Genome sequence of the agarwood tree <i>Aquilaria sinensis</i> (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

Ding, Xuezhi; Mei, Wen‐Li; Lin, Qiang; Wang, Hao; Wang, Jun; Peng, Shi-Qing; Li, Hui‐Liang; Zhu, Jiahong; Li, Wei; Wang, Pei; Chen, Huiqin; Dong, Wei; Guo, Dong; Cai, Cai-Hong; Huang, Sheng‐Zhuo; Cui, Peng; Dai, Hao‐Fu

doi:10.1093/gigascience/giaa013

Cited by 49 publications

(45 citation statements)

References 72 publications

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“…In particular, recursive polyploidization, polyploidization of different ploidy, and genome rearrangement have been observed in angiosperms [9,10]. As a valuable plant, the genome of A. sinensis has been sequenced by two independent groups [11,12]. It was reported that the genome of A. sinensis experienced a recent WGD event [11].…”

Section: Introductionmentioning

confidence: 99%

A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis

et al. 2021

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Background Agarwood, generated from the Aquilaria sinensis, has high economic and medicinal value. Although its genome has been sequenced, the ploidy of A. sinensis paleopolyploid remains unclear. Moreover, the expression changes of genes associated with agarwood formation were not analyzed either. Results In the present work, we reanalyzed the genome of A. sinensis and found that it experienced a recent tetraploidization event ~ 63–71 million years ago (Mya). The results also demonstrated that the A. sinensis genome had suffered extensive gene deletion or relocation after the tetraploidization event, and exhibited accelerated evolutionary rates. At the same time, an alignment of homologous genes related to different events of polyploidization and speciation were generated as well, which provides an important comparative genomics resource for Thymelaeaceae and related families. Interestingly, the expression changes of genes related to sesquiterpene synthesis in wounded stems of A. sinensis were also observed. Further analysis demonstrated that polyploidization promotes the functional differentiation of the key genes in the sesquiterpene synthesis pathway. Conclusions By reanalyzing its genome, we found that the tetraploidization event shaped the A. sinensis genome and contributed to the ability of sesquiterpenes synthesis. We hope that these results will facilitate our understanding of the evolution of A. sinensis and the function of genes involved in agarwood formation.

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Section: Introductionmentioning

confidence: 99%

A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis

et al. 2021

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“…Thailand (Ding et al 2020). It is one of the most important plant species for producing agarwood, and A. sinensis material has long been used as a sedative, digestive and anti-emetic drug in traditional medicine and as unique perfume and incense (Ding et al 2020;Xu et al 2020 The AsTal1 cDNA sequence containing class-speci c TAL conserved domains and nucleotide sequences was obtained from the A. sinensis callus transcriptomic dataset. To isolate this gene from A. sinensis calli, open reading frames (ORFs) were isolated via RT-PCR using speci c primers ( Table 1).…”

Section: Introductionmentioning

confidence: 99%

A Transaldolase From Aquilaria Sinensis Involves in Aba-mediated Seed Germination and Root Growth

Rong

Liu

et al. 2021

Preprint

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Transaldolase, the key enzyme of the pentose-phosphate pathway, plays an important role in plant growth and defense. Seed germination is a key factor that influences the cultivation of Aquilaria sinensis, the plant source of agarwood, which is widely used as a traditional medicine, perfume and incenses. However, little is known about the function of transaldolase in abscisic acid (ABA)-mediated seed germination. In the present study, the full-length AsTal1 gene was isolated and characterized from A. sinensis calli. Sublocalization analysis indicated that AsTal1 was localized in the cytoplasm. In addition, phenotypic analysis indicated that AsTal1-overexpressing Nicotiana benthamiana (OE) plants were less sensitive to ABA during seed germination and root growth than wild-type (WT) plants. Overexpression of AsTal1 regulated the expression of genes involved in ABA metabolism, biosynthesis and signal transduction under ABA treatment. In addition, expression of NbRbohA and NbRbohB was inhibited in the overexpression lines, whereas the abundance and activities of the antioxidative enzymes SOD, APX, and POD were higher in the transgenic plants than in the WT lines after ABA treatment. Taken together, our results indicated that AsTal1 is involved in the ABA response during seed germination and root growth by regulating the expression of genes involved in the ABA signaling pathway and the enzymes responsive to ROS.

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“…Moreover, Hi-C technology has emerged as a robust tool to reconstruct genomes at the chromosome level, providing long-range information about the grouping and linear organization of sequences along entire chromosomes ( Burton et al 2013 ). Recently, several high-quality plant genomes had been obtained by using Nanopore sequencing and Hi-C technologies, including Eriobotrya japonica ( Jiang et al 2020 ), Aquilaria sinensis ( Ding et al 2020 ), and Asparagus setaceus ( Li et al 2020 ).…”

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Genome Assembly of SalicaceaePopulus deltoides(Eastern Cottonwood)I-69Based on Nanopore Sequencing and Hi-C Technologies

Bai

Zhang

et al. 2021

Journal of Heredity

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Populus deltoides is of significantly ecological and economic values, widely used in poplar breeding programs due to its superior characteristics such as rapid growth and resistance to disease. Although the genome sequence of P. deltoides WV94 is available, the assembly is fragmented. Here, we reported an improved chromosome-level assembly of the P. deltoides cultivar I-69 by combining Nanopore sequencing and chromosome conformation capture (Hi-C) technologies. The assembly was 429.3 Mb in size and contained 657 contigs with a contig N50 length of 2.62 Mb. Hi-C scaffolding of the contigs generated 19 chromosome-level sequences, which covered 97.4% (418 Mb) of the total assembly size. Moreover, repetitive sequences annotation showed that 39.28% of the P. deltoides genome was composed of interspersed elements, including retroelements (23.66%), DNA transposons (6.83%), and unclassified elements (8.79%). We also identified a total of 44,362 protein-coding genes in the current P. deltoides assembly. Compared with the previous genome assembly of P. deltoides WV94, the current assembly had some significantly improved qualities: the contig N50 increased 3.5-fold and the proportion of gaps decreased from 3.2% to 0.08%. This high-quality, well-annotated genome assembly provides a reliable genomic resource for identifying genome variants among individuals, mining candidate genes that control growth and wood quality traits, and facilitating further application of genomics-assisted breeding in populations related to P. deltoides.

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Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

Cited by 49 publications

References 72 publications

A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis

A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis

A Transaldolase From Aquilaria Sinensis Involves in Aba-mediated Seed Germination and Root Growth

Genome Assembly of SalicaceaePopulus deltoides(Eastern Cottonwood)I-69Based on Nanopore Sequencing and Hi-C Technologies

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