This first telomere-to-telomere gap-free reference genome for P. volubilis is presented and the elucidated PvMYB14-PvFAD3 regulatory module provide a foundational resource and potential target for the metabolic engineering of high-quality oil.
Abstract
Alpha-linolenic acid (ALA) is an essential polyunsaturated fatty acid for the human body, possessing a broad spectrum of pharmacological effects. Plukenetia volubilis has garnered widespread cultivation interest for its exceptionally high ALA content. However, the lack of a high-quality reference genome has constrained in-depth genetic and functional research on this species. Here, we present the first telomere-to-telomere gap-free reference genome for P. volubilis. The assembled 665.29 Mb genome spans 29 chromosomes and demonstrates exceptional continuity and completeness (contig N50 = 22.88 Mb). The results of evolutionary analyses showed that the species divergence time of P. volubilis are significantly later than those of other oil crops. Moreover, comparative genomics revealed that P. volubilis underwent a lineage-specific whole-genome triplication around 39.83–48.39 million years ago, coinciding with its divergence from Ricinus communis. To elucidate the genetic basis of its high ALA content, we integrated comparative lipidomic, transcriptomic and genomic analyses, identifying the transcription factor PvMYB14 as a key regulator. The PvMYB14 localizes to the nucleus and directly activates the expression of PvFAD3, by binding to a specific CNGTTA-box motif. We used electrophoretic mobility shift assay to identify conserved nucleotide sites of the CNGTTA-box, with MT4 and MT6 mutations abolishing binding to PvMYB14. Heterologous expression demonstrated that PvMYB14 simultaneously increases total seed oil yield and the proportional content of ALA. This high-quality genome assembly and the elucidated PvMYB14-PvFAD3 regulatory module provide a foundational resource and potential target for the metabolic engineering of high-quality oil.
The first telomere-to-telomere genome assembly for Asparagus cochinchinensis is presented, illuminating both centromere evolution and the genomic basis of steroidal saponin biosynthesis.
Pteroceltis tatarinowii
is a monotypic relict species endemic to China. It belongs to the genus
Pteroceltis
in the family Cannabaceae, and is an economically and culturally valuable fiber-producing tree species. We integrated PacBio HiFi, Oxford Nanopore Technology (ONT), and Hi-C chromatin conformation capture data to generate a near-complete telomere-to-telomere genome assembly of a millennium-old
P. tatarinowii
tree. The final assembly spanned approximately 689 Mb, with a contig N50 of 35.0 Mb; 99.88% of the sequences were successfully mapped onto chromosomes, with only two gaps remaining in the genome, showing a marked improvement in assembly continuity over previously published
P. tatarinowii
assemblies. We predicted a total of 47,241 protein-coding genes; repetitive sequences accounted for 48.37% of the genome, with long terminal repeat retrotransposons as the dominant component (18.92%). Benchmarking Universal Single-Copy Orthologs assessment confirmed genome completeness of 98.6% and gene annotation completeness of 98.7%. We resolved key complex genomic regions, including telomeres and centromeres, and this high-quality assembly provided a foundational genomic resource to clarify the taxonomic status of
P. tatarinowii
and formulate scientific genetic conservation strategies for this endangered relict species.
Zhi-Cheng Wu, Qi Jing, Wei Liu et al.· Scientific Data· 0 citations
The genus Rhododendron is a well-known group of ornamental plants, which includes many rare and endangered species. The work of protecting and saving these rare and endangered plants is increasingly gaining attention. Whole-genome sequencing offers possibilities for a deeper understanding of key issues in conservation biology and for conducting precise conservation efforts. The Rhododendron yuefengense, as a critically endangered endemic species with high ornamental value, is a priority for conservation. In this study, we utilized PacBio HiFi, ONT ultra-long, and Hi-C data to achieve nearly a T2T genome assembly of the R. yuefengense, making it the first species of the genus Rhododendron to be fully assembled. The genome size is 637.95 Mb, with an N50 of 50.16 Mb and only four gaps. All 637.95 Mb were anchored to 13 pseudochromosomes, with a BUSCO completeness of 98.27%. Repetitive sequences account for 53.67% of the assembly, 37.79% of which are LTR retrotransposons. We predicted 49,250 protein-coding genes and functionally annotated 42,646 of them. Comparative genomic analyses were also performed, providing a comprehensive reference for future studies.
Wen Liu, Xinyu He, Jihua Wang et al.· Scientific Data· 0 citations
The mangrove red snapper (Lutjanus argentimaculatus) is a commercially important marine fish species in the Indo-Pacific region. Despite its significant economic value for aquaculture, existing genomic resources remain fragmented, limiting the advancement of molecular breeding and functional genomic studies. Here, we present a gap-free, telomere-to-telomere (T2T) genome assembly of L. argentimaculatus, generated using a hybrid approach combining PacBio HiFi, Oxford Nanopore ultra-long reads and Hi-C technology. The resulting assembly comprises exactly 24 scaffolds spanning 1.03 Gb, perfectly matching the haploid chromosome number with a contig N50 of 46.17 Mb. Notably, this assembly resolves all physical gaps present in previous versions, achieving a BUSCO completeness score of 98.2%. Comprehensive genome annotation successfully predicted 23,167 protein-coding genes. Among these, 22,067 genes (95.25%) were functionally annotated across major public databases, including eggNOG, InterPro, and Swiss-Prot. Furthermore, structural analysis successfully identified 19 telomeres and 20 centromeres, validating the chromosomal integrity. This high-fidelity, gap-free reference genome provides a robust foundation for comparative genomics, population genetics, and the genetic improvement of Lutjanidae species.
Yang Xiang, Zhen-Cheng Lu, Hao-Ling Jiang et al.· Scientific Data· 0 citations
The olive family (Oleaceae) comprises numerous species of economic, horticultural, and medicinal importance. Despite its significance, the evolutionary history of this complex family remains enigmatic. Here, we generated a high-quality haplotype-resolved genome of Forsythia suspensa, a distylous species that occupies a key phylogenetic position in Oleaceae. The two haplotypes exhibit significant allelic divergence with potential allele-specific regulation. We reconstructed the polyploidization history of Oleaceae by confirming and precisely dating a shared whole-genome triplication (WGT) and an independent whole-genome duplication (WGD) event. We revealed a complex reticulate evolution that gave rise to the tribe Oleeae: an initial hybridization between Forsythieae (♂) and Jasmineae (♀), a subsequent backcrossing event, and a final WGD. We identified a novel tandemly duplicated pectin methylesterase inhibitor (PMEI) gene cluster that regulates filament length and pollen size via restricting cell elongation in the long-styled morph. Dosage augmentation via stepwise cluster formation (0.99-3.83 Mya) may contribute to maintaining stamen traits of the long-styled morph. These FsPMEIs are co-expressed with many cell wall-related genes, suggesting a functional link in cell wall modification. Our study reveals the reticulate evolution in Oleaceae and a novel gene cluster controlling stamen development in F. suspensa, provides valuable haplotype-resolved genomic resources for heterostylous species, offering novel framework and molecular pathways to understand plant adaptive evolution.
Quanling Zhang, Ezi Zhao, Xiao-Min Fu et al.· Plant Physiology· 0 citations
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