Project | 01
LATEST PROJECTS
Project | 01
Project | 01 Evolution of specialized metabolite biosynthetic pathways in the Lamiaceae: sources of chemical diversity for molecules essential for human use and plant defense
The Lamiaceae (mint family) with ~7,000 species, produces a wide range of chemicals and includes culinary herbs, decorative foliage, and species with medicinal and health-promoting properties. To elucidate the mechanisms underlying the chemical diversity, a panel of 48 species representative of major clades within the Lamiaceae and 4 outgroup species were surveyed for their transcriptomes and metabolomes (monoterpenes, sesquiterpenes, iridoids). For this project, I’ve been working and contributing to the identification of gene expansion events, gene expression variation, and parallel evolution events that led to the chemical diversity within the mint family.
Project | 02
Project | 02
Decoding genome sequence of teak (Tectona grandis) for timber quality using single-molecule sequencing and chromatin interaction mapping
I sequenced the genome of teak, a key timber species, using long read sequencing technology (PacBio) and chromatin proximity data (Hi-C) as a first step in understanding at a genome level, genes that contribute to the high quality of teak timber.
FINISHED PROJECTS
Project | 01 The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum
Pack-MULEs are transposable elements capable of acquiring gene sequences and forming novel genes, with over 3,000 in the rice genome. An integrated survey of transcriptome, translatome, and epigenome indicated over 1/3 of Pack-MULEs resemble protein-coding genes by frequent transcription and translation, abundant active histone marks, low DNA methylation and repressive histone marks, suggesting that these Pack-MULEs have the potential to contribute to the functional components of the rice genome.
Project | 02
Project | 02 De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin
Camptotheca acuminata is one of a limited number of species that produce camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity due to its ability to inhibit DNA topoisomerase. Analyses of the genome sequence and annotation revealed extensive tandem duplication and physical clustering of candidate genes involved in camptothecin biosynthetic pathway. This is the first genome sequence for a camptothecin-producing species, and access to the genome will permit not only discovery of genes encoding the camptothecin biosynthetic pathway but also reagents that can be used for heterologous production of camptothecin and camptothecin analogs with novel pharmaceutical applications.
Project | 03
Project | 03 Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation
Using Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq), translatomes of three rice tissues were surveyed. Analyses showed that most transcribed genes were translated whereas few transposable elements were translated. Genes with short and GC-rich coding regions were overrepresented in the translatomes, transcripts with retained introns and extended 5’ untranslated regions were underrepresented, and genes belonging to different evolutionary lineages exhibited differential enrichment in the translatomes, suggestive of important mechanisms of gene regulation, which may have a role in evolution and diversification.