Jinming Chen

Wuhan Botanical Garden

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i-10 index

Research Trends

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Co-Authors

Qing‐Feng Wang

Wuhan Botanical Garden

Zhizhong Li

Anhui Normal University

Andrew W. Gichira

Chinese Academy of Sciences

Tao Shi

Wuhan Botanical Garden

Guang‐Wan Hu

University of Chinese Academy of Sciences

Jun-Ke Song

Northwest A&F University

De-Liang Tao

Northwest A&F University

Xingyu Yang

Kunming Institute of Botany

Guang‐Hui Zhao

Northwest A&F University

Xing‐Quan Zhu

Shanxi Agricultural University

Cooperative Institutions

Institute for Forecasting of the Slovak Academy of Sciences

295

Cytoskeleton (United States)

291

Chinese Academy of Sciences

220

University of Chinese Academy of Sciences

131

Wuhan Botanical Garden

Wuhan University

Zhejiang University

Sun Yat-sen University

Chinese Academy of Medical Sciences & Peking Union Medical College

Peking University

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Identification of hybrids in broad-leaved Potamogeton species (Potamogetonaceae) in China using nuclear and chloroplast DNA sequence data

Plant Systematics and Evolution (2010)

Zhi‐Yuan Du Chun‐Feng Yang Jinming Chen You‐Hao Guo

Potamogetonaceae

10.1007/s00606-010-0289-y

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Citations (15)

The dual role of POSTN in maintaining glioblastoma stem cells and the immunosuppressive phenotype of microglia in glioblastoma

Journal of Experimental & Clinical Cancer Research (2024)

Hao Wang Lin Yao Jinming Chen Yanyan Li Zuopeng Su

10.1186/s13046-024-03175-9

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Citations (2)

Development of microsatellite markers in Hagenia abyssinica (Bruce) J.F. Gmel, an endangered tropical tree of eastern Africa, using next-generation sequencing

Genetics and Molecular Research (2016)

Andrew W. Gichira Zhicheng Long Guangming Hu Robert Wahiti Gituru Qi Wang

Hagenia abyssinica (Bruce) J.F. Gmel is an endangered tree species endemic to the high mountains of tropical Africa. We used Illumina paired-end technology to sequence its nuclear genome, aiming at creating the first genomic data library and developing the first set of genomic microsatellites. Seventeen microsatellite markers were validated in 24 individuals. The average number of alleles per locus was 7.6, while the observed and expected heterozygosities ranged from 0.000 to 0.958 and from 0.354 to 0.883, respectively. These polymorphic markers will be used as tools for further molecular studies to facilitate formulation of appropriate conservation strategies for this species.

10.4238/gmr.15028168

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Citations (2)

Additional file 3 of RNA sequencing reveals dynamic expression of lncRNAs and mRNAs in caprine endometrial epithelial cells induced by Neospora caninum infection

Figshare (2022)

Shanshan Zhao De-Liang Tao Jinming Chen Jiangping Wu Xin Yang

Additional file 3: Data S3. Length, exon numbers and classification of the long noncoding RNAs (lncRNAs).

10.6084/m9.figshare.20580983

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Additional file 13 of RNA sequencing reveals dynamic expression of lncRNAs and mRNAs in caprine endometrial epithelial cells induced by Neospora caninum infection

Figshare (2022)

Shanshan Zhao De-Liang Tao Jinming Chen Jiangping Wu Xin Yang

Additional file 13: Data S11. Gene Ontology (GO) enrichment analysis of all cis-target genes for the differentially expressed lncRNAs (DElncRNAs).

Neospora

10.6084/m9.figshare.20580944

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Genetic variation in wild populations of the tuber crop Amorphophallus konjac (Araceae) in central China as revealed by AFLP markers

Genetics and Molecular Research (2015)

Cheng Pan Andrew W. Gichira Jinming Chen

Amorphophallus konjac is an economically important crop.In order to provide baseline information for sustainable development and conservation of the wild plant resources of A. konjac, we studied the genetic diversity and population structure of this species using amplified fragment length polymorphism (AFLP) molecular markers.We sampled 139 individuals from 10 wild populations of A. konjac in central China.Using five AFLP primer combinations, we scored a total of 270 DNA fragments, most of which were polymorphic (98.2%).Percentage of polymorphic loci, Nei's genetic diversity index, and Shannon's information index showed high levels of genetic variation within A. konjac populations.Analysis of molecular variance indicated that most of the variance (68%) resided within populations.The coefficient of genetic differentiation between populations was 0.348 and the estimated gene flow was 0.469, indicating that there was limited gene flow among the populations.Unweighted pair group method with arithmetic mean cluster analysis and principal coordinates analysis indicated that geographically close populations were more likely ©FUNPEC-RP www.funpecrp.com.brGenetics and Molecular Research 14 (4): 18753-18763 (2015) to cluster together.The Mantel test revealed a significant correlation between geographic and genetic distances (R 2 = 0.2521, P < 0.05).The special insect-pollination system of A. konjac and the complex geography of central China are likely to have contributed to the current pattern of genetic variation of this species.In the present study, we provide several suggestions on the future protection of the wild plant genetic resources of A. konjac.

Amorphophallus

Mantel test

Molecular marker

Araceae

10.4238/2015.december.28.24

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Citations (8)

Plastome Phylogenomics and Historical Biogeography of Aquatic Plant Genus Hydrocharis (Hydrocharitaceae)

Research Square (Research Square) (2021)

Zhizhong Li Samuli Lehtonen Andrew W. Gichira Karina Martins Efremov Andrey

Abstract Background Hydrocharis L. and Limnobium Rich. are small aquatic genera, including three and two species, respectively. The taxonomic status, phylogenetic relationships and biogeographical history of these genera have remained unclear, owing to the lack of Central African endemic H. chevalieri from all previous studies. We sequenced and assembled plastomes of all three Hydrocharis species and Limnobium laevigatum to explore the phylogenetic and biogeographical history of these aquatic plants. Results All four newly generated plastomes were conserved in genome structure, gene content, and gene order. However, they differed in size, the number of repeat sequences, and inverted repeat borders. Our phylogenomic analyses recovered non-monophyletic Hydrocharis . African species H. chevalieri was fully supported as sister to the rest of the species, and L. laevigatum was nested in Hydrocharis as a sister to H . dubia . Hydrocharis-Limnobium initially diverged from the remaining genera at ca. 53.3 Ma, then began to diversify at ca. 30.9 Ma. The biogeographic analysis suggested that Hydrocharis probably originated in Europe and Central Africa. Conclusion Based on the phylogenetic results, morphological similarity and small size of the genera, the most reasonable taxonomic solution to the non-monophyly of Hydrocharis is to treat Limnobium as its synonym. The African endemic H. chevalieri is fully supported as a sister to the remaining species. Hydrocharis mainly diversified in the Miocene, during which rapid climate change may have contributed to the speciation and extinctions. The American species of former Limnobium probably dispersed to America through the Bering Land Bridge during the Miocene.

Monophyly

Phylogenomics

Sister group

10.21203/rs.3.rs-1022437/v1

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Environmental determinants of the current and future distribution of seven Ottelia Pers. species in African freshwater bodies

Research Square (Research Square) (2021)

Boniface K. Ngarega John M. Nzei Josphat K. Saina Marwa Waseem A. Halmy Jinming Chen

Abstract Understanding the influence of environmental covariates on plants’ distribution is critical, especially for aquatic plant species. Climate change is likely to alter the distribution of aquatic species. However, knowledge of this change on the burden of aquatic macroorganisms is often fraught with difficulty. Ottelia Pers., a model genus for studying the evolution of the aquatic family Hydrocharitaceae, is mainly distributed in slow-flowing creeks, rivers or lakes throughout the world’s pantropical areas. Due to recent rapid climate changes, the natural Ottelia populations have declined significantly. In the present study, we use maximum entropy (MaxEnt) to explore the environmental drivers of seven Ottelia species distribution in African freshwater bodies. The models use known background points to determine how environmental covariates vary spatially and produce continental maps of these species’ distribution. We also estimate the possible influences of the optimistic and extreme pessimistic Intergovernmental Panel on Climate Change (IPCC) pathway scenarios and identify high suitability areas under these scenarios. Model performances were statistically significant than random expectations with Area Under Curve (AUC) values above 0.831, indicating the good performance of the models. We observe that our studied Ottelia species had distinct spatial patterns influenced by climate variations (e.g. Bio9- mean temperature of driest quarter, Bio12- annual precipitation, and Bio14- Precipitation of the driest month). While there is a lack of accord in defining the limiting factors for the distribution of the seven species, it is clear that water-temperature conditions have promising effects when kept within optimal ranges. Niche overlap analyses showed that most Ottelia species have similar but not equivalent climatic niches. In addition, considering the expected warming in the future, the persistence and survival of the Ottelia species in Africa could be compromised. The present findings provide a theoretical basis for the distribution of various Ottelia species in Africa.

Species distribution

Pantropical

Environmental niche modelling

10.21203/rs.3.rs-588497/v1

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The complexity and robustness of gene network inside the story between miRNAs and splicing isoforms in sacred lotus

Research Square (Research Square) (2019)

Yue Zhang Razgar Seyed Rahmani Xingyu Yang Jinming Chen Tao Shi

Abstract BACKGROUND. Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, coordination of interaction between miRNAs with different splicing isoforms, and the role of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus ( Nelumbo nucifera ), an economically important flowering plant. RESULTS. Through RNA-seq expression analyses among six lotus tissues, the negative regulatory roles of most miRNAs are reflected by their tissue-biased expression and the negative correlation with their targets in expression. Further, the central roles of miRNAs in the gene network was unveiled as there are more frequent interactions between miRNAs and hub isoforms than between miRNAs and non-hub isoforms. Surprisingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. The gene function enrichment analysis of miRNA targeted reveals that miRNAs are involved in regulation of lotus growth and development by regulating plant hormone-related pathway genes. CONCLUSION. Taken together, we carry out a comprehensive and deep analysis between miRNA and mRNA transcriptome to study coordination of interaction between miRNAs with different splicing isoforms. Our study on lotus highlights not only the complicate interactions between the miRNAs and transcript isoforms but also functional divergence of many transcript isoforms from the same locus in plant.

10.21203/rs.2.19330/v1

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Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement

Ecology and Evolution (2024)

Xiangyan He Jinming Chen Zhizhong Li

Abstract Scheuchzeria palustris , the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris , with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein‐coding genes (PCGs) and 142 in pt‐PCGs. Notably, abundant RNA editing sites in pt‐PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt‐PCGs ( atp4 , ccmB , nad3 , and sdh4 ) and one pt‐PCG ( rps7 ), which may contribute to the adaptation of S. palustris to low‐temperature and high‐altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt‐ and pt‐PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt‐ and pt‐PCGs ( p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris .

Phylogenomics

10.1002/ece3.70248

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