Characterization of the complete chloroplast genome of Dalbergia odorifera (Leguminosae), a rare and critically endangered legume endemic to China

The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain

BACKGROUND

Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method.

RESULTS

Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2 + trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2 + trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades.

CONCLUSIONS

The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2 + trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis.

Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae)

Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives.

Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms "amino acid binding," "cellulase activity," and "DNA beta-glucosyltransferase activity". Further, KEGG pathway annotation showed significant enrichment in "fatty acid elongation" and "biosynthesis of unsaturated fatty acids". These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.

Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia

Dalbergia is a pantropical genus with more than 250 species, many of which are highly threatened due to overexploitation for their rosewood timber, along with general deforestation. Many Dalbergia species have received international attention for conservation, but the lack of genomic resources for Dalbergia hinders evolutionary studies and conservation applications, which are important for adaptive management. This study produced the first reference transcriptomes for 6 Dalbergia species with different geographical origins and predicted ~ 32 to 49 K unique genes. We showed the utility of these transcriptomes by phylogenomic analyses with other Fabaceae species, estimating the divergence time of extant Dalbergia species to ~ 14.78 MYA. We detected over-representation in 13 Pfam terms including HSP, ALDH and ubiquitin families in Dalbergia. We also compared the gene families of geographically co-occurring D. cochinchinensis and D. oliveri and observed that more genes underwent positive selection and there were more diverged disease resistance proteins in the more widely distributed D. oliveri, consistent with reports that it occupies a wider ecological niche and has higher genetic diversity. We anticipate that the reference transcriptomes will facilitate future population genomics and gene-environment association studies on Dalbergia, as well as contributing to the genomic database where plants, particularly threatened ones, are currently underrepresented.

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.

Morphological and physiological responses of Dalbergia odorifera T. Chen seedlings to different culture substances

Dalbergia odorifera T. Chen seedlings do not grow well in the typical red soils of tropical regions. Eighteen culture substances filled with different substrate combinations and proportions of red soil, coconut coir powder, deciduous leaf powder, and sand were used as to determine their effects on the growth, root system development, dry matter accumulation and allocation, leaf relative electrolyte leakage, chlorophyll content, root superoxide dismutase activity, root malondialdehyde content, and total soluble sugar content of D. odorifera. Results demonstrated that different substrate combinations and proportions had different effects on the performance of D. odorifera. All mixed substrates were better than any single substrate. The suitable substrate combinations and proportions of sand, coconut coir powder, and deciduous leaf powder mixed with red soil improved the growth, root architecture, and physiological characteristics of D. odorifera seedling. For example, groups C1-2 (coconut coir/red soil = 2/2, v/v, the same below) and C3-2 (red soil/sand = 2/2) exerted the best effects on plant growth and biomass accumulation. Groups C1-2, C2-2 (deciduous leaf powder/red soil = 2/2), and C3-2 remarkably enhanced root system development. Group C6 (coconut coir/red soil/sand = 1/1/1) substantially promoted root nodule development. Group C3-1 (red soil/sand = 3/1) exhibited the best effects on physiological characteristics. On the basis of the comprehensive evaluation of Euclid's multidimensional space mathematical model, we found that the suitable substrate combinations followed the order of C1-2 > C3-1 > C2-2. This research provides scientific guidance for the proper seedling culture of D. odorifera and the rational utilization of solid wastes such as coconut coir and deciduous leaves of Ficus elastica.

Characterization of the complete chloroplast genome of Dalbergia cultrata (Leguminosae)

Dalbergia cultrata is a Near Threatened species with high ecological and economic values. In this study, its chloroplast genome was assembled using Illumina pair-end sequencing dataset. The chloroplast genome has a quadripartite structure with 156,385 bp in length and contains a pair of 16,392 bp inverted repeat (IR) regions, which were separated by large single copy (LSC: 86,040 bp) region and small single copy (SSC: 37,561 bp) region. A total of 121 genes were annotated, including 77 protein-coding genes (PCGs), 36 tRNAs, and 8 rRNAs. The overall GC content was 36.1%. The phylogenetic analysis revealed that D. cultrata has close relationship to D. hainanensis and D. odorifera. This complete chloroplast genome can be readily used for population genetic studies of D. cultrata.

De Novo Transcriptome Analysis of Dalbergia odorifera and Transferability of SSR Markers Developed from the Transcriptome

Dalbergia odorifera T. Chen (Fabaceae), indigenous to Hainan Island, is a precious rosewood (Hainan hualimu) in China. However, only limited genomic information is available which has resulted in a lack of molecular markers, limiting the development and utilization of the germplasm resources. In this study, we aim to enrich genomic information of D. odorifera, and develop a series of transferable simple sequence repeat (SSR) markers for Dalbergia species. Therefore, we performed transcriptome sequencing for D. odorifera by pooling leaf tissues from three trees. A dataset of 138,516,418 reads was identified and assembled into 115,292 unigenes. Moreover, 35,774 simple sequence repeats (SSRs) were identified as potential SSR markers. A set of 19 SSR markers was successfully transferred across species of Dalbergia odorifera T. Chen, Dalbergia tonkinensis Prain, and Dalbergia cochinchinensis Pierre ex Laness. In total, 112 alleles (3–13 alleles/locus) were presented among 60 Dalbergia trees, and polymorphic information content ranged from 0.38 to 0.75. The mean observed and mean expected heterozygosity was 0.34 and 0.40 in D. odorifera, 0.27 and 0.32 in D. tonkinensis, and 0.29 and 0.33 in D. cochinchinensis, respectively. The cluster analysis classified these 60 trees into three major groups according to the three Dalbergia species based on the genetic similarity coefficients, indicating these newly developed transferable markers can be used to explore the relationships among Dalbergia species and assist genetic research. All these unigenes and SSR markers will be useful for breeding programs in the future.