Background & Summary

The genus Aquilaria of Thymelaeaceae, which is consisted of 21 accepted species so far, is native to Indomalesia region. The members of Aquilaria are known to be the primary source of the fragrant non-wood product - agarwood, which is sold as a valuable ingredient for the making of incense, perfume, and traditional medicine1. However, the high demand for natural agarwood is ever increasing; yet, natural agarwood is rare to be obtained in the wild. The collection of agarwood from the trees is considered a destructive act, and the over-harvesting and indiscriminate felling of these trees have endangered the survival of the species in the wild2,3. At present, all the species of Aquilaria has been listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) under the category Appendix II4.

Aquilaria yunnanensis S. C. Huang is a precious agarwood-producing tree species native to the Yunnan Province of China5 (Fig. 1). Based on the latest assessment, A. yunnanensis is categorized as “Vulnerable” under the criteria B1ab(i) by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species6. Due to the decline of suitable habitat for survival, the species is now experiencing a narrow distribution and diminishing populations7. Unlike its congener, Aquilaria sinensis, A. yunnanensis is only confined to 10 locations in Yunnan, while A. sinensis is widely distributed in at least six provinces of China. Despite a new population of A. yunnanensis was recently discovered in the northern region of Vietnam, there were only less than 10 mature individuals recorded in that area8. Such phenomenon has somewhat gained the attention of local researcher to conserve its population. Although sufficient genetic information of this tree could lay out a foundation to strategizing the conservation effort of this vulnerable species, when compared to its congener, A. sinensis, the genomic information for A. yunnanensis is still very limited at present, however.

Fig. 1
figure 1

Aquilaria yunnanensis S. C. Huang. (a) habitat and individuals, (b) fruit, and (c) twigs and leaves.

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In order to provide genome-scale insights into this vulnerable species, we assembled the first high-quality chromosome-level reference genome sequence for A. yunnanensis using BGI short reads and PacBio long reads, coupled with the Hi-C technology. We determined that the primary genome assembly was approximately 846.95 Mb and had a contig N50 of 87.04 Mb. Using Hi-C data, we determined that 805.49 Mb (95.10%) of the assembled bases were assigned to eight pseudo-chromosomes. The final genome assembly of A. yunnanensis was 847.04 Mb. A total of 74.65% of the genome was occupied by repetitive sequences, of which the long terminal repeats (LTR) were predominant (48.28% of the whole genome). Gene prediction identified 27,955 protein-coding genes, of which 22,096 of them were presumably functional.

The availability of the genome information provides a valuable foundation not only for the studies of phylogenetic relationship, genetic diversity, functional genomics, and genomics-assisted breeding of A. yunnanensis, at the same time, also facilitates the comparative genetics and genomic research of Aquilaria.

Methods

Sample collection, library construction and sequencing

Total genomic DNA of A. yunnanensis were extracted from fresh leaves collected from Bubang village of Mengla County, Yunnan Province (21°35′59″N, 101°34′47″E; Fig. 1) using modified CTAB method9. The DNBSEQ-T7 library utilized 1 μg of DNA per sample as the input material, and the sequencing libraries were constructed using the VAHTS Universal DNA Library Prep Kit for MGI (Vazyme, Nanjing, China) according to the manufacturer’s protocol. The quantification and size of the library were measured using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and Bioanalyzer 2100 system (Agilent Technologies, CA, USA)10. The library was subjected to DNA nanoball (DNB) generation and was subsequently sequenced on a DNBSEQ-T7 (BGI, Shenzhen, China) sequencer with DNBSEQ-T7RS Sequencing Reagent in paired-end 150 bp mode11. In total, 441 million reads were generated, amounting to 132.30 Gb of raw sequence data.(Supplementary Table 1).

Fig. 2
figure 2

K-mer analysis (k = 21) for the genome size estimation of A. yunnanensis. The blue area denotes the observed 21-mer frequency distribution. The fitted model is indicated as a black line. The unique and putative error k-mer distributions are shown as yellow and red, respectively.

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To construct the PacBio HiFi library, the DNA template was sheared to an average size of 15 kb with g-TUBE (Covaris, Inc., MA, USA), and the target DNA fragments were recovered using BluePippin size selection System (Sage Science, Inc, MA, USA). The SMRTbell library was constructed using the SMRTbell Express Template Prep kit 2.0 (Pacific Biosciences, California, USA), according to the manufacturer’s instructions. The SMRTbell library was introduced to the PacBio Sequel II platform (Pacific Biosciences, Menlo Park, USA) for sequencing, and the consensus reads (HiFi reads) were generated utilizing the Circular Consensus Sequencing (CCS) software (https://github.com/pacificbiosciences/unanimity) with the parameter ‘-minPasses 3’12. Approximately 31.75 Gb data were obtained, in which the average length was 15,365 bp and the N50 length was 15,576 bp, after removing the adaptors in polymerase reads (Table 1).

Table 1 Sequencing data of A. yunnanensis genome based on four different types of libraries.
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Fresh leaf tissue of A. yunnanensis was used to construct a library for the Hi-C analysis. The fresh tissue was cross-linked with formaldehyde, and cells were lysed using Nuclear Isolation Buffer lysis solution. Then chromatin DNA were digested with restriction endonuclease (MboI), and sticky ends were formed at the cleavage sites. Sticky ends were biotinylated and proximity-ligated to form chimeric junctions that were enriched. Finally, the DNA samples were purified, impurities removed, and randomly interrupted into fragments of 300–500 bp size for library construction. Purified DNA was further blunt-end repaired, A-tailed and adaptor-added, prior to purification through biotin-streptavidin-mediated pull-down and PCR amplification. The Hi-C libraries were quantified and sequenced on the Illumina Nova-seq platform (Illumina, San Diego, CA, USA), which generated a total of 258,748,211 pairs of reads. The 77.62 Gb raw data had a coverage of 91.64× of the genome.

RNA preparation and sequencing

The RNA samples were extracted from roots, stems and leaves tissues using the standard Trizol reagent (Invitrogen, CA, USA) and equally mixed for sequencing. RNA purity and integrity was monitored with NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA)and an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). RNA contamination was assessed using 1.5% agarose gel electrophoresis. The full-length cDNA was synthesized using a Clontech SMARTer PCR cDNA Synthesis Kit (Takara Biotechnology, China). Then, the SMRTbell libraries were constructed using the Pacific Biosciences SMRTbell template prep kit (Pacific Biosciences, USA). The libraries’ quantification and size were measured using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Transcriptome sequencing was conducted using Iso-seq under the CCS model. Subsequently, SMRTbell sequencing was performed on a PacBio Sequel II platform by Frasergen Bioinformatics Co., Ltd. (Wuhan, China). After removing adaptors in polymerase reads, a total of 73.16 Gb subreads were obtained with an average length of 1,122 bp and an N50 length of 1,194 bp.

Genome size and heterozygosity estimation

The generated short reads from the DNBSEQ-T7 platform were subjected to qualitative filtering using SOAPnuke v2.1.613 based on the following approaches: the adaptors were removed from the sequencing reads; read pairs were excluded if either end had an average quality of <20; ends of reads were trimmed when the average quality was <20 in the 5-bp sliding window analysis; then removed the read pairs with either ends shorter than 75 bp. A clean data of 131.73 Gb was obtained for assessing the characteristics of the genome (Table 1). The 21-mer frequency distribution of sequencing reads from the short reads was generated using Jellyfish v2.1.414. Using the software GenomeScope v2.015, the genome size was estimated to be about 846.18 Mb, and the proportion of repeat sequences and heterozygosity rate of the genome were determined to be approximately 58.1% and 1.0% (Fig. 2), respectively.

De novo genome assembly

The PacBio HiFi reads were used for de novo assembly using hifiasm v.0.14-r31216 with default parameters. Gfatools (https://github.com/lh3/gfatools) was used to convert the sequence graphs from the GFA format into FASTA format. The primary assembly was corrected using short reads from the DNBSEQ-T7 library, and the correction process was completed using Pilon v1.2317. As a result, the A. yunnanensis genome assembly had a total length of about 846.95 Mb, which contained 575 contigs; while the contig N50 was 87.04 Mb (Table 2).

Table 2 Information of A. yunnanensis genome assembly based on the Hifiasm-derived contigs and Hi-C scaffolded assembly.
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The raw Hi-C data were primarily filtered using Fastp18, followed by mapping the filtered Hi-C data to the A. yunnanensis genome using Bowtie2 v2.3.219 with the default parameters. An iterative mapping strategy was employed, retaining only read pairs with uniquely mapped both ends for the subsequent analysis, to increase the ratio of interactive Hi-C reads. Self-ligation, non-ligation, and other invalid reads, including StartNearRsite, PCR amplification, random break, LargeSmallFragments, and ExtremeFragments, were filtered out by HiCUP20. A total of 20.56 Gb clean data were retained (Table 1). The order and orientation of the clustered contigs were arranged with D-DNA v180922 pipeline21. The construction of the chromosome was manually carried out using the Juicebox tool package v1.22.0122. A total of 575 contigs were used to construct scaffolds with Hi-C data, which generated 415 scaffolds consequently (Table 2). The scaffolds were anchored on eight pseudo-chromosomes (Fig. 3). Among them, six pseudo-chromosomes contained a total of 16 gaps, each with a length of 500 bp, while the other two pseudo-chromosomes were gapless (Fig. 4, Supplementary Table 2). The Hi-C-assisted chromosome-length scaffolds yielded a final size of 805.49 Mb accounting for the 95.10% draft genome, ranging from 86.64 Mb to 119.54 Mb in length (Table 3).

Fig. 3
figure 3

Hi-C interaction heatmap at chromosome-level of A. yunnanensis. The heatmap indicates that the intra-chromosome interactions (blocks on the diagonal line) are stronger compared to the inter-chromosome interactions.

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Fig. 4
figure 4

A circos plot of eight chromosomes of A. yunnanensis genome. The tracks from outside to inside represent: gene density, transposon density, repeat sequence density, GC content, and collinear blocks. The red vertical lines on the outside track indicate the gaps.

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Table 3 Information of the A. yunnanensis genome at chromosomal-level.
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Repeat annotation

The de novo- and homology-based approaches were used to identify the repeat sequences in the A. yunnanensis genome assembly. RepeatModeler v2.0.423 was used to construct a de novo repeat library, which employed the results from RECON v1.0.824 and RepeatScout v1.0.625. For the homology-based approach, repeats was identified using RepeatMasker v4.1.526, integrating both the Repbase library (http://www.girinst.org/repbase/) and the de novo repeat library, to detect known transposable elements (TEs) within the genome assembly. The results indicated a total of 632.35 Mb repetitive sequences identified, representing 74.65% of the A. yunnanensis genome assembly. The LTR elements, accounting for 48.28% of the whole genome, were the most abundant. For other classes, the DNA transposons, long interspersed nuclear elements (LINE), and short interspersed nuclear elements (SINE) had accounted for 6.09%, 1.65%, and 0.01% of the whole genome, respectively (Table 4)

Table 4 Information on the repeat annotation in the A. yunnanensis genome assembly.
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Gene prediction and functional annotation of the genome

For annotation of the protein-coding genes, we employed a method integrating transcriptome-based, ab initio, and homologue-based strategies to identify the gene models using Maker v3.0127. For the transcriptome-based gene prediction, we used the CCS, lima (https://github.com/pacificbiosciences/barcoding/) and IsoSeq (https://github.com/pacificBiosciences/pbbioconda) pipelines to obtain the transcript sequences. Error correction was carried out on the raw sequencing data using the CCS v6.4.0; while the adaptor sequences were filtered using lima v2.7.1. Further sequence filtering and clustering were conducted using IsoSeq v4.0.0 to produce accurate full-length transcript sequences, which were used as input data for the Maker software. The ab initio gene prediction was conducted using Augustus v3.4.028; while the proteins sequences from Aquilaria sinnsis29, Arabidopsis thaliana30, Gossypium hirsutum31, Stellera chamaejasme32 and Theobroma cacao33 were aligned with the genome of A. yunnanensis using TBLASTN34. The homologous genes were identified using Exonerate v2.2.235. As the gene prediction via Maker is based on the transcript sequences, the gene structure models generated by Maker were used as input to train the species-specific model files in Augustus. The gene model prediction was carried out another round using Maker, but with an automatic annotation integration of data, including the transcript evidence, protein evidence, and Augustus gene predictions, into a consensus annotation based on their evidence-based weights. After filtering off genes with protein-encoding sequence that were shorter than 50 amino acids, as well as genes that contained internal stop codons, and illegal start or stop codons, the gene prediction identified a total of 27,955 protein-coding genes being annotated in the A. yunnanensis genome.

Functional annotation was performed using eggNOG-mapper v2.1.736 with reference to the eggNOG orthology database and sequence searches were carried out using DIAMOND37. Additionally, protein annotation was conducted using eggNOG-mapper by referring to the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. As a result, a total of 22,096 genes that are presumably functional were annotated, while as much as 12,560 and 7,259 genes were assigned to a specific GO term and a KEGG pathway, respectively.

Data Records

The BGI short reads, PacBio HiFi long reads, Hi-C reads, and RNA-Seq data were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database with the accession number SRP45741838 under BioProject accession number PRJNA100891839. The genome assembly had been deposited in DDBJ/ENA/GenBank under the accession number JBDJPA00000000040. The genome assembly and annotation files were submitted to Figshare41.

Technical Validation

Accuracy assessment of genome assembly

The software BWA v0.7.17-r118842 was used to align the short reads of DNBSEQ-T7 library of A. yunnanensis to the assembled genome, achieving 99.51% of mapping rate, with coverage of 99.9%. Merqury v1.343 was used to assess the consensus quality value (QV) of the A. yunnanensis genome assembly. The QVs were 65.60 and 46.38 estimated with HiFi and BGI k-mers, respectively, indicating high accuracy of the genome assembly (Supplementary Figure 1).

Integrity assessment of genome assembly

The integrity of the final genome assembly was assessed by using BUSCO v5.1.244 with the embryophyta_odb10 orthologous database (https://busco-data.ezlab.org/v5/data/lineages/) including 1,614 widely conserved single-copy genes in embryophytes. The BUSCO analysis revealed that 98.1% of the complete genes were retrieved in the genome, with 95.0% being single-copy and 3.1% duplicated. Only 0.7% and 1.2% of BUSCO genes were fragmented and missing, respectively (Fig. 5). LTR_finder v.1.5.1045, LTR_harvest v1.0646 and LTR_retriver v2.9.047 were employed to assess the LTR Assembly Index (LAI) value of the genome assembly. The obtained LAI value was 22.16, which achieved the gold standard for genome assembly. The above evaluation results indicate that the A. yunnanensis genome assembly has high integrity.

Fig. 5
figure 5

BUSCO scores of the genome assembly of A. yunnanensis. C: the number of complete genes, S: the number of complete and single-copy genes, D: the number of complete and duplicated genes, F: the number of incomplete genes, M: the number of missing genes.

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