Biology subjects

Li, W.-H.

Publications and source records attributed to Li, W.-H..

8 recordsLinked to original sources

bioRxiv2026

Assembling and annotating the Tainung 67 rice genome to trace its japonica and indica ancestries

Here we reported the 409.0 Mb assembly of the Tainung 67 (TNG67) genome, an early hybrid of japonica and indica cultivars. We used different platforms to sequence the TNG67 genome with a total coverage of 209.8x, from a combination of Illumina paired-end reads, Illumina mate-pair reads, and Oxford Nanopore Technology long reads. The assembly has an N50 of 32.3 Mb with the longest scaffold = 45.2 Mb. We have annotated 38,938 genes where 28,376 (72.9%) finished with the Blast2GO annotation stage. There were 4,821 genes, (98.4%) of the total gene count that have complete BUSCOs. 48.33% (197.5Mb) of the TNG67 genome is composed of repeats. We predicted a total of 527 blast-resistant genes in TNG67. We also analyzed a total of 20 grain size genes and 38 photoperiod-related genes of TNG67, Nipponbare and TN1, and grouped them in terms of whether the TNG67 genes are more similar to Nipponbare, more similar to TN1, hybrid, same, or unique. We also determined whether the sequences of the TNG67 genome were derived from its japonica or indica ancestors. This TNG67 genome may help rice researchers improve yield, develop resistance against biotic and abiotic stress, and understand the evolution of a hybrid cultivar of japonica and indica.

genomics↗

bioRxiv2025

Eco-genomic analysis uncovers precision-conservation targets for the western Pacific's southernmost salmonid

Understanding how isolated small populations persist and adapt in adverse environments is instrumental to evolutionary and conservation biology. We combine a chromosome-level genome assembly, population resequencing and forward-time simulations to reconstruct the history and viability of the Formosan landlocked salmon (Oncorhynchus formosanus), now restricted to a handful of high-mountain headwaters in Taiwan. We estimate that this lineage has diverged from Japanese masu salmon over one million years ago and has no detectable gene flow for [~]50,000 years. It has accumulated extensive chromosome fusions and expansions of cold-adaptation gene families, qualifying it as a new species rather than a subspecies of Japanese masu salmon. Whole-stream sampling reveals an overlooked Hehuan-Creek population that retains high heterozygosity and has gained unique alleles. Life-table simulations show that the Hehuan population has a notably lower extinction risk and can persist or even grow under low-to-moderate typhoon frequency, whereas Qijiawan-Creek population would decline precipitously under the same or higher frequency . These findings contradict the notion that peripheral populations are likely genetically depleted and support stream-specific "precision conservation" in place of broad, untargeted translocations that could erode local adaptation potential. Thus, our genomic-ecological analysis has uncovered hidden strong resilience in a critically endangered, climate-threatened salmonid lineage.

genomics↗

bioRxiv2025

Rediscovery of the Enigmatic Paroxygraphis in Xizang, China: Phylogenetic Evidence for its Reclassification Within Oxygraphis (Ranunculaceae)

The enigmatic monotypic genus Paroxygraphis (Ranunculaceae, trib. Ranunculeae), represented solely by P. sikkimensis, has long posed taxonomic uncertainties due to its rarity. Through field rediscovery in southern Xizang province, China, and comprehensive molecular phylogenetic analyses combining nrITS and four plastid regions, we resolve its phylogenetic position within the Oxygraphis clade, with an estimated divergence time of about 3.73 Ma (95% HPD: 1.98-5.77 Ma) from its sister clade. Morphological and ecological characteristics, including small herb with a rosette of basal simple leaves, longitudinally ribbed achenes, and its alpine adaptations, further support this relationship. Furthermore, the results showed that persistent sepals and unisexual flowers in trib. Ranunculeae reflects multiple independent evolutionary origins. We propose the new combination Oxygraphis sikkimensis and highlight its critically endangered status due to habitat vulnerability. Lectotypification of P. sikkimensis is also made. This study provides new data for the floristic research of China and resolves the long-standing taxonomic controversy of this problematic genus within trib. Ranunculeae.

evolutionary biology↗

bioRxiv2022

Enhanced expression of 4-Cl-IAA and 6-Cl-IAA by touch stimulus for rapid and differential growths of the Madeira vine

Madeira vine (MV) grows 30 times faster after encountering a support. In vivo x-ray diffraction made on live MV stems revel the appearance of crystallized IAA (C10H9NO2), 4-Cl-IAA (C10H8ClNO2) and 6-Cl-IAA (C10H8ClNO2) in the stems. Small angle neutron scattering spectra of the IAA extracted from MVs stem reveal a progressive increase in the size of crystallized IAA transported downward from the apex of the shoots. High resolution X-ray diffractions made on the extracted IAA reveal significantly larger amounts of 4-Cl-IAA and 6-Cl-IAA in the climbing MVs than in the swaying around MVs. The gas chromatography-mass spectrometry spectra reveal the production of 9% more IAA and 90% more 4-Cl-IAA+6-Cl-IAA at the apexes of climbing MVs than swaying MVs. More 4-Cl-IAA+6-Cl-IAA were transported to the contact-free side than to the contact side of the vine. In vivo neutron tomography of naturally climbing MVs reveals a substantially higher H+ concentration in the contact-free parts than in the contact parts. The absorption spectra also reveal more expansin in the contact-free parts than in the contact parts. These results provide a view, at the molecular level, of what triggers the faster and differential growths in MVs in response to touching a support.

plant biology↗

bioRxiv2021

Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution

BackgroundTaichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits. ResultsAligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response. ConclusionsWe have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1s blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.

genomics↗

bioRxiv2020

GAMYB modulates bHLH142 and is homeostatically regulated by TDR during rice anther tapetal and pollen development

GAMYB, UDT1, TIP2/bHLH142, TDR, and EAT1/DTD are important transcription factors (TFs) that play a crucial role during rice pollen development. This study demonstrates that bHLH142 acts downstream of UDT1 and GAMYB and works as a "hub" in these two pollen pathways. We show that GAMYB modulates bHLH142 expression through specific binding to the MYB motif of bHLH142 promoter during early stage of pollen development; while TDR acts as a transcriptional repressor of the GAMYB modulation of bHLH142 by binding to the E-box close to the MYB motif on the promoter. The up- and down-regulation of TFs highlights the importance that a tight, precise, and coordinated regulation among these TFs is essential for normal pollen development. Most notably, this study illustrates the regulatory pathways of GAMYB and UDT1 that rely on bHLH142 in a direct and an indirect manner, respectively, and function in different tissues with distinct biological functions during pollen development. This study advances our understanding of the molecular mechanisms of rice pollen development. HighlightGAMYB can directly modulate the transactivation of the bHLH142, but the modulation is repressed by TDR to keep the homeostasis of bHLH142 gene expression to ensure normal pollen development.

molecular biology↗

bioRxiv2019

Trevolver: simulating non-reversible DNA sequence evolution in trinucleotide context on a bifurcating tree

SummaryRecent de novo mutation data allow the estimation of non-reversible mutation rates for trinucleotide sequence contexts. However, existing tools for simulating DNA sequence evolution are limited to time-reversible models or do not consider trinucleotide context-dependent rates. As this ability is critical to testing evolutionary scenarios under neutrality, we created Trevolver. Sequence evolution is simulated on a bifurcating tree using a 64 x 4 trinucleotide mutation model. Runtime is fast and results match theoretical expectation for CpG sites. Simulations with Trevolver will enable neutral hypotheses to be tested at within-species (polymorphism), between-species (divergence), within-host (e.g., viral evolution), and somatic (e.g., cancer) levels of evolutionary change.\n\nAvailability and ImplementationTrevolver is implemented in Perl and available on GitHub under GNU General Public License (GPL) version 3 at https://github.com/chasewnelson/trevolver.\n\nContactcnelson@amnh.org\n\nSupplementary informationFurther details and example data are available on GitHub.

evolutionary biology↗

bioRxiv2019

Recent origin of an XX/XY sex-determination system in the ancient plant lineage Ginkgo biloba

Sexual dimorphism like dioecy (separate male and female individuals) have evolved in diverse multicellular eukaryotes while the molecular mechanisms underlying the development of such a key biological trait remains elusive (1). The living fossil Ginkgo biloba represents an early diverged lineage of land plants with dioecy. However, its sex-determination system and molecular basis have long been controversial or unknown. In the present research, we assembled the first and largest to date chromosome-level genome of a non-model tree species using Hi-C data. With this reference genome, we addressed both questions using genome resequencing data gathered from 97 male and 265 female trees of ginkgo, as well as transcriptome data from three developmental stages for both sexes. Our results support vertebrate-like XY chromosomes for ginkgo and five potential sex-determination genes, which may originate ~14 million years ago. This is the earliest diverged sex determination region in all reported plants as yet. The present research resolved a long-term controversy, lay a foundation for future studies on the origin and evolution of plant sexes, and provide genetic markers for sex identification of ginkgo which will be valuable for both nurseries and field ecology of ginkgo.

evolutionary biology↗