Dalbergia odorifera
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ABSTRACT:
PROVIDER: PRJNA397853 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Plastome barcodes of Dalbergia odorifera and D. tonkinensis
| PRJNA553296 | ENA
Project description:Dalbergia cultrata Genome sequencing and assembly
| PRJNA524072 | ENA
Project description:Serratia odorifera strain:KCTC 2937 Genome sequencing and assembly
| PRJNA484650 | ENA
Project description: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.
| S-EPMC7433187 | biostudies-literature
Project description:Dalbergia odorifera T. Chen is a medium-sized evergreen tree that produces purple-brown heartwood called JiangXiang in traditional Chinese medicine, the formation process of which takes several decades. In this study, a standard culture method was used to isolate fungi from the wounded and normal stems of D. odorifera aiming to investigate the difference between the two types of wood. To characterize the spatial colonisation of endophytic fungi, an anatomical study was undertaken using the two different types of wood of D. odorifera. A total of 320 wood segments were placed on PDA plates and 87 fungal isolates were obtained. Only two fungi were isolated from the healthy white wood tissue, whereas 85 fungi were found in the purple-brown wounded-wood tissues. The two isolates from 160 white healthy wood tissues were assigned to Bionectriaceae sp., and the rest in wounded wood tissues were analyzed to 12 fungal species, indicating both a high fungal diversity and colonization rate in the purple-brown wounded wood. There was a difference in fungal species composition between coloured and white wood samples collected from the same tree. Eutypa sp. was the most commonly isolated species in the purple-brown wounded wood.
| S-EPMC4329543 | biostudies-literature