The jacktree genome and population genomics provides insights for the mechanisms of the germination obstacle and the conservation of endangered ornamental plants.

Sinojackia Hu represents the first woody genus described by Chinese botanists, with all species classified as endangered ornamental plants endemic to China. Their characteristic spindle-shaped fruits confer high ornamental value to the plants, making them favored in gardens and parks. Nevertheless, the fruits likely pose a germination obstacle, contributing to the endangered status of this lineage. Here we report the chromosome-scale genome of S. xylocarpa, and explore the mechanisms underlying its endangered status, as well as its population dynamics throughout evolution. Population genomic analysis has indicated that S. xylocarpa experienced a bottleneck effect following the recent glacial period, leading to a continuous population reduction. Examination of the pericarp composition across six stages of fruit development revealed a consistent increase in the accumulation of lignin and fiber content, responsible for the sturdiness of mature fruits' pericarps. At molecular level, enhanced gene expression in the biosynthesis of lignin, cellulose and hemicellulose was detected in pericarps. Therefore, we conclude that the highly lignified and fibrotic pericarps of S. xylocarpa, which inhibit its seed germination, should be its threatening mechanism, thus proposing corresponding strategies for improved conservation and restoration. This study serves as a seminal contribution to conservation biology, offering valuable insights for the study of other endangered ornamental plants.

Population Variation and Phylogeography of Cherry Blossom (Prunus conradinae) in China.

Prunus conradinae (subgenus Cerasus, Rosaceae) is a significant germplasm resource of wild cherry blossom in China. To ensure the comprehensiveness of this study, we used a large sample size (12 populations comprising 244 individuals) which involved the fresh leaves of P. conradinae in Eastern, Central, and Southwestern China. We combined morphological and molecular evidence (three chloroplast DNA (cpDNA) sequences and one nuclear DNA (nr DNA) sequence) to examine the population of P. conradinae variation and differentiation. Our results revealed that Central, East, and Southwest China are important regions for the conservation of P. conradinae to ensure adequate germplasm resources in the future. We also found support for a new variant, P. conradinae var. rubrum. We observed high genetic diversity within P. conradinae (haplotype diversity [Hd] = 0.830; ribotype diversity [Rd] = 0.798), with novel genetic variation and a distinct genealogical structure among populations. There was genetic variation among populations and phylogeographic structure among populations and three geographical groups (Central, East, and Southwest China). The genetic differentiation coefficient was the lowest in the Southwest region and the gene exchange was obvious, while the differentiation was obvious in Central China. In the three geographic groups, we identified two distinct lineages: an East China lineage (Central China and East China) and a Southwest China lineage ((Central China and Southwest China) and East China). These two lineages originated approximately 4.38 million years ago (Mya) in the early Pliocene due to geographic isolation. P. conradinae expanded from Central China to East China at 3.32 Mya (95% HPD: 1.12-5.17 Mya) in the Pliocene. The population of P. conradinae spread from East China to Southwest China, and the differentiation time was 2.17 Mya (95% (HPD: 0.47-4.54 Mya), suggesting that the population of P. conradinae differentiated first in Central and East China. The population of P. conradinae experienced differentiation from Central China to Southwest China around 1.10 Mya (95% HPD: 0.11-2.85 Mya) during the early Pleistocene of the Quaternary period. The southeastern region of East China, near Mount Wuyi, likely serves as a refuge for P. conradinae. This study establishes a theoretical foundation for the classification, identification, conservation, and exploitation of germplasm resources of P. conradinae.

Molecular and morphological evidence support a new species of RosaceaePrunus subg. Cerasus from Wuyishan National Park, southeast China.

Prunustongmuensis, a new species of cherry blossom, is described and illustrated from Wuyishan National Park, southeast China. This species is characterized by its tubular to nearly bottle-shaped receptacles and dark purple drupes. It can be distinguished from other wild cherry trees by its flowers and leaves, reddish brown young leaves, presence of 1-2 glands at the base of leaves, petioles densely covered with yellowish brown villi, longer pedicels (0.6-2.5 cm), villous pistil, and dark purple drupes. In the present study, we conducted a comprehensive morphological study based on specimens of the new species and its morphologically close species, field observations, and examination of pollen morphology. In addition, our phylogenetic analysis based on the complete plastid genome sequences further confirms the status of the new species and indicates that it is closely related to Prunusclarofolia, however, it notably differs in leaf shape, size, petiole villus color, gland location, timing of flower and leaf openings, and reflexed or spread sepals, as well as drupe color.

Inter- and Intra-Population Variation of Foliage Calcium and Magnesium in Two Chinese Pine Species.

Calcium and magnesium are major nutrient elements of plants, and both play an important role in plant growth and development. Pinus massoniana and P. hwangshanensis are important afforestation tree species in barren mountains in China. However, observation and research on calcium and magnesium nutrition of dominant forest species in China are still limited. This study determined the concentration of calcium and magnesium in needles for two species from five sites in East China by inductively coupled plasma optical emission spectrometry (ICP-OES). We then explored the inter- and intra-population variation pattern of calcium and magnesium and their relationship with environmental factors. There were significant differences in traits among populations. The strongest factors, which impacted the variation of calcium and magnesium concentration, were elevation and individual differences, respectively. Element concentration was correlated to environmental factors such as longitude, latitude, elevation, and mean annual temperature. The results of this study can be helpful for a better understanding of tree growth, population survival, and forest succession.

Scale-dependent effects of species diversity on aboveground biomass and productivity in a subtropical broadleaved forest on Mt. Huangshan.

The relationship between species diversity and biomass/productivity is a major scientific question in ecology. Exploring this relationship is essential to understanding the mechanisms underpinning the maintenance of biodiversity. Positive, negative, and neutral relationships have been identified in controlled experiments and observational research. However, increasing evidence suggests that the effects of species diversity on aboveground biomass and productivity are influenced by biotic and abiotic factors, but it remains unclear whether scale-dependent effects affect aboveground biomass and productivity. Herein, we used a generalized linear regression model and a structural equation model to explore relationships between species diversity and productivity/aboveground biomass under different scales and to investigate the effects of topographical factors and species diversity on ecosystem functioning. The results revealed a positive relationship between biodiversity and ecosystem functioning based on species diversity and aboveground biomass. Different sampling scales may impact the relationship between species diversity and ecosystem functioning. A positive relationship was found between species richness and productivity at medium and large scales; however, ambiguous relationships were found in productivity and other species diversity indices. Elevation was a key factor affecting both biomass and productivity. These results suggest that species diversity is not the only factor affecting biomass and productivity, and the positive correlation between species diversity and ecosystem functioning is mediated by abiotic factors.

Characterization of the complete chloroplast genome of Prunus clarofolia C.K. Schneid (Rosaceae).

Prunus clarofolia is an endemic species that widely distributed in subtropical regions of China. Here we present its complete plastome. The plastome of P. clarofolia is successfully assembled from raw reads sequenced by Illumina Hiseq 2500 platform system. The complete chloroplast of this species is 158,053 bp in length with 36.7% overall GC content, including a pair of invert repeat regions (IR) (26,393bp) that is divided by a large single copy region (LSC) (86,088bp) and a small single copy region (SSC) (19,179bp). The plastid genome contained a total of 130 genes, including 85 coding genes, 8 rRNA genes, and 37 tRNA genes. Each of rps16, atpF, rpoC1, clpP, petB, petD, rpl16, rpl2, ndhB, and ndhA contains one intron, rps12 and ycf3 contains two introns. Phylogenetic analysis indicates that P. clarofolia has a closer relationship with P. avium.

The complete plastid genome of cherry plants Prunus sargentii (Rosaceae) and its phylogenetic implication.

Prunus sargentii is an ornamental flowering cherry species, spread in Japan, Korea, Russia, and Northeast China. Little information is available regarding its genomic, with limited phylogenetic relationship study performed on P. sargentii until now. In this research, we reported the complete plastid genome of P. sargentii. The complete chloroplast of this species is 158,138 bp in length, including a pair of invert repeat regions (IR) (26,463bp) that is divided by a large single-copy region (LSC) (85,959bp) and a small single-copy region (SSC) (19,253bp). The plastid genome contained a total of 128 genes, including 84 coding genes, eight rRNA genes, and 36 tRNA genes. Phylogenetic analysis indicates that P. sargentii has a closer relationship with P. kumanoensis.

Phylogeography and the population genetic structure of flowering cherry Cerasus serrulata (Rosaceae) in subtropical and temperate China.

Cerasus serrulata (Rosaceae) is an important flowering cherry resource which is valuable for developing new cultivars of flowering cherries. It is broadly distributed and possesses abundant variations. In this study, phylogeographic analysis was conducted to reveal the evolutionary history to better understand the genetic diversity and genetic structure of C. serrulata so as to provide more accurate molecular insights into better conservation and utilization of the germplasm resources. A total of 327 individuals from 18 wild populations were collected. Three chloroplast DNA (cpDNA) fragments (matK, trnD-E, and trnS-G) and the nuclear internal transcribed spacer (ITS) were utilized. The results showed a high genetic diversity at both species level and population level of C. serrulata. High genetic differentiation and the existence of the phylogeographic structure were detected. No significant expansion events were discovered. Two geographic lineages were inferred. One was confined to the Qinling Mountains and the Taihang Mountains. The other was from the Wuling Mountains to the Jiangnan Hilly Regions and then went northeast to the coast of Asia. In addition, some taxonomic treatments of the C. serrulata complex are discussed and reconsidered. Conservation and utilization strategies of wild C. serrulata germplasm resources were recommended.

The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species.

Cerasus serrulata is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of C. serrulata by the use of Nanopore and Hi-C sequencing technologies. The assembled C. serrulata genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that C. serrulata and C. avium have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of C. serrulata are distributed on all chromosomes of C. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that C. serrulata has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present C. serrulata species diverged from Prunus yedoensis ~17.34 million years ago (Mya), while the divergence of C. serrulata and C. avium was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in C. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in C. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching C. serrulata within the PRGdb. This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.

The complete chloroplast genome of Pinus yunnanensis Franchet (Pinaceae).

Pinus yunnanensis is distributed in Southwestern China which is one of the main forest tree species. It is used for construction, railway sleepers, boards, furniture, and wood pulp. Due to the genetic infiltration hybridization between P. yunnanensis with P. densata and P. kesiya, the classification boundary between these groups is blurred and the identification is difficult. In this study, the complete chloroplast (cp) genome sequence of P. yunnanensis was determined using next-generation sequencing. The entire cp genome was determined to be 119,707 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 65,619 and 53,098 bp, respectively, which were separated by a pair of 495bp inverted repeat (IR) regions. The genome contained 116 genes, including 76 protein-coding genes, 36 tRNA genes, and 4 rRNA genes. The overall GC content of the genome is 38.5%. A phylogenetic tree reconstructed by 23 chloroplast genomes reveals that P. yunnanensis is most related with P. kesiya.

Complete chloroplast genome of Cerasus kumanoensis (Rosaceae), a wild flowering cherry endemic to Kii Peninsula, Japan.

Cerasus kumanoensis is a recently described wild cherry species from the Kii Peninsula, Japan. Here we determined the first complete chloroplast genome of C. kumanoensis using genome skimming approach. The cp genome was 157,898 bp long, with a large single-copy region (LSC) of 85,926 bp and a small single-copy region (SSC) of 19,070 bp separated by a pair of inverted repeats (IRs) of 26,451 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Besides, we reconstructed the phylogeny of Prunus using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that C. kumanoensis is close related with a group including Prunus takesimensis and P. speciosa.

The complete chloroplast genome of Osmanthus serrulatus rehd., a natural sweet olive endemic to China.

Osmanthus serrulatus is an endemic tree in southwest China. Here, the complete chloroplast genome of this species was assembled and characterised from high-throughput data. The entire circular genome of O. serrulatus was 155,465 bp in size, which composed of large single-copy (LSC) and small single-copy (SSC) regions of 86,545 bp and 17,494 bp, respectively, and separated by a pair of inverted repeat (IR) regions of 25,713 bp each. The genome contained 133 genes, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 37.8%. A phylogenetic tree reconstructed by 35 chloroplast genomes reveals that O. serrulatus is most related with O. yunnanensis.

Complete chloroplast genome of Prunus emarginata and its implications for the phylogenetic position within Prunus sensu lato (Rosaceae).

Prunus emarginata is a species of Prunus native to western North America.We determined the first complete chloroplast genome of P. emarginata using genome skimming approach. The cp genome was 157,458 bp long, with a large single-copy region (LSC) of 85,567 bp and a small single-copy region (SSC) of 19,121 bp separated by a pair of inverted repeats (IRs) of 26,385 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. emarginata is closely related with Prunus subhirtella var. subhirtella and Prunus yedoensis.

The complete plastid genome of cherry plants Prunus discoidea (Rosaceae) and its phylogenetic implication.

Prunus discoidea is an endemic cherry species with ornamental value, spread in eastern China (Anhui, Jiangxi, Zhejiang provinces). Little information is available regarding its genomic, with limited phylogenetic relationship study performed on P. discoidea until now. The plastid genome was 158,024 bp in length consisting of four regions: large single-copy region (85,953 bp), small single-copy region (19,113 bp), and a pair of inverted repeat regions (26,469 bp each). The plastid genome contained a total of 129 genes, including 84 coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis for 20 reported genomes within the Prunus sensu lato showed three main clades of Prunus s.l. with strong supports.

The complete chloroplast genome of Changnienia amoena S. S. Chien (Orchidaceae) and its phylogenetic implication.

Changnienia amoena S. S. Chien is mainly distributed in the mid-subtropical hilly areas of central and eastern China at an altitude of 200-1700 m. It has important academic significance in the orchid phylogeny, and is an excellent wild flower and precious medicinal plant. The species was once abundant but has become rare and endangered in recent years and has been identified as Endangered (EN) under criteria A2c (The IUCN Red List and Threatened Specis) because of the habitat fragmentation and unduly commercial collections. In this study, the complete chloroplast (cp) genome sequence of C. amoena was determined using next-generation sequencing. The entire cp genome was determined to be 156,818 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 84,847 and 18,141bp, respectively, which were separated by a pair of 26,915 bp inverted repeat (IR) regions. The genome contained 133 genes, including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes.The overall GC content of the genome is 37.1%. A phylogenetic tree reconstructed by 48 chloroplast single-copy coding gene reveals that C. amoena is closely related with Calypso bulbosa.

Complete chloroplast genome of the wild Japanese Mountain cherry (Prunus jamasakura, Rosaceae).

Prunus jamasakura is a species of Prunus native to eastern Asia. We determined the first complete chloroplast genome of Prunus jamasakura using genome skimming approach. The cp genome was 157,905 bp long, with a large single-copy region (LSC) of 85,910 bp and a small single-copy region (SSC) of 19,123 bp separated by a pair of inverted repeats (IRs) of 26,436 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. jamasakura is closely related with Prunus speciosa.