Biology subjects

Yao, E.

Publications and source records attributed to Yao, E..

8 recordsLinked to original sources

bioRxiv2025

Genome assembly and population genomic analysis of Aegilops caudata uncover a rich source for disease and insect pest resistance for wheat improvement

Aegilops caudata L. is a rich source of resistance genes to major wheat pathogens and pests, yet its complex genome structure and lack of a reference sequence have hindered genetic analysis, gene discovery, and introgression. Here, we report a high-quality genome sequence assembly of Ae. caudata accession S740-69, integrated with optical mapping to precisely delineate introgressed segments from structurally altered genomic regions in wheat-Ae. caudata translocation lines carrying a novel stem rust resistance gene. Resequencing and phenotyping of 95 diverse accessions, coupled with k-mer-based association mapping, enabled population-level identification of several novel loci for resistance to wheat pests and diseases, such as greenbug and stem rust. Virus-induced gene silencing confirmed Aecau6C01G127270 (SrAect1) as the first functionally characterized stem rust resistance gene from Ae. caudata. This new genomic framework provides a foundation for systematic mining of resistance genes in this species and their efficient introgression into wheat.

genomics↗

bioRxiv2025

Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs

Lung size control and cell type specification are key unresolved issues. In this study, we have engineered mosaic patterns of Hippo signaling to reveal the developmental potential of SOX9+ progenitors at the distal lung buds. Our results show that the distal SOX9+ subdomain is sufficient to direct lung outgrowth through bifurcation, providing a mechanism for lung size control. Through single-cell analyses, we identify transitional cell states and candidates for promoting cell fates. Moreover, genetic analysis reveals that Hippo signaling induces distinct cell fates at different SOX9+ subdomains to produce the conducting airways and the alveolar epithelium. These results provide the first extensive map of the developmental paths of lung cells. Some of the developmental paths of transitional cell states in mice correspond to those in human lungs. Together, these studies provide mechanistic insight into how Hippo signaling controls the sequential expansion and differentiation of SOX9+ progenitors to construct the mammalian lungs.

developmental biology↗

bioRxiv2024

Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb, and 166,325 predicted gene models. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. The G genome was also more closely related to the S genome of Aegilops speltoides than to the B genome of hexaploid or tetraploid wheat. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.

plant biology↗

bioRxiv2023

Effect of growing regions on morphological characteristics, protein nutrition, rumen degradation and molecular structures of various whole-plant silage corn cultivars

Little information exists on the variation of morphological characteristics, nutritional value, ruminal degradability, and molecular structural makeup of diverse whole-plant silage corn (WPSC) cultivars among different growing regions. This study investigated the between-regions discrepancies in five widely used WPSC cultivars in China (FKBN, YQ889, YQ23, DK301 and ZD958) in terms of 1) morphological characteristics; 2) crude protein (CP) chemical profile; 3) Cornell Net Carbohydrate and Protein System (CNCPS) CP subfractions; 4) in situ CP degradation kinetics; and 5) CP molecular structures. Our results revealed that significant difference were observed on growing region and WPSC cultivar interaction for all estimated morphological characteristics (P < 0.001), CP chemical profile (P < 0.001), CNCPS subfractions (P < 0.001) and CP molecular structural features (P < 0.05). Except ear weight (P = 0.18), all measured morphological characteristics varied among different growing regions (P < 0.001). Besides, WPSC cultivars planted in different areas had remarkably different (P < 0.01) CP chemical profiles and CNCPS subfractions. All spectral parameters of protein primary structure of WPSC differed (P < 0.05) due to the various growing regions, except amide II area (P = 0.28). Finally, the area ratio of amide I to II was negatively correlated with the contents of soluble CP ({delta} = -0.66; P = 0.002), CP ({delta} = - 0.61; P = 0.006), non-protein N ({delta} = -0.56; P = 0.004) and acid detergent insoluble CP ({delta} = - 0.43; P = 0.008), in conjunction with positively correlated with moderately degradable CP (PB1;{delta} = 0.58; P = 0.01). In conclusion, the current study suggested that even for the same WPSC cultivar, the morphological characteristics, protein nutritional values and rumen degradability significantly varied among different grown regions due to distinguished molecular structures. Author summaryAs the major roughage source, whole plant silage corn plays an essential role in ruminant feed industry. The quality and quantity of it largely influenced by environmental and climate conditions except genetic factors. However, there was limited information to systematically analyze whole plant silage corn from morphological characteristics, nutritional components, rumen degradation to its inherent molecular structures. Thus, this study was conducted to investigate the discrepancies of various silage-corn cultivars grown in different regions from internal structure to phenotype based novel technology - fourier transform infrared spectroscopy.

biochemistry↗

bioRxiv2021

Acquisition of cellular properties during alveolar formation requires differential activity and distribution of mitochondria

Alveolar formation requires coordinated movement and interaction between alveolar epithelial cells, mesenchymal myofibroblasts and endothelial cells/pericytes to produce secondary septa. These processes rely on the acquisition of distinct cellular properties to enable ligand secretion for cell-cell signaling and initiate morphogenesis through cell migration and cell shape change. In this study, we showed that mitochondrial activity and distribution play a key role in bestowing cellular functions on both alveolar epithelial cells and mesenchymal myofibroblasts for generating secondary septa to form alveoli. These results suggest that mitochondrial function is tightly regulated to empower cellular machineries in a spatially specific manner. Indeed, such regulation via mitochondria is required for secretion of platelet-derived growth factor from alveolar epithelial cells to influence myofibroblast proliferation and migration. Moreover, mitochondrial function enables myofibroblast migration during alveolar formation. Together, these findings yield novel mechanistic insights into how mitochondria regulate pivotal steps of alveologenesis. They highlight selective utilization of energy and diverse energy demands in different cellular processes during development. Our work serves as a paradigm for studying how mitochondria control tissue patterning.

developmental biology↗

bioRxiv2019

Pulmonary acini exhibit complex changes during postnatal rat lung development

Pulmonary acini represent the functional gas-exchanging units of the lung. Due to technical limitations, individual acini cannot be identified on microscopic lung sections. To overcome these limitations, we imaged the right lower lobes of instillation-fixed rat lungs from postnatal days P4, P10, P21, and P60 at the TOMCAT beamline of the Swiss Light Source synchrotron facility at a voxel size of 1.48 m. Individual acini were segmented from the three-dimensional data by closing the airways at the transition from conducting to gas exchanging airways. For a subset of acini (N=268), we followed the acinar development by stereologically assessing their volume and their number of alveoli. We found that the mean volume of the acini increases 23 times during the observed time-frame. The coeffcients of variation dropped from 1.26 to 0.49 and the difference between the mean volumes of the fraction of the 20 % smallest to the 20 % largest acini decreased from a factor of 27.26 (day 4) to a factor of 4.07 (day 60), i.e. shows a smaller dispersion at later time points. The acinar volumes show a very large variation early in lung development and homogenize during maturation of the lung by reducing their size distribution by a factor of 7 until adulthood. The homogenization of the acinar sizes hints at an optimization of the gas-exchange region in the lungs of adult animals and that acini of different size are not evenly distributed in the lungs. This likely leads to more homogeneous ventilation at later stages in lung development.

physiology↗

bioRxiv2019

JBrowse Connect: A server API to connect JBrowse instances and users

We describe JBrowse Connect, an optional expansion to JBrowse that allows live messaging via WebSockets, notifications for new annotation tracks, heavy-duty analyses initiated by the user from within the browser, and other dynamic features. We present JBlast, an example application of JBrowse Connect that allows users to specify and execute BLAST searches, managed by a Galaxy instance, as well as tracking job progress and viewing results, all in the context of the browser.

bioinformatics↗

bioRxiv2019

Apollo: Democratizing genome annotation

Genome annotation is the process of identifying the location and function of a genomes encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, Apollo is an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform.\n\nIn this paper we first outline some of Apollos newer user interface features, which were driven by the needs of this expanding genomics community. These include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible. O_LISource: https://github.com/GMOD/Apollo\nC_LIO_LILicense (BSD-3): https://github.com/GMOD/Apollo/blob/master/LICENSE.md\nC_LIO_LIDocker: https://hub.docker.com/r/gmod/apollo/tags/, https://github.com/GMOD/docker-apollo\nC_LIO_LIRequirements: JDK 1.8, Node v6.0+\nC_LIO_LIUser guide: http://genomearchitect.org; technical guide: http://genomearchitect.readthedocs.io/en/latest/\nC_LIO_LIMailing list: apollo@lists.lbl.gov\nC_LI

bioinformatics↗