Songtao Gui, Ph.D.

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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

Major Projects in Agricultural Biological Breeding, Sub-task, 2024ZD0408001

GUI SONGTAO

Major Projects in Agricultural Biological Breeding, 2024-2025 fundings Host

National Key Research and Development Project of China, Sub-task, 2024YFF1000700

GUI SONGTAO

National Key Research and Development Project of China, 2025-2027 fundings Host

National Natural Science Foundation of China, 32470659

GUI SONGTAO

National Natural Science Foundation of China, 2025-2028 fundings Host

SDAU 811 Special

GUI SONGTAO

Shandong Agriculture University, 2024-2026 fundings Host

Taishan Scholar

GUI SONGTAO

Shandong Provincial Department of Education, 2024-2026 fundings Host

SDAU Start-up funding

GUI SONGTAO

Shandong Agriculture University, 2023 fundings Host

National Natural Science Foundation of China, 32000396

GUI SONGTAO

National Natural Science Foundation of China, 2021-2023 fundings Host

National Key Research and Development Project of China, 0120200395

..., GUI SONGTAO, ...

National Key Research and Development Project of China, 2020-2024 fundings Participate

Outstanding Postdoctoral funding

GUI SONGTAO

College of Plant Science, HZAU, 2019-2021 fundings Host

National Natural Science Foundation of China, 31271310

..., GUI SONGTAO, ...

National Natural Science Foundation of China, 2013-2016 fundings Participate

Awards

TaiShan Scholars (for Young expert)

GUI SONGTAO

Shandong Provincial Department of Education, 2023 awards Wheat Scholars

Big Data Driven Crop Intelligent Breeding Platform, Winner's Price

Luo Jingyun, GUI SONGTAO, Xiao Yingjie, Jianyu Yuan, Shenshen Wu, Wenjie Wei, Shuyan Li

Hubei Postdoctoral Innovation and Entrepreneurship Competition, 2022 awards Zea Competition

1st National Crop Science Postdoctoral Academic Forum, Outstanding Award

GUI SONGTAO

1st National Crop Science Postdoctoral Academic Forum, 2020 awards Conference report

7th Hubei Congress of Plant Biology, 1st Reporter Award

GUI SONGTAO

7th Hubei Congress of Plant Biology, 2017 awards Conference report

National Congress of Plant Biology, 3rd Poster Award

GUI SONGTAO

National Congress of Plant Biology, 2016 awards Conference report

National Scholarship for PhD. students

GUI SONGTAO

National Scholarship of China, 2016 awards Scholarship

Publications

#: Co-first authors; *: Correspondence

Regulation of tillering and panicle branching in rice and wheat

Zhang*# Ning, Liu# Yuhao, GUI SONGTAO, Wang* Yonghong

Journal of Genetics and Genomics, 2024 article Rice Wheat Crop architecture Tillering Panicle branching

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.