Chromosomal‐level reference genome of the incense tree Aquilaria sinensis

This is the author accepted manuscript. The final version is available on open access from Wiley via the DOI in this recordData Accessibility: The raw genome and RNA sequencing data have been deposited in the SRA under Bioproject numbers SRR10737433 and PRJNA534170. The final chromosome assembly was submitted to NCBI Assembly under accession number VZPZ00000000 in NCBI.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, 10X Genomics 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.Chinese University of Hong KongAgriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative RegionBiotechnology and Biological Sciences Research Council (BBSRC

Case studies of seasonal rainfall forecasts for Hong Kong and its vicinity using a regional climate model

Seasonal climate forecasts are one of the most promising tools for providing early warnings for natural hazards such as floods and droughts. Using two case studies, this paper documents the skill of a regional climate model in the seasonal forecasting of below normal rainfall in southern China during the rainy seasons of July-August-September 2003 and April-May-June 2004. The regional model is based on the Regional Spectral Model of the National Centers for Environmental Prediction of the United States. It is the first time that the model has been applied to a region dominated by the East Asian Monsoon. The article shows that the regional climate model, when being forced by reasonably good forecasts from a global model, can generate useful seasonal rainfall forecasts for the region, where it is dominated by the East Asia monsoon. The spatial details of the dry conditions obtained from the regional climate model forecast are also found to be comparable with the observed distribution. © Springer Science+Business Media, Inc. 2007.link_to_subscribed_fulltex