Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses

Dalbergia cultrata Pierre Graham ex Benth (D. cultrata) is a precious rosewood tree species that grows in the tropical and subtropical regions of Asia. In this study, we used PacBio long-reading sequencing technology and Hi-C assistance to sequence and assemble the reference genome of D. cultrata. We generated 171.47 Gb PacBio long reads and 72.43 Gb Hi-C data and yielded an assembly of 10 pseudochromosomes with a total size of 690.99 Mb and Scaffold N50 of 65.76 Mb. The analysis of specific genes revealed that the triterpenoids represented by lupeol may play an important role in D. cultrata's potential medicinal value. Using the new reference genome, we analyzed the resequencing of 19 Dalbergia accessions and found that D. cultrata and D. cochinchinensis have the latest genetic relationship. Transcriptome sequencing of D. cultrata leaves grown under cold stress revealed that MYB transcription factor and E3 ubiquitin ligase may be playing an important role in the cold response of D. cultrata. Genome resources and identified genetic variation, especially those genes related to the biosynthesis of phytochemicals and cold stress response, will be helpful for the introduction, domestication, utilization, and further breeding of Dalbergia species.

Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods

In the billion-dollar global illegal wildlife trade, rosewoods have been the world's most trafficked wild product since 2005. Dalbergia cochinchinensis and Dalbergia oliveri are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here, we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic offset to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge of Vietnam suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on hotspots of genomic offset in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change.

Dalbergia odorifera, a new host of Colletotrichum tropicale causing anthracnose in China

Dalbergia odorifera T. Chen (Family: Fabaceae) is an endangered, wild and second class key protected tree species in China. It has been cultivated widely in south China because of its valuable rosewood and pharmacological uses. During January and September 2022, anthracnose was observed on D. odorifera in Chikan, Zhanjiang, Guangdong (N21°15' 9.4" E110°22' 25.9"). All of the D. odorifera plants were infected and the leaf disease incidence was above 30%. The lesions were 0.35 to 0.65 cm in size, greyish-white, and gradually expanded into brown black circular spots surrounded by a yellowish halo. Later, the centers of spots were white with dark-brown borders. In severe cases, the leaves turned yellow, withered and fell off. To isolate the pathogen, about 5×5 mm tissues at the disease-health junction of spots were sterilized with 75% ethanol for 30s and 3% hydrogen peroxide for 3 min, rinsed with sterile water three times, and plated onto PDA for incubation at 25-28℃ in the dark. Isolates were obtained by picking the tip of hypha growing from the tissues, further purified by coating the diluted spore suspension to obtain single-spore isolates. Colonies with abundant aerial mycelium were white to light gray, 4.0 to 5.0 cm in diameter after 5 days at 25 to 28℃ in the dark. Conidiogenous cells were hyaline, cylindrical and monoblastic. Conidia were unicellular, subcylindrical, hyaline, guttulate, 3.5 to 5.6×11.1 to 16.8 (av. 4.6±0.48 × 14.0±1.25) μm (n>50). Appressoria were dark brown subglobose, clavate, fusiform, occasionally lobed, terminal, 7.8 to 16.3×4.6 to 8.9 μm. No swollen cells and setae were observed. To further confirm identity of the fungus, partial regions of six genetic loci of isolate ACCC 35246 (stored in Agricultural Culture Collection of China) were amplified and sequenced: actin (ACT), chitin synthase (CHS), glyceraldehyde-3-phosphate dehydrogenase (GPDH), histone (HIS), beta-tubulin (TUB) and internal transcribed spacer (ITS) utilizing the primer pairs (Damm et al. 2012; Weir et al. 2012; White et al 1990) (OP314900-OP314904 and OP269660, respectively). Based on a BLAST analysis, the six sequences were about 99% identical to those of Colletotrichum tropicale holotype strain CBS124949 (ACT: JX009489 270/272; CHS: JX009870 295/299; GPDH: JX010007 274/279; HIS: KY856395 638/670; ITS: JX010264 546/548 and TUB: JX010407 494/497, respectively) (Weir et al. 2012). Phylogenetic analyses, using a combined dataset of ACT, CHS, GPDH, ITS and TUB were carried out in MEGA X using the maximum likelihood method, placed the fungus within the C. tropicale clade. Based on morphogical and molecular analyses, the fungus was identified as C. tropicale (Rojas et al 2010). To test the pathogenicity, five healthy leaves of 1 year-old potted plants were stab-wounded with a sterile needle and inoculated with 10 µL of spore suspension (105 conidia/mL). Another five healthy leaves were inoculated with sterile water as the control. Symptoms expressed by the inoculated leaves, 10 days after inoculation, were the same as those of the diseased plants, while the non-inoculated leaves remained asymptomatic. The same fungus based on morphogical and molecular criteria was re-isolated from the spots. As an endophyte or plant pathogen, C. tropicale inhabits a wide host range of plant species belonging to 31 genera in 25 families (Farr and Rossman 2022), D. odorifera is a new host of C. tropicale causing anthracnose in China. This work will be helpful for the diagnosis and control of this disease.

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macroevolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with (i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots; (ii) scaling the numbers of individuals analysed and loci sequenced; and (iii) building tools for reproducible bioinformatic analyses of such data sets. To address these challenges, we developed target capture probes for genomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built the general purpose bioinformatic pipeline CaptureAl. Phylogenomic analyses of Malagasy Dalbergia species yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatic resources, including the Fabaceae1005 and Dalbergia2396 probe sets, will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

amazonica Ducke) Essential Oil: Chemical Composition, Antibacterial, Antioxidant and Antitrypanosomal Activity

Aniba rosaeodora is one of the most widely used plants in the perfumery industry, being used as medicinal plant in the Brazilian Amazon. This work aimed to evaluate the chemical composition of A. rosaeodora essential oil and its biological activities. A. rosaeodora essential oil presented linalool (93.60%) as its major compound. The A. rosaeodora essential oil and linalool showed activity against all the bacteria strains tested, standard strains and marine environment bacteria, with the lower minimum inhibitory concentration being observed for S. aureus. An efficient antioxidant activity of A. rosaeodora essential oil and linalool (EC₅₀: 15.46 and 6.78 µg/mL, respectively) was evidenced by the inhibition of the 2,2-azinobis- (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical. The antitrypanosomal activity of A. rosaeodora essential oil and linalool was observed at high concentrations against epimatigote forms (inhibitory concentration for 50% of parasites (IC₅₀): 150.5 ± 1.08 and 198.6 ± 1.12 µg/mL, respectively), and even higher against intracellular amastigotes of T. cruzi (IC₅₀: 911.6 ± 1.15 and 249.6 ± 1.18 µg/mL, respectively). Both A. rosaeodora essential oil and linalool did not exhibit a cytotoxic effect in BALB/c peritoneal macrophages, and both reduced nitrite levels in unstimulated cells revealing a potential effect in NO production. These data revealed the pharmacological potential of A. rosaeodora essential oil and linalool, encouraging further studies.

Chemical and Genotypic Variations in Aniba rosiodora from the Brazilian Amazon Forest

Aniba rosiodora has been exploited since the end of the nineteenth century for its essential oil, a valuable ingredient in the perfumery industry. This species occurs mainly in Northern South America, and the morphological similarity among different Aniba species often leads to misidentification, which impacts the consistency of products obtained from these plants. Hence, we compared the profiles of volatile organic compounds (essential oils) and non-volatile organic compounds (methanolic extracts) of two populations of A. rosiodora from the RESEX and FLONA conservation units, which are separated by the Tapajós River in Western Pará State. The phytochemical profile indicated a substantial difference between the two populations: samples from RESEX present α-phellandrene (22.8%) and linalool (39.6%) in their essential oil composition, while samples from FLONA contain mainly linalool (83.7%). The comparison between phytochemical profiles and phylogenetic data indicates a clear difference, implying genetic distinction between these populations.

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.