in allopolyploids like the water hyacinth remain (Eichhornia crassipes or Pontederia crassipes) poorly understood. In our study, we analyzed five typ-ical tandem repeats in the allotetraploid water hyacinth using genomic and cytogenetic methods. We found non-random distribution and copy number variation across the genome. The highly abundant centromeric tandem repeat, putative CentEc, co-localized with the centromeric re-trotransposon CREc, indicating conserved centromeric features. Putative CentEc sequences showed high conservation (91%-100%), suggesting ongoing concerted evolution post-subgenome divergence. Fluorescence in situ hybridization (FISH) analysis showed telomere sequences on all chromosomes, with tandem repeat of interstitial chromosome regions (ICREc) only on certain chromosomes, both exhibiting copy number variation. Moreover, 5S rDNA was detected on one chromosome pair, and 35S rDNA on multiple chromosomes with varying intensities. Examination of the genome assembly also revealed sequence heterogeneity in copies of 5S and 35S rDNA from the two subgenomes, implying divergent evolution of these two rDNA families within their re-spective subgenomes. Our findings highlight the role of tandem repeats in the water hyacinth genome's structure and evolution, with implications for understanding the genomic dynamics of invasive species.