Vertical stratification in trees may respond to selective pressures to enhance light interception and utilization; therefore, the vertical functional variation in leaf traits may indicate niche partitioning within forests. In this study, vertical variations in leaf and crown structure traits of seven common tree species were analysed with respect to differences between species in different height groups, within the same height range, in the same species across tree height, and different parts of the individual tree crown to reveal coexistence mechanisms in subtropical forest tree species. There were multiple levels of trait variation in the vertical dimension, validating the existence of vertical niche differentiation in subtropical forest species. The functional trait differences arose among different height groups, among species co-occurring within the same height range, in the same species across tree height, and among different parts of the individual tree crown. Variation in comparative advantages, which was characterised by those traits between species across different height ranges, was also one of the manifestations of niche differentiation in the vertical dimension. Moreover, contrasting results between lower height ranges and higher ranges in the relationship between species’ differences in functional traits and species’ difference of abundance were found, further confirming that there was obvious vertical niche separation in the community. This study emphasised the importance of vertical variation in species’ performances in elucidating the mechanisms of tree species coexistence in subtropical forests.

Objectives: Nepenthes belongs to the monotypic family Nepenthaceae, one of the largest carnivorous plant families. Nepenthes species show impressive adaptive radiation and suffer from being overexploited in nature. Nepenthes mirabilis is the most widely distributed species and the only Nepenthes species that is naturally distributed within China. Herein, we reported the genome and transcriptome assemblies of N. mirabilis. The assemblies will be useful resources for comparative genomics, to understand the adaptation and conservation of carnivorous species. Data description: This work produced ~ 139.5 Gb N. mirabilis whole genome sequencing reads using leaf tissues, and ~ 21.7 Gb and ~ 27.9 Gb of raw RNA-seq reads for its leaves and flowers, respectively. Transcriptome assembly obtained 339,802 transcripts, in which 79,758 open reading frames (ORFs) were identified. Function analysis indicated that these ORFs were mainly associated with proteolysis and DNA integration. The assembled genome was 691,409,685 bp with 159,555 contigs/scaffolds and an N50 of 10,307 bp. The BUSCO assessment of the assembled genome and transcriptome indicated 91.1% and 93.7% completeness, respectively. A total of 42,961 genes were predicted in the genome identified, coding for 45,461 proteins. The predicted genes were annotated using multiple databases, facilitating future functional analyses of them. This is the first genome report on the Nepenthaceae family.

Objectives: OtteliaPers. is in the Hydrocharitaceae family. Species in the genus are aquatic, and China is their centre of origin in Asia.Ottelia alismoides(L.) Pers., which is distributed worldwide, is a distinguishing element in China, while other species of this genus are endemic to China. However,O. alismoidesis also considered endangered due to habitat loss and pollution in some Asian countries.Ottelia alismoidesis the only submerged macrophyte that contains three carbon dioxide-concentrating mechanisms, i.e. bicarbonate (HCO₃⁻) use, crassulacean acid metabolism and the C4 pathway. In this study, we present its first genome assembly to help illustrate the various carbon metabolism mechanisms and to enable genetic conservation in the future.Data description: Using DNA and RNA extracted from oneO. alismoidesleaf, this work produced ∼ 73.4 Gb HiFi reads, ∼ 126.4 Gb whole genome sequencing short reads and ∼ 21.9 Gb RNA-seq reads. Thede novogenome assembly was 6,455,939,835 bp in length, with 11,923 scaffolds/contigs and an N50 of 790,733 bp. Genome assembly completeness assessment with Benchmarking Universal Single-Copy Orthologs revealed a score of 94.4%. The repetitive sequence in the assembly was 4,875,817,144 bp (75.5%). A total of 116,176 genes were predicted. The protein sequences were functionally annotated against multiple databases, facilitating comparative genomic analysis.

Aquilaria sinensis, endemic to China, is an economically important evergreen tree species and a source of agarwood. Due to the high market demand for agarwood, this species is heavily overexploited in the wild and is now listed as an endangered species. Although its nuclear and chloroplast genomes have been previously reported, little is known about its mitochondrial genome. Using the paired-end short reads generated by the Illumina sequencing platform, we assembled and herein report the mitochondrial genome of A. sinensis for future phylogenetic, evolutionary, and preservative studies. The length of the A. sinensis mitochondrial genome was found to be 341,829 bp and the GC content was 45.01%. A total of 32 protein-coding genes, 19 tRNA genes, and three rRNA genes were annotated. The phylogenetic tree indicated that A. sinensis is most closely genetically related to Vigna radiata.

Background: The genus Ormosia belongs to the Fabaceae family; almost all Ormosia species are endemic to China, which is considered one of the centers of this genus. Thus, genomic studies on the genus are needed to better understand species evolution and ensure the conservation and utilization of these species. We performed a chromosome-scale assembly of O. purpureiflora and updated the chromosome-scale assemblies of O. emarginata and O. semicastrata for comparative genomics. Findings: The genome assembly sizes of the 3 species ranged from 1.42 to 1.58 Gb, with O. purpureiflora being the largest. Repetitive sequences accounted for 74.0–76.3% of the genomes, and the predicted gene counts ranged from 50,517 to 55,061. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis indicated 97.0–98.4% genome completeness, whereas the long terminal repeat (LTR) assembly index values ranged from 13.66 to 17.56, meeting the “reference genome” quality standard. Gene completeness, assessed using BUSCO and OMArk, ranged from 95.1% to 96.3% and from 97.1% to 98.1%, respectively. Characterizing genome architectures further revealed that inversions were the main structural rearrangements in Ormosia. In numbers, density distributions of repetitive elements revealed the types of Helitron and terminal inverted repeat (TIR) elements and the types of Gypsy and unknown LTR retrotransposons (LTR-RTs) concentrated in different regions on the chromosomes, whereas Copia LTR-RTs were generally evenly distributed along the chromosomes in Ormosia. Compared with the sister species Lupinus albus, Ormosia species had lower numbers and percentages of resistance (R) genes and transcription factor genes. Genes related to alkaloid, terpene, and flavonoid biosynthesis were found to be duplicated through tandem or proximal duplications. Notably, some genes associated with growth and defense were absent in O. purpureiflora. By resequencing 153 genotypes (∼30 Gb of data per sample) from 6 O. purpureiflora (sub)populations, we identified 40,146 single nucleotide polymorphisms. Corresponding to its very small populations, O. purpureiflora exhibited low genetic diversity. Conclusions: The Ormosia genome assemblies provide valuable resources for studying the evolution, conservation, and potential utility of both Ormosia and Fabaceae species.