A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers.

BACKGROUND: Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. RESULTS: We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. CONCLUSION: For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.

Changes in Non-Structural Carbohydrates, Wood Properties and Essential Oil During Chemically-Induced Heartwood Formation in Dalbergia odorifera.

The highly valuable heartwood of Dalbergia odorifera T. Chen, known as Jiang Xiang in traditional Chinese medicine, is formed very slowly, and there is a need to better understand the process and promote heartwood formation. Chemical induction is considered to be one of the promising methods to induce heartwood formation. However, to date no method has been proved effective for D. odorifera as little is known about biochemical and physiological changes during heartwood development. Three potential heartwood induction substances viz. acetic acid, sodium chloride, and hydrogen peroxide solutions were injected into the trunk of D. odorifera to determine the effect on heartwood formation and physiological activity. Non-structural carbohydrates, lipids, wood properties, and essential oil were assessed in the post-treatment period. As also observed in the formation of natural heartwood, chemical-induced Jiang Xiang production was accompanied by sapwood dehydration, non-structural carbohydrates consumption, and synthesis of heartwood substances. As the heartwood substances accumulated, basic density and essential oil content increased gradually, thereby Jiang Xiang was finally produced. In this process, physiological parameters of discolored sapwood gradually evolved to resemble those of natural heartwood. Hydrogen peroxide-induced Jiang Xiang was closest to natural heartwood, and the essential oil components met the standards for high-quality Jiang Xiang, while the induction effects of acetic acid and sodium chloride were unsatisfactory. Thus, this study indicates that hydrogen peroxide has the potential to induce Jiang Xiang production in Dalbergia odorifera.

The chromosome-level draft genome of Dalbergia odorifera.

BACKGROUND: Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation. FINDINGS: We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ∼92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan. CONCLUSIONS: We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.

Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae).

Pterocarpus is a genus of trees mainly distributed in tropical Asia, Africa, and South America. Some species of Pterocarpus are rosewood tree species, having important economic value for timber, and for some species, medicinal value as well. Up to now, information about this genus with regard to the genomic characteristics of the chloroplasts has been limited. Based on a combination of next-generation sequencing (Illumina Hiseq) and long-read sequencing (PacBio), the whole chloroplast genomes (cp genomes) of five species (rosewoods) in Pterocarpus (Pterocarpus macrocarpus, P. santalinus, P. indicus, P. pedatus, P. marsupium) have been assembled. The cp genomes of five species in Pterocarpus have similar structural characteristics, gene content, and sequence to other flowering plants. The cp genomes have a typical four-part structure, containing 110 unique genes (77 protein coding genes, 4 rRNAs, 29 tRNAs). Through comparative genomic analysis, abundant simple sequence repeat (SSR)loci (333-349) were detected in Pterocarpus, among which A /T single nucleotide repeats accounted for the highest proportion (72.8-76.4%). In the five cp genomes of Pterocarpus, eight hypervariable regions, including trnH-GUG_psbA, trnS-UGA_psbC, accD-psaI, ndhI-exon2_ndhI-exon1, ndhG_ndhi-exon2, rpoC2-exon2, ccsA, and trnfM-CAU, are proposed for use as DNA barcode regions. In the comparison of gene selection pressures (P. santalinus as the reference genome), purifying selection was inferred as the primary mode of selection in maintaining important biological functions. Phylogenetic analysis shows that Pterocarpus is a monophyletic group. The species P. tinctorius is resolved as early diverging in the genus. Pterocarpus was resolved as sister to the genus Tipuana.

Genetic Diversity and Population Structure Analysis of DalbergiaOdorifera Germplasm and Development of a Core Collection Using Microsatellite Markers.

Dalbergia odorifera T. Chen (Fabaceae) is a woody tree species indigenous to Hainan Island in China. Due to its high medicinal and commercial value, this tree species has been planted over 3500 ha² in southern China. There is an urgent need for improvement of the D. odorifera germplasm, however, limited information on germplasm collection, conservation, and assessment of genetic resources is available. Therefore, we have built a database of 251 individuals collected across the whole of southern China, which included 42 wild trees and 210 cultivated trees, with the following objectives. (1) Evaluate genetic diversity and population structure of the database using 19 microsatellite markers and (2) develop a core collection for improvement and breeding programs. Totally, the 19 microsatellite markers harbored 77 alleles across the database with the polymorphic information content (PIC) ranging from 0.03 to 0.66. Medium genetic diversity level was inferred by Nei's gene diversity (0.38), Shannon's information index (0.65), and observed (0.33) and expected heterozygosity (0.38). Structure analysis showed that four was the optimum cluster size using the model-based Bayesian procedure, and the 251 D. odorifera individuals were grouped into five populations including four pure ones (RP1-4) and one mixed one (MIX) based on their maximum membership coefficients. Among these populations, the expected heterozygosity varied from 0.30 (RP3) to 0.38 (RP4). Analysis of molecular variance (AMOVA) showed 11% genetic variation existed among populations, and moderate population differentiation was inferred by the matrix of pairwise Fst (genetic differentiation among populations), which was in the range of 0.031 to 0.095. Moreover, a core collection of 31 D. odorifera individuals including six wild and 25 cultivated trees was developed, which was only 12.4% of the database but conserved the whole genetic diversity. The results of this study provided additional insight into the genetic structure of the large D. odorifera germplasm, and the core collection will be useful for the efficient and sustainable utilization of genetic resources, as well as efficient improvement in breeding programs.

Synergistic Roles of Biphasic Ethylene and Hydrogen Peroxide in Wound-Induced Vessel Occlusions and Essential Oil Accumulation in Dalbergia odorifera.

The heartwood of Dalbergia odorifera (D. odorifera), named "Jiang Xiang" in traditional Chinese medicine, is highly valuable. Mechanical wounding induced the production of "Jiang Xiang" in D. odorifera. Ethylene and hydrogen peroxide (H2O2) are proposed to play vital roles in wound signaling. However, little is known about the role of ethylene or H2O2 in the wound-induced formation of vessel occlusions and biosynthesis of "Jiang Xiang" in D. odorifera. In this study, the pruning of D. odorifera saplings resulted in the synergistic biosynthesis of biphasic ethylene and H2O2, which was followed by formation of vessel occlusions and "Jiang Xiang" in the pruned stems. In this process, the H2O2 production stimulated higher biosynthesis of ethylene. Treatments with aminoethoxyvinylglycine (AVG), an inhibitor for ethylene biosynthesis and ascorbate acid (AsA), a scavenger of H2O2, markedly reduced the production of ethylene and H2O2, respectively, and the corresponding the percentage of vessels with occlusions (PVO), oil content, and the amount of "Jiang Xiang" formed. These results indicate that ethylene and H2O2 might be important wound signals in D. odorifera that induce vessel occlusions and formation of "Jiang Xiang," and thus ethylene and H2O2 might play vital roles in "Jiang Xiang" formation in pruned stems of D. odorifera.

Characterization of the chloroplast genome of Cassia siamea Lain, a rosewood species from southeast China.

Cassia siamea is a rosewood species in Southwest China with high wood and medicinal value. To clarify genetic background of C. siamea, we sequenced chloroplast genome by Illumina Hiseq and PacBio Sequel. The whole genome was 148,437 bp in length, containing a large single copy region (77,723 bp), a small single copy region (18,462 bp) and a pair of inverted repeats regions (26,126 bp). The cp genome contained 102 genes (71 protein-coding genes, 27 tRNAs and 4 rRNAs). The phylogenetic analysis indicated that C. siamea is close to Senna tora within Cassiinae/Caesalpiniaceae. The complete chloroplast genome of C. siamea will provide useful resources for the development and utilization of this species and the phylogenetic study of Fabaceae.

The environment, not space, dominantly structures the landscape patterns of the richness and composition of the tropical understory vegetation.

The mechanisms driving the spatial patterns of species richness and composition are essential to the understanding of biodiversity. Numerous studies separately identify the contributions of the environment (niche process) and space (neutral process) to the species richness or composition at different scales, but few studies have investigated the contributions of both types of processes in the two types of data at the landscape scale. In this study, we partitioned the spatial variations in all, exotic and native understory plant species richness and composition constrained by environmental variables and space in 134 plots that were spread across 10 counties in Hainan Island in southern China. The 134 plots included 70 rubber (Hevea brasiliensis) plantation plots, 50 eucalyptus (Eucalyptus urophylla) plantation plots, and 14 secondary forest plots. RDA based variation partitioning was run to assess the contribution of environment and space to species richness and composition. The results showed that the environmental variables alone explained a large proportion of the variations in both the species richness and composition of all, native, and exotic species. The RDA results indicated that overstory composition (forest type here) plays a leading role in determining species richness and composition patterns. The alpha and beta diversities of the secondary forest plots were markedly higher than that of the two plantations. In conclusion, niche differentiation processes are the principal mechanisms that shape the alpha and beta diversities of understory plant species in Hainan Island.

[Growth effect of eucalyptus-acacia mixed plantation in South China].

Eucalyptus U6 and Acacia crassicarpa were mixed planted with different ratios and modes to investigate the growth parameters of the two tree species. In the 2-3 years old mixed plantation, the wind-throw of A. crassicarpa decreased markedly with increasing ratio of Eucalyptus U6, the decrement being 26.14% when the Eucalyptus U6/A. crassicarpa ratio was 3 : 1, but the survival rates of Eucalyptus U6 and A. crassicarpa had no significant difference under different planting modes. Mixed planting retarded the A. crassicarpa growth to some extent, with the DBH being 90% of that in pure A. crassicarpa stand. The mixed planting had little effects on the height growth of Eucalyptus U6, but promoted its DBH growth markedly, and the beneficial effect increased with increasing ratio of A. crassicarpa. In the 6 years old 1 : 1 Eucalyptus U6/A. crassicarpa plantation, the Eucalyptus U6 individuals with DBH > 15 cm occupied 32.1%; while in pure Eucalyptus U6 stand, they only accounted for 5.83%. Mixed planting with 2 : 1 Eucalyptus U6/A. crassicarpa could obtain a maximum total biomass of 198.8 m3 x hm(-2), which was 118.8% of the total biomass in pure Eucalyptus U6 stand, or 169.9% of that in pure A. crassicarpa stand. Mixture of Eucalyptus with Acacia would be a good choice to produce Eucalyptus trees with larger DBH.