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Songtao Gui, Ph.D.

  • Researcher in population genetics, pan-genomics and graph genome;

  • Trying to solve the \( V_{Geno} \sim V_{Pheno} \) problem using multi-omics evidences;

  • Developing tools and databases related to omics-analyses;

Contacts

songtaogui@sina.com Blog GitHub Twitter ORCID GoogleScholar

Skills

  • Programming Languages: Bash; Perl; R; Julia; Python(Read&Edit); Rust(Trying);

  • Systems: Linux(Debian, Ubuntu, Red Hat); Windows; HPC cluster(CentOS7-based)

  • Bioinformatics:

    • State-of-art NGS/omics-seq analyses: DNA/RNA-seq(Illumina, PB-SMRT/RSII, ONT), ChIP/HiC/WGS/ATAC etc.

    • Downstream analyses: Population Genetics, Phylogenetics, Genomics, Epigenetics etc.

    • Visualisation: R/ggplot-x, Julia/Makie, AdobeIllustrator, Photoshop etc.

    • DIY pipelines when necessary: Pan-genomic, SV calling, GWAS and post-GWAS etc.

    • Web development: more a designer than a developer, dealing with data more than code

  • Biological:

    • Evolutionary > Functional: tends to understand questions through large data supports

    • Theoretical > Practical: embracing cooperations for making bioinfo-data practical

Research/Work Experience

 
 
 
 
 

Professor(tenure track)

SDAU

Jan 2023 – Now Tai'an
Responsibilities include:

  • Pan-genomics and multi-omics integration based Crop improvements

  • Wheat genomics and population genetics

  • Crop domestication and adaptation

 
 
 
 
 

PostDoc

Huazhong Agricultural University; Supervisor: Prof. Jianbing Yan

Jan 2018 – Dec 2022 Wuhan
Responsibilities include:

  • Study the pan-genomics of Zea

  • Study the genomics and genetic variations in Zea

  • Construct and maintain the Zea multi-omics database Zeamap

 
 
 
 
 

Developer(concurrent post)

BGI Genomics

Dec 2018 – Dec 2019 Shenzhen
Cooperate with/Lead a group of 5 members to develop the Zeamap database.
 
 
 
 
 

PhD candidate

Wuhan University; Mentor: Prof. Yi Ding

Sep 2012 – Dec 2017 Wuhan
Responsibilities include:

  • Construct the genetic linkage map of Nelumbo nucifera

  • Study the genome of Nelumbo nucifera and comparative genomics among eudicots

  • Study the organelle genomes of Nelumbo nucifera

  • Study the CenH3 and centromere of Nelumbo nucifera

  • Identify DNA fingerprints for Rice germplasms

Interests & Education

Interests

  • Population genetics
  • Graph genomics
  • Cool codes in julia
  • Ping-Pong
  • Cat

Education

  • PostDoc in Crop Breeding, 2018-2022

    Huazhong Agricultural University

  • PhD in Genetics, 2012-2017

    Wuhan University

  • BSc in Biological Science, 2008-2012

    Shandong Normal University

Foundings/Achievements

  • 2025-2028, National Natural Science Foundation of China, 32470659; Host

  • 2021-2023, National Natural Science Foundation of China, 32000396; Host

  • 2022, Hubei Postdoctoral Innovation and Entrepreneurship Competition, Winner's Price

  • 2020, 1st National Crop Science Postdoctoral Academic Forum, Outstanding Award;

  • 2019-2021, College of Plant Science, HZAU, Outstanding Postdoctoral funding;

  • 2017, 7th Hubei Congress of Plant Biology, 1st reporter award;

  • 2016, 2016 National Congress of Plant Biology, 3rd poster award;

  • 2016, National Scholarship for PhD. students;

Bibliography

#: Co-first authors; *: Correspondence

Historic wheat for modern breeding: the breeding application and prospect of wheat germplasm resources

Wang Yonghong*, GUI SONGTAO, Li Jiayang*
SCIENTIA SINICA Vitae, 1310-1314, 54, 2024     article Wheat Landrace

LAZY4 acts additively with the starch–statolith-dependent gravity-sensing pathway to regulate shoot gravitropism and tiller angle in rice

Wang Wenguang#, Huang Linzhou#, Song Yuqi#, GUI SONGTAO, Cao Jiajia, Zhang Han, Du Mengchen, Chen Jiaze, Wang Zihao, Zhou Jie, Meng Xiangbing, Zeng Dali, Li Jiayang, Wang Yonghong*
Plant Communications, doi: 10.1016/j.xplc.2024.100943, 2024     article Rice LAZY4 gravity-sensing

Uncover the mystery of pleiotropic effects of PROG1 during rice domestication

Wang Wenguang, GUI SONGTAO, Wang Yonghong*
Molecular Plant, 1722--1723, 16, 2023     article PROG1 rice

ZmWAK02 encoding an RD-WAK protein confers maize resistance against gray leaf spot

Dai Zhikang, Pi Qianyu, Liu Yutong, Hu Long, Li Bingchen, Zhang Bao, Wang Yanbo, Jiang Min, Qi Xin, Li Wenqiang, GUI SONGTAO, Llaca Victor, Fengler Kevin, Thatcher Shawn, Li Ziwei, Liu Xiangguo, Fan Xingming, Lai Zhibing*
New Phytologist, 1780--1793, 241, 2024     article ZmWAK02 gray leaf spot maize

LAZing around: The intricate dance of amyloplast sedimentation and gravity sensing in plants

Zhang Ning, GUI SONGTAO, Wang Yonghong*
Molecular Plant, 1887--1889, 16, 2023     article gravity LAZY amyloplast sedimentation

Two teosintes made modern maize

Yang# Ning, Wang# Yuebin, Liu# Xiangguo, Jin Minliang, Vallebueno-Estrada Miguel, Calfee Erin, Chen Lu, Dilkes P. Brian, GUI SONGTAO, Fan Xingming, Harper K. Thomas, Kennett J. Douglas, Li Wenqiang, Lu Yanli, Ding Junqiang, Chen Ziqi, Luo Jingyun, Mambakkam Sowmya, Menon Mitra, Snodgrass Samantha, Veller Carl, Wu Shenshen, Wu Siying, Zhuo Lin, Xiao Yingjie, Yang Xiaohong, Stitzer C. Michelle, Runcie Daniel, Yan* Jianbing, Ross-Ibarra* Jeffrey
Science, eadg8940, 382, 2023     article teosintes maize domestication

Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication

GUI SONGTAO, Martinez-Rivas Juan Felix, Wen Weiwei, Meng Minghui, Yan Jianbing, Usadel Björn, Fernie R.* Alisdair
The Plant Journal, 446-459, 113, 2022     article sequencing pangenome single-cell domestication physiology

A pan-Zea genome map for enhancing maize improvement

GUI SONGTAO, Wei Wenjie, Chenglin Jiang, Luo Jingyun, Wu Shenshen, Li Wenqiang, Wang Yuebin, Li Shuyan, Yang Ning, Li Qing, Fernie R. Alisdair, Yan Jianbing*
Genome Biology, 178, 23, 2022     article Zea pan-genome structural variation GAB

Genome sequencing reveals evidence of adaptive variation in the genus Zea

Chen Lu#, Luo Jingyun#, Jin Minliang#, Yang Ning#*, Liu Xiangguo, Peng Yong, Li Wenqiang, Philips Alyssa, Cameron Brenda, Bernal Julio, Rubén Rellán-Álvarez, Sawers JH Ruairidh, Qing Liu, Yin Yuejia, Ye Xinnan, Yan Jiali, Zhang Qinghua, Zhang Xiaoting, Wu Shenshen, GUI SONGTAO, Wei Wenjie, Wang Yuebin, Luo Yun, Jiang Chengling, Deng Min, Jin Min, Jian Liumei, Yu Yanhui, Zhang Maolin, Yang Xiaohong, Hufford B. Matthew, Fernie R. Alisdair, Warburton L. Marilyn, Ross-Ibarra Jeffrey*, Yan Jianbing*
Nature Genetics, 1-10, 2022     article Zea WGS adaptation selection

A Heavy Metal Transporter Gene ZmHMA3a Promises Safe Agricultural Production on Cadmium-Polluted Arable Land

Chen Yuanyuan#, Chao Zhen-Fei#, Jin Min, Wang Ya-Ling, Li Yaoyao, Wu Jia-Chen, Xiao Yingjie, Peng Yong, Lv Qiao-Yan, GUI SONGTAO, Wang Xiaqing, Han Mei-Ling, Fernie R. Alisdair, Chao Dai-Yin*, Yan Jianbing*
Journal of Genetics and Genomics, S1673852722002156, 2022     article Zea GWAS Heavy metal ZmHMA3a

Three Types of Genes Underlying the Gametophyte Factor1 Locus Cause Unilateral Cross Incompatibility in Maize

Wang Yuebin#, Li Wenqiang#, Wang Luxi, Yan Jiali, Lu Gang, Yang Ning, Xu Jieting, Wang Yuqing, GUI SONGTAO, Chen Gengshen, Li Shuyan, Wu Chengxiu, Guo Tingting, Xiao Yingjie, Warburton L. Marilyn, Fernie R. Alisdair, Dresselhaus Thomas, Yan Jianbing*
Nature Communications, 4498, 13, 2022     article Zea Unilateral Cross Incompatibility ga1

The Transcription Factor GATA10 Regulates Fertility Conversion of a Two‐line Hybrid Tms5 Mutant Rice via the Modulation of Ub_L40 Expression

Jin Jing, GUI SONGTAO, Li Qian, Wang Ying, Zhang Hongyuan, Zhu Zhixuan, Chen Hao, Sun Yueyang, Zou Yu, Huang Xingguo, Ding Yi*
Journal of Integrative Plant Biology, 1034--1056, 62, 2020     article rice TF-GATA10 atac-seq

ZEAMAP, a Comprehensive Database Adapted to the Maize Multi-Omics Era

GUI SONGTAO, Yang Linfeng, Li Jianbo, Luo Jingyun, Xu Xiaokai, Yuan Jianyu, Chen Lu, Li Wenqiang, Yang Xin, Wu Shenshen, Li Shuyan, Wang Yuebin, Zhu Yabing, Gao Qiang, Yang Ning, Yan Jianbing*
iScience, 101241, 23, 2020     article maize database multi-omics Integration

Genome Assembly of a Tropical Maize Inbred Line Provides Insights into Structural Variation and Crop Improvement

Yang Ning#, Liu Jie#, Gao Qiang#, GUI SONGTAO, Chen Lu, Yang Linfeng, Huang Juan, Deng Tianquan, Luo Jingyun, He Lijuan, Wang Yuebin, Xu Pengwei, Peng Yong, Shi Zhuoxing, Lan Liu, Ma Zhiyun, Yang Xin, Zhang Qianqian, Bai Mingzhou, Li San, Li Wenqiang, Liu Lei, Jackson David, Yan Jianbing*
Nature Genetics, 1052--1059, 51, 2019     article maize genome assembly structural variation crop improvement

Improving Nelumbo Nucifera Genome Assemblies Using High‐resolution Genetic Maps and BioNano Genome Mapping Reveals Ancient Chromosome Rearrangements

GUI SONGTAO, Peng Jing, Wang Xiaolei, Wu Zhihua, Cao Rui, Salse Jérôme, Zhang Hongyuan, Zhu Zhixuan, Xia Qiuju, Quan Zhiwu, Shu Liping, Ke Wedong, Ding Yi*
The Plant Journal, 721--734, 94, 2018     article Nelumbo nucifera genetic map bionano ancient chromosome rearrangements

A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna Unguiculata

Pan Lei, Wang Nian, Wu Zhihua, Guo Rui, Yu Xiaolu, Zheng Yu, Xia Qiuju, GUI SONGTAO, Chen Chanyou*
Frontiers in Plant Science, 1544, 8, 2017     article RAD sequencing genetic map vigna unguiculata

The NnCenH3 Protein and Centromeric DNA Sequence Profiles of Nelumbo Nucifera Gaertn. (Sacred Lotus) Reveal the DNA Structures and Dynamics of Centromeres in Basal Eudicots

Zhu Zhixuan, GUI SONGTAO, Jin Jing, Yi Rong, Wu Zhihua, Qian Qian, Ding Yi*
The Plant Journal, 568--582, 87, 2016     article Nelumbo nucifera centromeric DNA centromeric protein

Development and Characterization of Polymorphic MicroRNA-Based Microsatellite Markers in Nelumbo Nucifera (Nelumbonaceae)

Wang Xiaolei, GUI SONGTAO, Pan Lei, Hu Jihong, Ding Yi*
Applications in Plant Sciences, 1500091, 4, 2016     article Nelumbo nucifera microsatellite microRNA

The Mitochondrial Genome Map of Nelumbo Nucifera Reveals Ancient Evolutionary Features

GUI SONGTAO#, Wu Zhihua#, Zhang Hongyuan, Zheng Yinzhen, Zhu Zhixuan, Liang Dequan, Ding Yi*
Scientific Reports, 30158, 6, 2016     article Nelumbo nucifera mitochondrial genome evolution

Genome-Wide Identification of SSR and SNP Markers Based on Whole-Genome Re-Sequencing of a Thailand Wild Sacred Lotus (Nelumbo Nucifera)

Hu Jihong#, GUI SONGTAO#, Zhu Zhixuan, Wang Xiaolei, Ke Weidong, Ding Yi*
PLOS ONE, e0143765, 10, 2015     article Nelumbo nucifera WGS SSR SNP

A Precise Chloroplast Genome of Nelumbo Nucifera (Nelumbonaceae) Evaluated with Sanger, Illumina MiSeq, and PacBio RS II Sequencing Platforms: Insight into the Plastid Evolution of Basal Eudicots

Wu Zhihua, GUI SONGTAO, Quan Zhiwu, Pan Lei, Wang Shuzhen, Ke Weidong, Liang Dequan, Ding Yi*
BMC Plant Biology, 289, 14, 2014     article Nelumbo nucifera Evolutionary Chloroplast Genome Sanger Illumina MiSeq PacBio RS II

Molecular Evolution and Functional Characterisation of an Ancient Phenylalanine Ammonia-Lyase Gene (NnPAL1) from Nelumbo Nucifera: Novel Insight into the Evolution of the PAL Family in Angiosperms

Wu Zhihua, GUI SONGTAO, Wang Shuzhen, Ding Yi*
BMC Evolutionary Biology, 100, 14, 2014     article Nelumbo nuciferaEvolutionaryNnPAL1

Refer to Achievements for more.

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