Chromosomal-level reference genome of the incense treeAquilaria sinensis

Abstract

Trees in the genus Aquilaria (Thymelaeaceae) are known as lign aloes, and are native to the forests of southeast Asia. Lign aloes produce agarwood as an antimicrobial defence.Agarwood has a long history of cultural and medicinal use, and is of considerable commercial value. However, due to habitat destruction and over collection, lign aloes are threatened in the wild. We present a chromosomal-level assembly for Aquilaria sinensis, a lign aloe endemic to China known as the incense tree, based on Illumina short-read, 10XGenomics linked-read, and Hi-C sequencing data. Our 783.8Mbp A. sinensis genome assembly is of high physical contiguity, with a scaffold N50 of 87.6Mbp, and high completeness, with a 95.8% BUSCO score for eudicotyledon genes. We include 17 transcriptomes from various plant tissues, providing a total of 35,965 gene models. We reveal the first complete set of genes involved in sesquiterpenoid production, plant defence, and agarwood production for the genus Aquilaria, including genes involved in the biosynthesis of sesquiterpenoids via the mevalonic acid (MVA), 1-deoxy-D-xylulose-5-phosphate (DXP), and methylerythritol phosphate (MEP) pathways. We perform a detailed repeat content analysis, revealing that transposable elements account for ~61% of the genome, with major contributions from gypsy-like and copia-like LTR retroelements. We also provide a comparative analysis of repeat content across sequenced species in the order Malvales. Our study reveals the first chromosomal-level genome assembly for a tree in the genus Aquilaria and provides an unprecedented opportunity to address a variety of applied, genomic and evolutionary questions in the Thymelaeaceae more widely.

A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

“…Recently, the first chromosome-level assemblies have been published for tree and shrub species, e.g., the tea tree [Camellia sinensis (Chen et al, 2020)], loquat [Eriobotrya japonica (Jiang et al, 2020)], walnut [Juglans regia (Marrano et al, 2020)], Chinese tupelo [Nyssa sinensis (Yang et al, 2019)], fragrant rosewood [Dalbergia odorifera (Hong et al, 2020)], wheel tree [Trochodendron aralioides (Strijk at. Al., 2019)], azalea [Rhododendron simsii (Yang et al, 2020)], agarwood tree [Aquilaria sinensis (Nong et al, 2020)], and tea olive [Osmanthus fragrans (Yang et al, 2018)]. However, such resources are currently lacking for species of the Fagaceae, which includes the economically and ecologically important genera Castanea, Fagus, and Quercus (Kermer at al., 2012).…”

Chromosomal-Level Reference Genome of the Moth Heortia Vitessoides (Lepidoptera: Crambidae), A Major Pest of Agarwood-Producing Trees

“…Gene models were predicted as previously described [48,59]. Briefly, gene models were trained and predicted using funannotate (v1.7.4, htt ps://github.com/nextgenusfs/funannotate) [61] specifying the parameters "-repeats2evm -protein_evidence uniprot_sprot.fasta -gene-mark_mode ET -busco_seed_species fly -optimize_augustus -busco_db arthropoda -organism other -max_intronlen 350000".…”

Migrators Within Migrators: Exploring Transposable Element Dynamics in the Monarch Butterfly, Danaus plexippus

“…The D. plexippus genome was annotated using a bespoke automated in-house TE annotation pipeline, as previously described [99][100][101][102][103][104]. For this, known repeats were first identified and masked using RepeatMasker (version 4.1.0) [105] using the Arthropoda library from RepBase (version 23.08) and Dfam (release 3.3) [106,107].…”