Zhixia Xiao

Zhixia Xiao

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Zhixia Xiao

School of Life Sciences, Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong , Shatin, Hong Kong

Research Focus & Metrics

Academic Career Length

5Years (2022-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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5 September 2022 in Plant Physiology
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Journal Article
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ZXZhixia Xiao
Zhixia Xiao
QWQianwen Wang
Qianwen Wang
MLMan-Wah Li
Man-Wah Li
MHMingkun Huang
Mingkun Huang
ZWZhili Wang
Zhili Wang
Hon-Ming LamHon-Ming Lam
Hon-Ming Lam
Dear Editor, The rapid development of sequencing technology in the last decade has ushered soybean (Glycine max and Glycine soja) research into the genomic age. Mining information out of these datasets is challenging for biologists without intensive bioinformatic training, but web applications with intuitive data retrieval and visualization functions can empower general users to access both the genome sequences and genomics resources. Although there are some online platforms for soybean ( Machado et al., 2020; Yu et al., 2022), they are primarily focused on RNA-Seq data and lack the association to gene regulation information, like chromatin accessibility. While the leading platform Soybase (https://soybase.org/) has deposited multiomic data, most of their data are based on prior versions of the soybean reference genome (Wm82 a1v1.1, Wm82 a2v1) ( Brown et al., 2021). Furthermore, none of the aforementioned platforms allow biologists to easily retrieve intergenic sequences (e.g. promoters) or design primers. With the increasing amount of sequencing data generated from various cultivars, there is a growing demand for a curated web portal hosting multiple reference genomes with associated multiomic data. To address this gap, we created an integrated online platform Wildsoydb DataHub (https://datahub.wildsoydb.org/) hosting four high-quality genome assemblies, including two G. max cultivars: Williams 82 (Wm82 a2v1 and Wm82 a4v1) ( Schmutz et al., 2010; Valliyodan et al., 2019) and Zhonghuang 13 (v2) ( Liu et al., 2020) and a G. soja cultivar: W05 (v1) ( Xie et al., 2019). We aim to provide an easy-to-use web interface for biologists to fully benefit from the genomic resources. Aside from comprehensive functional annotations of all the genes, the sequencing data from 21 soybean genomics studies and 11 public SRA BioProjects of various data types were integrated. Furthermore, a variety of functional modules were developed to provide an intuitive user-centric interface. Modules currently available on this platform include Gene Search, BLAST, Jbrowse, Synteny, SeqExtractor, and Primer3. All functions are aggregated to the Gene Search result and can also be invoked from their respective pages, allowing users to (1) retrieve functional annotations, genome sequences, and gene expressions; (2) cross-compare sequences of interest with BLAST and synteny analysis; (3) visualize expression and methylation levels as well as other genomics information from a well-organized browser; (4) design primers for selected genes; and (5) retrieve sequence from unannotated regions.