Biology subjects

Liu, Y.-C.

Publications and source records attributed to Liu, Y.-C..

32 records · Page 2Linked to original sources

bioRxiv2022

The Aphelenchoides genomes reveal major events of horizontal gene transfers in clade IV nematodes

Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the Aphelenchoididae family capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are amongst the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of horizontal gene transfer in nematodes.

genomics↗

bioRxiv2022

EZH2/ hSULF1 axis mediates receptor tyrosine kinase signaling to shape cartilage tumor progression

BackgroundChondrosarcomas are primary cancers of cartilaginous tissue and capable of alteration to highly aggressive, metastatic, and treatment-refractory states, leading to a poor prognosis with a five-year survival rate at 11 months for the dedifferentiated subtype. At present, the surgical resection of chondrosarcoma is the only effective treatment, and no other treatment options including targeted therapies, conventional chemotherapies, or immunotherapies are available for these patients. MethodsA non-biased ChIP sequence, cDNA microarray analysis, and validation of chondrosarcoma cell lines identified sulfatase 1(SULF1) as the top EZH2-targeted gene to regulate chondrosarcoma progression. Receptor tyrosine kinase (RTK) array of chondrosarcoma cells with vector control or ectopically expressed SULF1 revealed that cMET was the downstream signal. The regulation of the EZH2/SULF1/cMET axis was further validated in mice and patient samples with mice models and chondrosarcoma tissue array, respectively. ResultsThe EZH2/SULF1/cMET axis is identified, which contributes to the malignancy of chondrosarcoma and provides a potential therapeutic option for the disease. Ectopically expressed SULF1 or pharmaceutical inhibition of the cMET pathway significantly retards the chondrosarcoma growth and extends mice survival. ConclusionsThe results not only established a signal pathway promoting the malignancy of chondrosarcoma but also provided a therapeutic potential for further development of effective target therapy to treat chondrosarcoma.

cancer biology↗

bioRxiv2022

Statistical significance and biological relevance: The case of Nosema ceranae and winter colony losses.

Managed and wild insect pollinators play a key role in ensuring that mankind is adequately supplied with food. Among the pollinating insects, the managed Western honey bee providing about 90% of commercial pollination is of special importance. Hence, diseases as well as disease causing pathogens and parasites that threaten honey bees, have become the focus of many research studies. The ectoparasitic mite Varroa destructor together with deformed wing virus (DWV) vectored by the mite have been identified as the main contributors to colony losses, while the role of the microsporidium Nosema ceranae in colony losses is still controversially discussed. In an attempt to solve this controversy, we statistically analyzed a unique data set on honey bee colony health comprising data on mite infestation levels, Nosema spp. infections and winter losses continuously collected over 15 years. We used various statistical methods to investigate the relationship between colony mortality and the two pathogens, V. destructor and N. ceranae. Our multivariate statistical analysis confirmed that V. destructor is the major cause of colony winter losses. When using cumulative data sets, we also found a significant relationship between N. ceranae infections and colony losses. However, determining the effect size revealed that this statistical significance was of low biological relevance, because the deleterious effects of N. ceranae infection are normally masked by the more severe effects of V. destructor on colony health and therefore only detectable in the few colonies that are not infested with mites or are infested at low levels.

microbiology↗

bioRxiv2021

Genomes of keystone Mortierella species lead to better in silico prediction of soil mycobiome functions from Taiwan's offshore islands

The ability to correlate the functional relationship between microbial communities and their environment is critical to understanding microbial ecology. There is emerging knowledge on island biogeography of microbes but how island characteristics influence functions of microbial community remain elusive. Here, we explored soil mycobiomes from nine islands adjacent to Taiwan using ITS2 amplicon sequencing. Geographical distances and island size were positively correlated to dissimilarity in mycobiomes, and we identified 56 zero-radius operational taxonomic units (zOTUs) that were ubiquitously present across all islands, and as few as five Mortierella zOTUs dominate more than half of mycobiomes. Correlation network analyses revealed that seven of the 45 hub species were part of the ubiquitous zOTUs belonging to Mortierella, Trichoderma, Aspergillus, Clonostachys and Staphylotrichum. We sequenced and annotated the genomes of seven Mortierella isolates, and comparative predictions of KEGG orthologues using PICRUSt2 database updated with new genomes increased sequence reads coverage by 62.9% at the genus level. In addition, genes associated with carbohydrate and lipid metabolisms were differentially abundant between islands which remained undetected in the original database. Predicted functional pathways were similar across islands despite their geographical separation, difference in differentially abundant genes and composition. Our approach demonstrated the incorporation of the key taxa genomic data can improve functional gene prediction results and can be readily applied to investigate other niches of interests.

genomics↗

bioRxiv2021

Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories

The ecology and genetic diversity of model yeast Saccharomyces cerevisiae prior to human domestication remain poorly understood. Taiwan is regarded as part of this yeasts geographic birthplace where the most divergent natural lineage was discovered. Here, we deep sampled the broad-leaf forests across this continental island to probe the ancestral species diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages, the highest known in any region. Three lineages are endemic to Taiwan and six are widespread in Asia. Molecular dating placed the divergence of the Taiwanese and Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Extensive historical and recent admixture events were detected between natural lineages. In particular, the genetic component from a lineage associated with fruits that spanned the widest geographical range was present in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We detected prevalent purifying selection genome-wide, with lineage-specific signals of positive or directional selection independent between lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.

genomics↗

bioRxiv2020

Myosin XI drives polarized growth by vesicle clustering and local enrichment of F-actin in Physcomitrium (Physcomitrella) patens

In tip-growing plant cells, growth results from myosin XI and F-actin mediated deposition of cell wall polysaccharides contained in secretory vesicles. Previous evidence showed that myosin XI anticipates F-actin accumulation at the cells tip, suggesting a mechanism where vesicle clustering via myosin XI promotes F-actin polymerization. To evaluate this model, we used a conditional loss-of-function strategy by generating Physcomitrium (Physcomitrella) patens plants harboring a myosin XI temperature-sensitive allele. We found that loss of myosin XI function alters tip cell morphology, vacuolar homeostasis, and cell viability, but not following F-actin depolymerization. Importantly, our conditional loss-of-function analysis shows that myosin XI clusters and directs vesicles at the tip of the cell, which induces F-actin polymerization, increasing F-actins local concentration. Our findings support the role of myosin XI in vesicle clustering and F-actin organization, necessary for tip growth, and deepen our understanding of additional myosin XI functions.

cell biology↗

bioRxiv2020

Mycena genomes resolve the evolution of fungal bioluminescence

Mushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life, yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. We sequenced the genomes and transcriptomes of five bonnet mushroom species (Mycena spp.), a diverse lineage comprising the majority of bioluminescent fungi. Two species with haploid genome assemblies [~]150Mb are amongst the largest in Agaricales, and we found that a variety of repeats between Mycena species were differentially mediated by DNA methylation. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was maintained through at least 160 million years of evolution. Analyses of synteny across genomes of bioluminescent species resolved how the luciferase cluster was derived by duplication and translocation, frequently rearranged and lost in most Mycena species, but conserved in the Armillaria lineage. Luciferase cluster members were co-expressed across developmental stages, with highest expression in fruiting body caps and stipes, suggesting fruiting-related adaptive functions. Our results contribute to understanding a de novo origin of bioluminescence and the corresponding gene cluster in a diverse group of enigmatic fungal species. SignificanceWe present the genomes of five new bonnet mushroom Mycena species, formerly the last fungal bioluminescent lineage lacking reference genomes. These genome-scale datasets allowed us to construct an evolutionary model pinpointing all possible changes in the luciferase cluster across all fungi and additional genes involved in bioluminescence. We show that luciferase clusters were differentially lost in different fungal lineages and in particular a substantial loss was observed in the Mycena lineage. This can be attributed to genome regions of Mycena underwent different evolutionary dynamics. Our findings offer insights into the evolution of how a gene cluster that emerged 160 million years ago and was frequently lost or maintained due to differences in genome plasticity.

genomics↗

bioRxiv2020

Sequence variation among SARS-CoV-2 isolates in Taiwan

Taiwan experienced two waves of imported cases of coronavirus disease 2019 (COVID-19), first from China in January to late February, followed by those from other countries starting in early March. Additionally, several cases could not be traced to any imported cases and were suspected as sporadic local transmission. Twelve full viral genomes were determined in this study by Illumina sequencing either from virus isolates or directly from specimens, among which 5 originated from clustered infections. Phylogenetic tree analysis revealed that these sequences were in different clades, indicating that no major strain has been circulating in Taiwan. A deletion in open reading frame 8 was found in one isolate. Only a 4-nucleotide difference was observed among the 5 genomes from clustered infections.

genetics↗

bioRxiv2020

Regenerated Interneurons Integrate Into Locomotor Circuitry Following Spinal Cord Injury

Whereas humans and other adult mammals lack the ability to regain locomotor function after spinal cord injury, zebrafish are able to recover swimming behavior even after complete spinal cord transection. We have previously shown that zebrafish larvae regenerate lost neurons within 9 days post-injury (dpi), but the functional contribution of these neurons to motor recovery is unknown. Here we show that multiple interneuron subtypes known to play a role in locomotor circuitry are regenerated in injured spinal cord segments during the period of functional recovery. Further, we show that one subtype of newly-generated interneurons receives excitatory input and fires synchronously with motor output by 9 dpi. Taken together, our data show that regenerative neurogenesis in the zebrafish spinal cord produces interneurons with the physiological capacity to participate in the recovery of locomotor function.

neuroscience↗

bioRxiv2020

The Genomic Formation of Human Populations in East Asia

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE - 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to [~]3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.

genomics↗

bioRxiv2020

Electrical coupling between chromatophore muscle fibers allows for versatile control of chromatophore expansion in squid.

Camouflage color change in cephalopods is generated by the expansion and relaxation of hundreds to thousands of chromatophore pigment organs in the skin. Individual chromatophores display color when the central pigment sac is expanded to several times its original size by a ring of 20-30 radial muscles, which are electrically coupled and are innervated by multiple motoneurons. However, mechanisms for their neuromuscular control are unclear. Here we characterize chromatophore expansion kinematics and perform simultaneous whole-cell recordings on pairs of muscle fibers of a chromatophore in squid hatchlings. We show that activity is highly correlated between muscle fibers of a chromatophore due to a high ratio of electrical coupling between all muscles for slow currents. However, fast currents are filtered and decrease rapidly further away from the muscle receiving the inputs. This low-pass filtering property of electrical coupling allows fast inputs to activate one muscle while persistent inputs spread throughout the chromatophore to synchronously activate all muscles, providing a versatile mode of control for chromatophore expansion.

systems biology↗

bioRxiv2019

Inland-coastal bifurcation of southern East Asians revealed by Hmong-Mien genomic history

The early history of the Hmong-Mien language family and its speakers is elusive. A good variety of Hmong-Mien-speaking groups distribute in Central China. Here, we report 903 high-resolution Y-chromosomal, 624 full-sequencing mitochondrial, and 415 autosomal samples from 20 populations in Central China, mainly Hunan Province. We identify an autosomal component which is commonly seen in all the Hmong-Mien-speaking populations, with nearly unmixed composition in Pahng. In contrast, Hmong and Mien respectively demonstrate additional genomic affinity to Tibeto-Burman and Kra-Dai speakers. We also discover two prevalent uniparental lineages of Hmong-Mien speakers. Y-chromosomal haplogroup O2a2a1b1a1b-N5 diverged [~]2,330 years before present (BP), approximately coinciding with the estimated time of Proto-Hmong-Mien ([~]2,500 BP), whereas mitochondrial haplogroup B5a1c1a significantly correlates with Pahng and Mien. All the evidence indicates a founding population substantially contributing to present-day Hmong-Mien speakers. Consistent with the two distinct routes of agricultural expansion from southern China, this Hmong-Mien founding ancestry is phylogenetically closer to the founding ancestry of Neolithic Mainland Southeast Asians and present-day isolated Austroasiatic-speaking populations than Austronesians. The spatial and temporal distribution of the southern East Asian lineage is also compatible with the scenario of out-of-southern-China farming dispersal. Thus, our finding reveals an inland-coastal genetic discrepancy related to the farming pioneers in southern China and supports an inland southern China origin of an ancestral meta-population contributing to both Hmong-Mien and Austroasiatic speakers.

genetics↗

bioRxiv2019

Mechanistic and compositional studies of the autophagy-inducing areca nut ingredient

Areca nut (AN) is a popular chewing carcinogen worldwide causing a variety of diseases such as oral and esophageal carcinomas. We previously found that the partially purified 30-100 kDa fraction of AN extract (ANE 30-100K) induces autophagy in oral carcinoma OECM-1 cells and some other different types of cells. Since autophagy is known to play important roles in tumor establishment and development, the underlying mechanisms of ANE 30-100K-induced autophagy (AIA) is worthy of further investigation. In this study, we further demonstrated that the cytotoxic concentration of ANE 30-100K induces some typical autophagy hallmarks in esophageal carcinoma (CE81T/VGH) cells in an Atg5-dependent manner. Furthermore, the endocytosis inhibitor (methyl-{beta}-cyclodextrin) and two caveolin shRNAs, as well as two proteasome inhibitors (lactacystin and epoxomicin), were shown to attenuate ANE 30-100K-induced cytotoxicity and LC3-II accumulation significantly in OECM-1 and CE81T/VGH cells. Finally, we also analyzed the carbohydrate compositions of ANE 30-100K by phenol-sulfuric acid method and high performance anion exchange chromatography with pulse amperic detector. The results showed that ANE 30-100K contains about 67% carbohydrate and is composed of fucose (5.938%), arabinose (24.631%), glucosamine (8.066%), galactose (26.820%), glucose (21.388%), and mannose (13.157%). Collectively, these results suggest that caveolin-mediated endocytosis and proteasome are required for AIA and the major components of ANE 30-100K are carbohydrates. This study may have provided new knowledges of the action mechanisms and compositions of ANE 30-100K.

cancer biology↗

bioRxiv2018

Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution

We present reference-quality genome assembly and annotation for the stout camphor tree (SCT; Cinnamomum kanehirae [Laurales, Lauraceae]), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales, and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry relative to monocots. Two whole genome duplication events were inferred within the magnoliid lineage, one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history of Cinnamomum. For example, expansion of terpenoid synthase subfamilies within the Laurales spawned the diversity of Cinnamomum monoterpenes and sesquiterpenes.

genomics↗