Population structure and quantitative characteristics of Tetracentron sinense (Trochodendraceae) in Leigong Mountain Nature Reserve, China

Background: Knowledge of plant population structure facilitates conservation, management, and utilization of endangered plants. Research question: What is the current status of the natural populations of Tetracentron sinense in Leigong Mountain Nature Reserve (LMNR) and what future population development trends can be predicted? Studied species: Tetracentron sinense Study site and period of research: T. sinense populations in LMNR in China in 2018. Methods: The population structure and quantity dynamics of four typical patches were studied using static life tables, survival curves, survival analyses, and time series analyses. Results: The age structures of the T. sinense populations were spindle-shaped, with few seedlings and saplings, and Deevey type II and Ⅲ survival curves. The mortality rate (qx) of each patch increased quickly, and then plateaued, finally increasing again. Survival rate (Sx) showed a contrary trend to qx. Trends in cumulative mortality rate (F(i)), killing power (Kx), mortality density (f(ti)), and hazard rate (λ(ti)) with increasing age class were similar: increasing at a younger age, gradually stabilizing in middle age, and then increasing slightly in older age. The number of individuals in these T. sinense populations was predicted to decrease sharply in future, with younger individuals being seriously deficient. The results showed that the natural populations of T. sinense in the LMNR were relatively stable but were in an early stage of decline. Conclusions: The lack of younger individuals might reflect a bottleneck for regeneration of T. sinense populations, leading to a decline in population size.

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research

BackgroundThe wheel tree (Trochodendron aralioides) is one of only 2 species in the basal eudicot order Trochodendrales. Together with Tetracentron sinense, the family is unique in having secondary xylem without vessel elements, long considered to be a primitive character also found in Amborella and Winteraceae. Recent studies however have shown that Trochodendraceae belong to basal eudicots and demonstrate that this represents an evolutionary reversal for the group. Trochodendron aralioides is widespread in cultivation and popular for use in gardens and parks.FindingsWe assembled the T. aralioides genome using a total of 679.56 Gb of clean reads that were generated using both Pacific Biosciences and Illumina short-reads in combination with 10XGenomics and Hi-C data. Nineteen scaffolds corresponding to 19 chromosomes were assembled to a final size of 1.614 Gb with a scaffold N50 of 73.37 Mb in addition to 1,534 contigs. Repeat sequences accounted for 64.226% of the genome, and 35,328 protein-coding genes with an average of 5.09 exons per gene were annotated using de novo, RNA-sequencing, and homology-based approaches. According to a phylogenetic analysis of protein-coding genes, T. aralioides diverged in a basal position relative to core eudicots, ∼121.8–125.8 million years ago.ConclusionsTrochodendron aralioides is the first chromosome-scale genome assembled in the order Trochodendrales. It represents the largest genome assembled to date in the basal eudicot grade, as well as the closest order relative to the core-eudicots, as the position of Buxales remains unresolved. This genome will support further studies of wood morphology and floral evolution, and will be an essential resource for understanding rapid changes that took place at the base of the Eudicot tree. Finally, it can further genome-assisted improvement for cultivation and conservation efforts of the wheel tree.

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research

BackgroundThe wheel tree (Trochodendron aralioides) is one of only two species in the basal eudicot order Trochodendrales. Together with Tetracentron sinense, the family is unique in having secondary xylem without vessel elements, long considered to be a primitive character also found in Amborella and Winteraceae. Recent studies however have shown that Trochodendraceae belong to basal eudicots and demonstrate this represents an evolutionary reversal for the group. Trochodendron aralioides is widespread in cultivation and popular for use in gardens and parks.FindingsWe assembled the T. aralioides genome using a total of 679.56 Gb of clean reads that were generated using both PacBio and Illumina short-reads in combination with 10XGenomics and Hi-C data. Nineteen scaffolds corresponding to 19 chromosomes were assembled to a final size of 1.614 Gb with a scaffold N50 of 73.37 Mb in addition to 1,534 contigs. Repeat sequences accounted for 64.226% of the genome, and 35,328 protein-coding genes with an average of 5.09 exons per gene were annotated using de novo, RNA-seq, and homology-based approaches. According to a phylogenetic analysis of protein-coding genes, T. aralioides diverged in a basal position relatively to core eudicots, approximately 121.8-125.8 million years ago.ConclusionsTrochodendron aralioides is the first chromosome-scale genome assembled in the order Trochodendrales. It represents the largest genome assembled to date in the basal eudicot grade, as well as the closest order relative to the core-eudicots, as the position of Buxales remains unresolved. This genome will support further studies of wood morphology and floral evolution, and will be an essential resource for understanding rapid changes that took place at the base of the Eudicot tree. Finally, it can serve as a valuable source to aid both the acceleration of genome-assisted improvement for cultivation and conservation efforts of the wheel tree.