Biology subjects

Chan, T.-F.

Publications and source records attributed to Chan, T.-F..

15 recordsLinked to original sources

bioRxiv2025

A wild genome of the underutilized legume lablab (Lablab purpureus) reveals the genetic basis of domestication

BackgroundWith global food security threatened by climate change and the growing global population, underutilized crops offer sustainable solutions for diversifying current agricultural systems. Lablab (Lablab purpureus) is a highly versatile, climate-resilient underutilized legume native to Africa and widely, but locally, cultivated in Asia with untapped potential for sustainable agriculture. However, the lack of wild genome resource prevents a comprehensive genome utilization research for this underutilized crop. This paper presents the first chromosome-scale genome of wild lablab with its complete gene annotation and provides comprehensive population genomic analyses of its evolution and domestication by resequencing a panel of wild and domesticated accessions. ResultsThe genome was assembled into a total size of 478.2 Mb with a scaffold N50 of 39.7 Mb, and 96.4% (460.8 Mb) of the scaffolds anchored to 11 pseudochromosomes, the haploid chromosome number of lablab. We demonstrated that domestication was likely in Africa with several subsequent instances of transportation into Asia. Our analyses identified selective sweeps resulting from domestication as well as pseudogenes associated with yield-related traits and stress tolerance, representing candidate genes for further validation and targets for future breeding programs. ConclusionsOur genomic resource for wild lablab delineated its domestication history and identified key genes and pseudogenes under selection, bridging the gap between its untapped wild diversity and breeding for improved stress resilience and yield in underutilized legumes. This offers genomic and genetic insights for crop improvement of lablab.

evolutionary biology↗

bioRxiv2024

Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor

Platalea minor, the black-faced spoonbill (Threskiornithidae) is a wading bird that is confined to coastal areas in East Asia. Due to habitat destruction, it has been classified by The International Union for Conservation of Nature (IUCN) as globally endangered species. Nevertheless, the lack of its genomic resources hinders our understanding of their biology, diversity, as well as carrying out conservation measures based on genetic information or markers. Here, we report the first chromosomal-level genome assembly of P. minor using a combination of PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (1.24 Gb) contains 95.33% of the sequences anchored to 31 pseudomolecules. The genome assembly also has high sequence continuity with scaffold length N50 = 53 Mb. A total of 18,780 protein-coding genes were predicted, and high BUSCO score completeness (93.7% of BUSCO metazoa_odb10 genes) was also revealed. A total of 6,155,417 bi-allelic SNPs were also revealed from 13 P. minor individuals, accounting for [~]5% of the genome. The resource generated in this study offers the new opportunity for studying the black-faced spoonbill, as well as carrying out conservation measures of this ecologically important spoonbill species.

genomics↗

bioRxiv2024

Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)

The edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has also been used in food additives given its ability to synthesize long-chain glycolipids. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size of D. spathularia is 29.2 Mb and in high sequence contiguity and completeness, including scaffold N50 of 1.925 Mb and 92.0% BUSCO score, respectively. A total of 11,510 protein-coding genes, and 474.7 kb repeats accounting for 1.62% of the genome, were also predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology such as wood decaying capability, evolutionary relationships with other fungus, as well as their unique biology and applications in the food industry.

genomics↗

bioRxiv2024

Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific and can cause severe bioerosion on the reef community. Nevertheless, the lack of genomic information has hindered the study its ecology and evolution. Here, we report the chromosomal-level genome (885.8 Mb) of the long-spined sea urchin D. setosum using a combination of PacBio long-read sequencing and Omni-C scaffolding technology. The assembled genome contained scaffold N50 length of 38.3 Mb, 98.1 % of BUSCO (Geno, metazoa_odb10) genes, and with 98.6% of the sequences anchored to 22 pseudo-molecules/chromosomes. A total of 27,478 genes including 23,030 protein-coding genes were annotated. The high-quality genome of D. setosum presented here provides a significant resource for further understanding on the ecological and evolutionary studies of this coral reef associated sea urchin.

genomics↗

bioRxiv2024

Genome assembly of the rare and endangered Grantham's camellia, Camellia granthamiana

The Granthams camellia (Camellia granthamiana Sealy) is a rare and endangered tea species that is endemic to southern China, and was first discovered in Hong Kong in 1955. Despite its high conservation value, genomic resources of C. granthamiana remain limited. Here, we present a chromosome-scale draft genome of the tetraploid C. granthamiana (2n = 4x = 60) using a combination of PacBio long read sequencing and Omni-C data. The assembled genome size is [~]2.4 Gb with most sequences anchored to 15 pseudochromosomes that resemble a monoploid genome. The genome is of high contiguity, with a scaffold N50 of 139.7 Mb, and high completeness with a 97.8% BUSCO score. Gene model prediction resulted in a total 76,992 protein-coding genes with a BUSCO score of 85.9%. 1.65 Gb of repeat content was annotated, which accounts for 68.48% of the genome. The Granthams camellia genome assembly provides a valuable resource for future investigations on its biology, ecology, phylogenomic relationships with other Camellia species, as well as set up a foundation for further conservation measures.

plant biology↗

bioRxiv2024

Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)

Chitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. Nevertheless, there remains only two chiton genomes sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of [~]609 Mb with a scaffold N50 length of 37.34 Mb (96.1% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding genes. The repeat content (27.89%) was similar to the other Chitonidae species and approximately three times lower than in the genome of the Hanleyidae chiton. The genomic resources provided in this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.

genomics↗

bioRxiv2024

Genome assembly of the milky mangrove Excoecaria agallocha

The milky mangrove Excoecaria agallocha is a latex-secreting mangrove that are distributed in tropical and subtropical regions. While its poisonous latex is regarded as a potential source of phytochemicals for biomedical applications, the genomic resources of E. agallocha remains limited. Here, we present a chromosomal level genome of E. agallocha, assembled from the combination of PacBio long-read sequencing and Omni-C data. The resulting assembly size is 1,332.45 Mb and has high contiguity and completeness with a scaffold N50 of 58.9 Mb and a BUSCO score of 98.4 %. 73,740 protein-coding genes were also predicted. The milky mangrove genome provides a useful resource for further understanding the biosynthesis of phytochemical compounds in E. agallocha.

genomics↗

bioRxiv2024

Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

Troides aeacus, the golden birdwing (Lepidoptera, Papilionidae) is a large swallowtail butterfly widely distributed in Asia. Despite its occurrence, T. aeacus has been assigned as a major protective species in many places given the loss of their native habitats under urbanisation and anthropogenic activities. Nevertheless, the lack of its genomic resources hinders our understanding of their biology, diversity, as well as carrying out conservation measures based on genetic information or markers. Here, we report the first chromosomal-level genome assembly of T. aeacus using a combination of PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (351 Mb) contains 98.94% of the sequences anchored to 30 pseudo-molecules. The genome assembly also has high sequence continuity with scaffold length N50 = 12.2 Mb. A total of 28,749 protein-coding genes were predicted, and high BUSCO score completeness (98.9% of BUSCO metazoa_odb10 genes) was also revealed. This high-quality genome offers a new and significant resource for understanding the swallowtail butterfly biology, as well as carrying out conservation measures of this ecologically important lepidopteran species.

genomics↗

bioRxiv2023

Accurate identification of structural variations from cancer samples

Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion, and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the COMSV method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.

genomics↗

bioRxiv2022

rG4-seq 2.0: enhanced transcriptome-wide RNA G-quadruplex structure sequencing for low RNA input samples

RNA G-quadruplexes (rG4s) are non-canonical structural motifs that have diverse functional and regulatory roles such as transcription termination, alternative splicing, mRNA localization and stabilization and translational process. We recently developed RNA G-quadruplex structure sequencing (rG4-seq) technique and discovered many rG4s in both eukaryotic and prokaryotic transcriptomes. However, rG4-seq suffers from complicated gel purification step and limited PCR product yield and thus requires a high RNA input amount, limiting its applications for physiologically or clinically relevant studies. In this study, we have developed rG4-seq 2.0 by introducing a new ssDNA adapter containing deoxyuridine in the library preparation to enhance the library quality with no gel purification step, less PCR amplification cycles and higher yield of PCR products. We demonstrate that rG4-seq 2.0 produced high quality cDNA libraries that supported reliable and reproducible rG4 identification at varying RNA inputs (as low as 10 ng amount of RNA). rG4-seq 2.0 also improved the rG4-seq calling outcome and nucleotide bias in rG4 detection persistent in rG4-seq 1.0. Our new method can improve the identification and study of rG4s in low abundance transcripts, and our findings can provide insights to optimize cDNA library preparation in other related methods.

genomics↗

bioRxiv2021

Deep autoencoder enables interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis

Single-cell RNA-sequencing has become a powerful tool to study biologically significant characteristics at explicitly high resolution. However, its application on emerging data is currently limited by its intrinsic techniques. Here, we introduce Tissue-AdaPtive autoEncoder (TAPE), a deep learning method connecting bulk RNA-seq and single-cell RNA-seq to achieve precise deconvolution in a short time. By constructing an interpretable decoder and training under a unique scheme, TAPE can predict cell-type fractions and cell-type-specific gene expression tissue-adaptively. Compared with popular methods on several datasets, TAPE has a better overall performance and comparable accuracy at cell type level. Additionally, it is more robust among different cell types, faster, and sensitive to provide biologically meaningful predictions. Moreover, through the analysis of clinical data, TAPE shows its ability to predict cell-type-specific gene expression profiles with biological significance. We believe that TAPE will enable and accelerate the precise analysis of high-throughput clinical data in a wide range.

bioinformatics↗

bioRxiv2020

rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments

We recently developed the rG4-seq method to detect and map in vitro RNA G-quadruplex (rG4s) structures on a transcriptome-wide scale. rG4-seq of purified human HeLa RNA has revealed many non-canonical rG4s and the effects adjacent sequences have on rG4 formation. In this study, we aimed to improve the outcomes and false-positive discrimination in rG4-seq experiments using a bioinformatic approach. By establishing connections between rG4-seq library preparation chemistry and the underlying properties of sequencing data, we identified how to mitigate indigenous sampling errors and background noise in rG4-seq. We applied these findings to develop a novel bioinformatics pipeline named rG4-seeker(https://github.com/TF-Chan-Lab/rG4-seeker), which uses tailored noise models to autonomously assess and optimize rG4 detections in a replicate-independent manner. Compared with previous methods, rG4-seeker exhibited better false-positive discrimination and improved sensitivity for non-canonical rG4s. Using rG4-seeker, we identified novel features in rG4 formation that were missed previously. rG4-seeker provides a reliable and sensitive approach for rG4-seq investigations, laying the foundations for further elucidation of rG4 biology.

bioinformatics↗

bioRxiv2019

Cross-kingdom regulation of tRNAs/tRFs derived from Chinese yew

Plants containing countless chemical constituent have benefited mankind since the origin of life. Although secondary metabolites in plants, such as morphine, artemisinin and taxol, have been developed as therapeutic drugs for clinical therapy, few study focuses on the pharmacological activities of plant small RNAs with function of cross-kingdom regulations. Yew is widely considered as a \"superstar\" plant due to the discovery of paclitaxel, or taxol, which is a well-known natural drug for the treatment of multiple types of cancer1. Here we show the surprising finding that an RNA fragment, named tRF-T11, derived from tRNAHis(GUG) of Chinese yew strongly suppressed human ovarian cancer progression. In A2780 cells, tRF-T11 mimic (a double-stranded RNA with tRF-T11 as antisense chain) exhibited potent cytotoxicity comparable to that of taxol, but no significant cytotoxicity to normal ovarian surface epithelial cells. Moreover, the cytotoxicity of tRF-T11 mimic is 80-fold stronger than that of taxol in taxol-resistant A2780 cells. Bioinformatic and molecular biological studies revealed that tRF-T11 targets transient receptor potential cation channel subfamily A member 1 (TRPA1) to inhibit its expression levels. In a further in vivo investigation, the growth rate of ovarian tumor xenografts in nude mice was significantly reduced by treatment with tRF-T11 mimic, and the TRPA1 protein expression in tumors treated with tRF-T11 mimic was also down-regulated. Our findings are the first to provide evidence that plant-derived tRFs can regulate the expression of target genes in vitro and in vivo, indicating that they may become as a new source of druggable siRNA. Moreover, this discovery demonstrated a pilot example of an innovative approach for not only identifying pharmacologically-active tRFs from plants, but also for improving the efficiency and possibilities of discovering new drug target.

cell biology↗

bioRxiv2017

Systematic selection of reference genes for normalization of circulating RNA transcripts in pregnant women based on RNA-seq data

RNA transcripts circulating in peripheral blood represent an important source of non-invasive biomarkers. To accurately quantify the levels of a circulating transcript, one needs to normalize the data with internal control reference genes, which are detected at relatively constant levels across different blood samples. A few stably-expressed reference gene candidates have to be selected from transcriptome data before validation of their stable expression by reverse-transcription quantitative polymerase chain reaction. However, there is a lack of transcriptome, let alone whole-transcriptome, data from maternal blood. To overcome this shortfall, we performed RNA-seq on blood samples from women presented with preterm labor. Of 11215 exons detected in the maternal blood whole-transcriptome, we systematically identified a panel of 395 genes comprising exons that were detected at a coefficient of variation (CV) ranging from 7.75%-17.7%. Their levels were considerably less variable than any GAPDH exon (minimum CV, 27.3%). Upon validation, selected genes from this panel remained as more stably expressed than GAPDH in maternal blood. This panel is over-represented with genes involved with actin cytoskeleton, macromolecular complex and the integrin signaling pathway. This groundwork provides a starting point for systematically selecting reference gene candidates for normalizing the levels of circulating RNA transcripts in maternal blood.

genomics↗

bioRxiv2017

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

Human genomes contain structural variations (SVs) that are associated with various phenotypic variations and diseases. SV detection by sequencing is incomplete due to limited read length. Nanochannel-based optical mapping (OM) allows direct observation of SVs up to hundreds of kilo-bases in size on individual DNA molecules, making it a promising alternative technology for identifying large SVs. SV detection from optical maps is non-trivial due to complex types of error present in OM data, and no existing methods can simultaneously handle all these complex errors and the wide spectrum of SV types. Here we present a novel method, OMSV, for accurate and comprehensive identification of SVs from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with and without creating/destroying restriction sites. In an extensive series of tests based on real and simulated data, OMSV achieved both high sensitivity and specificity, with clear performance gains over the latest existing method. Applying OMSV to a human cell line, we identified hundreds of SVs >2kbp, with 65% of them missed by sequencing-based callers. Independent experimental validations confirmed the high accuracy of these SVs. We also demonstrate how OMSV can incorporate sequencing data to determine precise SV break points and novel sequences in the SVs not contained in the reference. We provide OMSV as open-source software to facilitate systematic studies of large SVs.

bioinformatics↗