Biology subjects

Lau, D. T. W.

Publications and source records attributed to Lau, D. T. W..

3 recordsLinked to original sources

bioRxiv2024

Chromosomal-level reference genome and microRNAs of the ricefield flatsedge Cyperus iria

BackgroundGrass-like plants in the Cyperaceae family, commonly known as sedges, have a global distribution and include many economically problematic weeds. The ricefield flatsedge, Cyperus iria, is an aggressive weed in rice crops in Asia. ResultHere, we present a chromosomal-level genome assembly for C. iria (461.2 Mb, scaffold N50 = 7.3 Mbp, 99.6% BUSCO score) providing potential targets for the control of this devastating weed. Based on the genome assembly and transcriptomes of vegetative tissues, 52,574 protein-coding genes were predicted to be encoded. A total of 26 conserved and 75 novel microRNAs, including 9 microRNA clusters, were also annotated. Synteny and microRNA cluster analyses further showed that C. iria had undergone at least one round of whole genome duplication. ConclusionThe genomic resource established in this study sets up a foundation to further address basic and applied questions in the Cyperaceae.

genomics↗

bioRxiv2024

Chromosomal-level genome of fish mint Houttuynia cordata Thunb. (Saururaceae)

Herbaceous flowering plants in the family Saururaceae, or commonly known as the lizards tail family, are native to Southeast Asia and North America. Fish mint Houttuynia cordata is native to Southeast Asia and widely cultivated as culinary herb and medicinal plant in traditional medicine. Here, using a combination of PacBio HiFi long-read sequencing and Omni-C data, we present the chromosomal-level genome assembly of H. cordata (genome size 499.6 Mb). The genome has high sequence contiguity (scaffold N50 = 64.3 Mb) and completeness (BUSCO score of 94.6 %). 40,451 protein coding genes were also predicted using two transcriptomes generated in this study. The fish mint genome provides a valuable resource for further understanding the bioactive compounds and evolution of plants in the Saururaceae more widely.

genomics↗

bioRxiv2020

Chromosomal-level reference genome of the incense tree Aquilaria sinensis

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.

genomics↗