Publications
Group highlights
(For a full list of publications and patents see below or go to Google Scholar)
We assemble a chromosome-scale reference genome for T. grandis, accompanied by transcriptome and methylome profiling in multiple tissues. Our data, through comparative genomic analyses, unravel interesting footprints associated with morphological diversity of major land plant lineages, and discover and validate two key enzymes that are responsible for SCA biosynthesis.
H Lou#, L Song#, X Li#, H Zi, W Chen, Y Gao, S Zheng, Z Fei*, X Sun*, J Wu*
Nature Communications 14:1315 (2023)
see ZAFU News
Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis.
L Wang#, X Sun#, Y Peng#, K Chen#, S Wu#, Y Guo, J Zhang, H Yang, T Jin, L Wu, X Zhou, B Liang, Z Zhao, D liu*, Z Fei*, L Bai*.
see News
Most of us are familiar with "spinach teeth" – the harmless but gritty-chalky mouthfeel caused by the vegetable. An international team led by us has identified candidate genes in spinach that regulate its concentration of oxalate, which is responsible for "spinach teeth", as well as genes that help the plant combat downy mildew, a major disease of commercial crops.
X Cai#, X Sun#, C Xu#, H Sun, X Wang, C Ge, Z Zhang, Q Wang*, Z Fei*, C Jiao*#, Q Wang*.
Nature Communications 12:7246 (2021)
see Cornell Chronicle, ZJU News, 中文报道
Penium margaritaceum belongs to a group of freshwater algae called charophytes, and specifically to a subgroup called the Zygnematophyceae, which had a common ancestor with the first land plants some 600 million years ago. In order to shift from water to land – a transition that still puzzles scientists – plants had to protect themselves from drying out and from ultraviolet (UV) radiation, and they had to develop structures to support themselves without the buoyancy provided by water. Through sequencing and analyzing the genome of P. margaritaceum, we and collaborators have found footprints of these adaptations, providing insight into the mechanisms and genetics that early terrestrial plants required.
C Jiao#, I Sørensen#, X Sun#, H Sun, H Behar, S Alseekh, G Philippe, KP Lopez, L Sun, R Reed, S Jeon, R Kiyonami, S Zhang, AR Fernie, H Brumer, DS Domozych*, Z Fei*, JKC Rose*.
see Cell Preview, Nature Plants Research Highlight, Cornell News
The fabled Silk Road – the 4,000-mile stretch between China and Western Europe where trade flourished from the second century B.C. to the 14th century A.D. – is responsible for one of our favorite and most valuable fruits: the domesticated apple (Malus domestica). Hybridizations with wild species have made the apple genome very complex and difficult to study, we tackled this problem by applying cutting-edge sequencing technologies and bioinformatics algorithms to assemble complete sets of both chromosomes for the domesticated apple and its two main wild progenitors. We discovered that the apple’s unique domestication history has led to untapped sources of genes that could be used for crop improvement, such as improving size, flavor, sweetness and texture.
X Sun#, C Jiao#, H Schwaninger#, T Chao, Y Ma, N Duan, A Khan, S Ban, K Xu, L Cheng, GY Zhong*, Z Fei*.
Nature Genetics 52:1423–1432 (2020)
Arbuscular mycorrhizal (AM) fungi form endosymbioses with most plants, and they themselves are hosts for Mollicutes/Mycoplasma‐related endobacteria (MRE). Despite their significance, genomic information for AM fungi and their MRE are relatively sparse, which hinders our understanding of their biology and evolution. We assembled the genomes of the AM fungus Diversispora epigaea (formerly Glomus versiforme) and its MRE and performed comparative genomics and evolutionary analyses.
X Sun, W Chen, S Ivanov, AM MacLean, H Wight, T Ramaraj, J Mudge, M Harrison*, Z Fei*.
New Phytologist 221:1556-1573 (2019)
Whitefly bacteriocytes have different microsatellite alleles from other somatic cells, the bacteriocyte genotype is stable over three sexual generations of the insect. Bacteriocyte genomes in different insects are genetically very similar and the single bacteriocyte transmitted to the sexual egg persists through embryogenesis.
J Luan#, X Sun#, Z Fei, AE Douglas*.
Current Biology 28:459-465 (2018)
Our first Riboseq paper done in yeast
Z Wang#, X Sun#, X Guo, H Jiang, Z Gu*.
Genome Biology and Evolution 7:1155–1167 (2015)
see our RiboseqTools developped for Riboseq data analysis.
Full List of publications
The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis
H Lou#, L Song#, X Li#, H Zi, W Chen, Y Gao, S Zheng, Z Fei*, X Sun*, J Wu*
Nature Communications 14:1315 (2023)
Differential regulation of red light- and ethephon-induced degreening in postharvest kumquat fruit
J Gong, H Yang, Y Xu, Y Zeng, P Liu, C Chen, P Wang*, X Sun*
Postharvest Biology and Technology 198:112264 (2023)
A MYB Transcription Factor Atlas Provides Insights into the Evolution of Environmental Adaptations in Plants
C Zhang, C Jiao, X Sun*, X Li*
International Journal of Molecular Science 24(3):2566 (2023)
Nanopore long-read RNAseq reveals transcriptional variations in citrus species
X Hu, C You, K Zhu, X Li, J Gong, H Ma, X Sun*
Frontiers in Plant Science 13:1077797 (2023)
Combining BN-PAGE and microscopy techniques to investigate pigment-protein complexes and plastid transitions in citrus fruit
J Gong, H Zhang, Y Zeng, Y Cheng, X Sun*, P Wang*
Plant Methods 18(1):124 (2022)
Highly efficient hairy root genetic transformation and applications in citrus
H Ma#, X Meng#, K Xu, M Li, FG Gmitter Jr, N Liu, Y Gai, S Huang, M Wang, M Wang, N Wang, H Xu, J Liu*, X Sun*, S Duan*
Frontiers in Plant Science 13:1039094 (2022)
Genomic and Transcriptomic Characterization of Alternaria alternata during Infection
Y Gai*, Q Niu, J Kong, L Li, X Liang, Y Cao, X Zhou, X Sun, H Ma, M Wang, N Shrivastava, H Li, C Jiao*
Agronomy 13(3),809 (2023)
Loss of function of bHLH transcription factor Nrd1 in tomato induces an arabinogalactan protein-encoding gene and enhances resistance to Pseudomonas syringae pv. tomato
N Zhang, C Hecht, X Sun, Z Fei, G Martin*.
Plant Physiology (2022)
Histone methylation is required for virulence, conidiation and multi-stress resistance of Alternaria alternata
S Meng, S Huang, J Liu, Y Gai, M Li, S Duan, S Zhang, X Sun, Q Yang, Y Wang, K Xu*, H Ma*.
Frontiers in Microbiology (2022)
Genomic insights into the origin, adaptive evolution and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields
L Wang#, X Sun#, Y Peng#, K Chen#, S Wu#, Y Guo, J Zhang, H Yang, T Jin, L Wu, X Zhou, B Liang, Z Zhao, D liu*, Z Fei*, L Bai*.
Molecular Plant (2022)
The protective role of MdATG10-mediated autophagy in apple plant under cadmium stress
L Huo, Z Guo, Q Wang, X Jia, X Sun, F MA*.
Ecotoxicology and Environmental Safety (2022)
Distinct and essential roles of bZIP transcription factors in the stress response and pathogenesis in Alternaria alternata
Y Gai*#, L Li, B Liu, H Ma, Y Chen, F Zheng, X Sun, M Wang, C Jiao, H Li*.
Microbiological Research 256:126915 (2022)
Comparative Transcriptome Profiling of Chinese Wild Grapes Provides Insights Into Powdery Mildew Resistance
C Jiao#, X Sun#, X Yan, X Xu, Q Yan, M Gao, Z Fei*, X Wang*.
Phytopathology 111(11):2041-2051 (2021)
Chromosome-scale genome sequence of Alternaria alternata causing Alternaria brown spot of citrus
Y Gai, H Ma, Y Chen, L Li, Y Cao, M Wang, X Sun, C Jiao, B Riely, H Li*.
Molecular Plant-Microbe Interactions 34(7):726-732 (2021)
Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits
X Cai#, X Sun#, C Xu#, H Sun, X Wang, C Ge, Z Zhang, Q Wang*, Z Fei*, C Jiao*#, Q Wang*.
Nature Communications 12:7246 (2021)
Cutin and suberin: assembly and origins of specialized lipidic cell wall scaffolds
G Philippe, I Sørensen, C Jiao, X Sun, Z Fei, DS Domozych, JKC Rose*.
Current Opinion in Plant Biology 55:11-20 (2020)
The Penium margaritaceum genome: hallmarks of the origins of land plants
C Jiao#, I Sørensen#, X Sun#, H Sun, H Behar, S Alseekh, G Philippe, KP Lopez, L Sun, R Reed, S Jeon, R Kiyonami, S Zhang, AR Fernie, H Brumer, DS Domozych*, Z Fei*, JKC Rose*.
Cell 181:1097-1111 (2020)
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication
X Sun#, C Jiao#, H Schwaninger#, T Chao, Y Ma, N Duan, A Khan, S Ban, K Xu, L Cheng, GY Zhong*, Z Fei*.
Nature Genetics 52:1423–1432 (2020)
A CLE–SUNN module regulates strigolactone content and fungal colonization in arbuscular mycorrhiza
LM Müller, K Flokova, E Schnabel, X Sun, Z Fei, J Frugoli, HJ Bouwmeester, MJ Harrison*.
Nature Plants 5:933-939 (2019)
Cellular and molecular characterization of a thick-walled variant reveal a pivotal role of shoot apical meristem in transverse development of bamboo culm
Y Wang#, X Sun#, Y Ding, Z Fei, C Jiao, M Fan, B Yao, P Xin, J Chu, Q Wei*.
Journal of Experimental Botany 70(15):3911–3926 (2019)
Diverse Sorghum bicolor accessions show marked variation in growth and transcriptional responses to arbuscular mycorrhizal fungi
SJ Watts-Williams, B Emmett, V Levesque-Tremblay, AM. MacLean, X Sun, JW. Satterlee, Z Fei, MJ Harrison*.
Plant Cell and Environment 42(5):1758-1774 (2019)
Morphological dissection and cellular and transcriptome characterizations of bamboo pith cavity formation reveal a pivotal role of genes related to programmed cell death
L Guo#, X Sun#, Z Li, Y Wang, Z Fei, C Jiao, J Feng, D Cai, X Feng, Y Ding, C Zhang, Q Wei*.
Plant Biotechnology Journal 17(5):982-997 (2019)
Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping
W Tang#, X Sun#, J Yue#, X Tang, C Jiao, Y Yang, X Niu, M Miao, D Zhang, S Huang, W Shi, M Li, C Fang, Z Fei*, Y Liu*.
GigaScience 8(4):giz027 (2019)
Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts
X Sun, W Chen, S Ivanov, AM MacLean, H Wight, T Ramaraj, J Mudge, M Harrison*, Z Fei*.
New Phytologist 221:1556-1573 (2019)
Novel insights into global translational regulation through Pumilio family RNA-binding protein Puf3p revealed by ribosomal profiling
Z Wang#*, X Sun#, J Wee, X Guo, Z Gu*.
Current Genetics 65:201-212 (2019)
Cell-wall-degrading enzymes required for virulence in the host selective toxin-producing necrotroph Alternaria alternata of citrus
H Ma#, B Zhang#, Y Gai, X Sun, KR Chung*, H Li*.
Frontiers in Microbiology 10:2514 (2019)
First report of Luffa aphid-borne yellows virus in Cucurbita mostchata in China
B Peng, B Qin, J Cai, X Sun, H Wu, Q Gu*.
Plant Disease 103, 2481 (2019)
A novel FADS2 isoform identified in human milk fat globule suppresses FADS2 mediated Δ6-desaturation of omega-3 fatty acids
KSD Kothapalli#*, HG Park#, X Guo, X Sun, J Zhou, SS Hyon, X Qin, P Lawrence, RR Ran-Ressler, JY Zhang, Z Gu*, JT Brenna*.
Prostaglandins Leukot Essent Fatty Acids 138:52-59 (2018)
Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation
Y Chen*#, J Wang#, N Yang, Z Wen, X Sun, Y Chai, Z Ma*.
Nature Communications 9:3429 (2018)
Maternal inheritance of a single somatic animal cell displayed by the bacteriocyte in the whitefly Bemisia tabaci
J Luan#, X Sun#, Z Fei, AE Douglas*.
Current Biology 28:459-465 (2018)
Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions
C Xu#, C Jiao#*, H Sun#, X Cai, X Wang, C Ge, Y Zheng, W Liu, X Sun, Y Xu, J Deng, Z Zhang, S Huang, S Dai, B Mou, Q Wang, Z Fei*, Q Wang*.
Nature Communications 8:15275 (2017)
Diversity, distribution, and evolution of tomato viruses in China uncovered by small RNA sequencing
C Xu#, X Sun#*, A Taylor, C Jiao, Y Xu, X Cai, X Wang, C Ge, G Pan, Q Wang, Z Fei, Q Wang*.
Journal of Virology 91:e00173-00117 (2017)
Functional analysis of two sterol regulatory element binding proteins in Penicillium digitatum
R Ruan, M Wang, X Liu, X Sun, K Chung, H Li*.
PLoS One 12:e0176485 (2017)
The citrus postharvest pathogen Penicillium digitatum depends on the PdMpkB kinase for developmental and virulence functions
H Ma, X Sun, M Wang, Y Gai, K Chung, H Li*.
International Journal of Food Microbiology 235:167-176 (2016)
Genomic and transcriptomic analyses of the tangerine pathotype of Alternaria alternata in response to oxidative stress
M Wang, X Sun, D Yu, J Xu K Chung, H Li*.
Scientific Reports 6:32437 (2016)
Coordinated transcriptional and post-transcriptional regulation of mitochondrial functions in yeast strains
X Sun#, Z Wang#, H Jiang, H Li, Z Gu*.
PLoS One 11:e0153523 (2016)
Evolution of gene regulation during transcription and translation
Z Wang#, X Sun#, X Guo, H Jiang, Z Gu*.
Genome Biology and Evolution 7:1155–1167 (2015)
Deletion of PdMit1, a homolog of yeast Csg1, affects growth and Ca 2+ sensitivity of the fungus Penicillium digitatum, but does not alter virulence
C Zhu, W Wang, M Wang, R Ruan, X Sun, M He, C Mao, H Li*.
Research in Microbiology 166:143-152 (2015)
Diminishing returns in next-generation sequencing (NGS) transcriptome data
R Lei, K Ye, Z Gu*, X Sun*.
Gene 557:82-87 (2015)
PdbrlA, PdabaA and PdwetA control distinct stages of conidiogenesis in¬ Penicillium digitatum
M Wang, X Sun, C Zhu, Q Xu, R Ruan, D Yu, H Li*.
Research in Microbiology 166:56-65 (2015)
Os2 MAP kinase-mediated osmostress tolerance in Penicillium digitatum is associated with its positive regulation on glycerol synthesis and negative regulation on ergosterol synthesis
M Wang, C Chen, C Zhu, X Sun, R Ruan, H Li*.
Microbiological Research 169:511-521 (2014)
Improvement of a gene targeting system for genetic manipulation in Penicillium digitatum
Q Xu, C Zhu, M Wang, X Sun, H Li*.
Journal of Zhejiang University Science B 15:116-124 (2014)
Genomewide investigation into DNA elements and ABC transporters involved in imazalil resistance in Penicillium digitatum
X Sun, R Ruan, L Lin, C Zhu, M Wang, H Li*, D Yu.
FEMS Microbiology Letters 348:11-18 (2013)
The pH signaling transcription factor PacC is required for full virulence in Penicillium digitatum
T Zhang, X Sun, Q Xu, C Luis González, H Li*.
Applied Microbiology and Biotechnology 97:9087-9098.
PdSNF1, a sucrose non-fermenting protein kinase gene, is required for Penicillium digitatum conidiation and virulence
T Zhang, X Sun, Q Xu, C Zhu, Q Li, H Li*.
Applied Microbiology and Biotechnology 97:5433-5445.
The calcineurin-responsive transcription factor Crz1 is required for conidation, full virulence and DMI resistance in Penicillium digitatum
T Zhang, Q Xu, X Sun, H Li*.
Microbiological Research 168:211-222 (2013)
PdMLE1, a specific and active transposon acts as a promoter and confers Penicillium digitatum with DMI resistance
X Sun, Q Xu, R Ruan, T Zhang, C Zhu, H Li*.
Environmental Microbiology Reports 5:135-142 (2013)
PdMfs1, a major facilitator superfamily transporter from Penicillium digitatum, is partially involved in the imazalil-resistance and pathogenicity
J Wang, X Sun, L Lin, T Zhang, Z Ma, H Li*.
African Journal of Microbiology Research 6:95-105 (2012)
Complete mitochondrial genome sequence of the phytopathogenic fungus Penicillium digitatum and comparative analysis of closely related species
X Sun, H Li, D Yu*.
FEMS Microbiology Letters 323:29-34 (2011)
PdCYP51B, a new putative sterol 14α-demethylase gene of Penicillium digitatum involved in resistance to imazalil and other fungicides inhibiting ergosterol synthesis
X Sun, J Wang, D Feng, Z Ma, H Li*.
Applied Microbiology and Biotechnology 91:1107-1119 (2011)
CRISPR/Cas系统及其在昆虫基因功能研究中的应用
张敏菁, 张春红, 孙学鹏, 李红叶, 祝增荣
生命科学 27(1):99-106 (2015)
柑橘绿霉病菌对咯菌腈的敏感基线的建立
符雨诗, 王明爽, 阮若昕, 朱从一, 孙学鹏, 李红叶
浙江农业学报 27(1):68-74 (2015)
浙江衢州地区柑橘绿霉病菌对抑霉唑和多菌灵的抗性水平及其分子机制
冯丹, 孙学鹏, 姜丽英, 陈健民, 李红叶
农药学学报 13(4):341-346 (2011)
Patents
孙学鹏, 李红叶. PCR法检测抗抑霉唑柑橘绿霉菌菌系的引物序列及方法, CN201010591618.1.