Selected Publications
*, corresponding author; †, co-first author.
2026
Lu YF, Zuo GH*, and Zhi XY*.
A structural backbone with sequestered plasticity organizes the Escherichia coli pangenome.
mSystems. 2026 Jun. In press.
DOI: 10.1128/msystems.00207-26
Zhao Y, Lu YF, Hai X, and Zhi XY*.
LSGFA: Domain-based infraspecific large-scale prokaryotic genomic orthologous gene inference.
BMC Bioinformatics. 2026 Jun. In press.
DOI: 10.1186/s12859-026-06506-z
Li CJ†, Zhao Y†, Tang M†, Chu X, Zhan PC, Jiang XW, Tian JY, Hai X, Lu YF, Yang LL* , Zhi XY*
Comparative population genomics reveal the genetic features associated with the plant host adaptation of Clostridium butyricum.
BMC Genomics. 2026 27:544.
DOI: 10.1186/s12864-026-12876-8
2023
Wang M†, Li CJ†, Zhang Z, Li PP, Yang LL, Zhi XY*.
The evolution of morphological development is congruent with the species phylogeny in the genus Streptomyces.
Front Microbiol. 2023 14:1102250.
DOI: 10.3389/fmicb.2023.1102250
Tang SK†, Zhi XY†, Zhang Y†, Makarova K-S†, Liu BB†, Zheng GS, ..., Yang LL, ..., Koonin EV*, Zhao GP*, Xu P*.
Cellular differentiation into hyphae and spores in halophilic archaea.
Nat Commun. 2023 14:1827.
DOI: 10.1038/s41467-023-37389-w
2020
Yang LL, Jiang Z, Li Y, Wang ET, Zhi XY*.
Plasmids related to the symbiotic nitrogen fixation are not only cooperated functionally, but also may have evolved over a time span in family Rhizobiaceae.
Genome Biol Evol. 2020 12(11):2002-2014.
DOI: 10.1093/gbe/evaa152
Tan W†, Liao TH†, Wang J, Ye Y, Wei YC, Zhou HK, Xiao Y, Zhi XY*, Zhao ZH*, Lyu LD*, Zhao GP*.
A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation.
J Biol Chem. 2020 295(15):5051-5066.
DOI: 10.1074/jbc.RA120.012859
2019
Jiang Z, Xiao M, Yang LL, Zhi XY*, Li WJ*.
Genome-based taxonomic classification within the family Thermoactinomycetaceae.
Int J Syst Evol Microbiol. 2019 69(7):2028-2036.
DOI: 10.1099/ijsem.0.003425
2017
Yin YR†, Meng ZH†, Hu QW, Jiang Z, Xian WD, Li LH, Hu W, Zhang F, Zhou EM, Zhi XY*, Li WJ*.
The Hybrid Strategy of Thermoactinospora rubra YIM 77501T for Utilizing Cellulose as a Carbon Source at Different Temperatures.
Front Microbiol. 2017 8:942.
DOI: 10.3389/fmicb.2017.00942
Zhi XY*, Jiang Z, Yang LL, Huang Y.
The underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach.
Mol Phylogenet Evol. 2017 107:246-255.
DOI: 10.1016/j.ympev.2016.11.009
2015
Yang LL, Tang SK, Huang Y, Zhi XY*.
Low Temperature Adaptation Is Not the Opposite Process of High Temperature Adaptation in Terms of Changes in Amino Acid Composition.
Genome Biol Evol. 2015 7(12):3426-33.
DOI: 10.1093/gbe/evv232
2014
Zhi XY†*, Yao JC†, Tang SK, Huang Y, Li HW, Li WJ*.
The futalosine pathway played an important role in menaquinone biosynthesis during early prokaryote evolution.
Genome Biol Evol. 2014 6(1):149-60.
DOI: 10.1093/gbe/evu007
Zhi XY†*, Yao JC†, Li HW, Huang Y, Li WJ*.
Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes.
Mol Phylogenet Evol. 2014 75:154-64.
DOI: 10.1016/j.ympev.2014.02.015
2012
Zhi XY†, Zhao W†, Li WJ, Zhao GP*.
Prokaryotic systematics in the genomics era.
Antonie Van Leeuwenhoek. 2012 101(1):21-34.
DOI: 10.1007/s10482-011-9667-x
2010
Zhou J*, Deng Y, Luo F, He Z, Tu Q, Zhi X.
Functional molecular ecological networks.
mBio. 2010 1(4):e00169-10.
DOI: 10.1128/mBio.00169-10
2009
Zhi XY, Li WJ*, Stackebrandt E*.
An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa.
Int J Syst Evol Microbiol. 2009 59(3):589-608.
DOI: 10.1099/ijs.0.65780-0