Weibo Xie

Huazhong Agricultural University

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Xingming Lian

Huazhong Agricultural University

Gongwei Wang

Third Affiliated Hospital of Sun Yat-sen University

Wen Yao

Henan Agricultural University

Qifa Zhang

Huazhong Agricultural University

Hu Zhao

Huazhong Agricultural University

Guangwei Li

Henan Agricultural University

Yongzhong Xing

Huazhong Agricultural University

Rod A. Wing

King Abdullah University of Science and Technology

Xianghua Li

Huazhong Agricultural University

Jayson Talag

University of Arizona

Cooperative Institutions

Huazhong Agricultural University

297

Chinese Academy of Sciences

Chinese Academy of Agricultural Sciences

Ministry of Agriculture and Rural Affairs

Shanghai Zhangjiang Laboratory

Sun Yat-sen University

University of Chinese Academy of Sciences

Zhejiang University

Peking University

Shanghai Jiao Tong University

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Transcriptome-based analysis of mitogen-activated protein kinase cascades in the rice response to Xanthomonas oryzae infection

Rice (2015)

Zeyu Yang Haigang Ma Hanming Hong Wen Yao Weibo Xie

Mitogen-activated protein (MAP) kinase cascades, with each cascade consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK), play important roles in dicot plant responses to pathogen infection. However, no single MAP kinase cascade has been identified in rice, and the functions of MAP kinase cascades in rice - pathogen interactions are unknown.To explore the contribution of MAP kinase cascade in rice in response to Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight, one of the devastating diseases of rice worldwide, we performed a comprehensive expression analysis of rice MAP kinase cascade genes. We transcriptionally analyzed all the 74 MAPKKK genes, 8 MAPKK, and 17 MAPK genes in two pairs of susceptible and resistant rice lines, with each pair having the same genetic background, to determine the rice response to Xoo infection. The expression of a large number of MAP kinase cascade genes changed in response to infection, and some of the genes also showed different expression in resistant and susceptible reactions. In addition, some MAPKKK genes co-expressed with MAPKK and/or MAPK genes, and MAPKK genes co-expressed with MAPK genes.These results provide a new perspective regarding the putative roles of rice MAP kinase gene candicates and potential cascade targets for further characterization in rice-pathogen interactions.

MAPK cascade

MAP2K7

c-Raf

Cyclin-dependent kinase 9

10.1186/s12284-014-0038-x

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Citations (39)

Additional file 8: Table S7. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Figshare (2015)

Wen Yao Guangwei Li Hu Zhao Gongwei Wang Xingming Lian

The alignment of predicted proteins of the indica dispensable genome to proteins coded by cloned genes of the Nipponbare genome using Blastp. (XLS 33Â kb)

Table (database)

Sequence assembly

10.6084/m9.figshare.c.3636791_d13

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Citations (0)

Additional file 17: Table S15. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Figshare (2015)

Wen Yao Guangwei Li Hu Zhao Gongwei Wang Xingming Lian

Sheet 1 shows the contigs of the indica dispensable genome related to exon/intron shuffling. Sheet 2 displays the contigs of the japonica dispensable genome related to exon/intron shuffling. (XLS 3716Â kb)

Table (database)

Sequence assembly

10.6084/m9.figshare.c.3636791_d2

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CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer

bioRxiv (Cold Spring Harbor Laboratory) (2020)

Ruidong Li Han Qu Shibo Wang John M. Chater Xuesong Wang

ABSTRACT MicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising diagnostic and prognostic biomarkers for human cancer. In particular, circulating miRNAs that are secreted into circulation exist in remarkably stable forms, and have enormous potential to be leveraged as non-invasive biomarkers for early cancer detection. Novel and user-friendly tools are desperately needed to facilitate data mining of the vast amount of miRNA expression data from The Cancer Genome Atlas (TCGA) and large-scale circulating miRNA profiling studies. To fill this void, we developed CancerMIRNome, a comprehensive database for the interactive analysis and visualization of miRNA expression profiles based on 10,998 samples from 33 TCGA projects and 21,993 samples from 40 public circulating miRNome datasets. A series of cutting-edge bioinformatics tools and machine learning algorithms have been packaged in CancerMIRNome, allowing for the pan-cancer analysis of a miRNA of interest across multiple cancer types and the comprehensive analysis of miRNome profiles to identify dysregulated miRNAs and develop diagnostic or prognostic signatures. The data analysis and visualization modules will greatly facilitate the exploit of the valuable resources and promote translational application of miRNA biomarkers in cancer. The CancerMIRNome database is publicly available at http://bioinfo.jialab-ucr.org/CancerMIRNome .

Profiling (computer programming)

10.1101/2020.10.04.325670

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Citations (4)

MOESM10 of Genome sequence of the model rice variety KitaakeX

Figshare (2019)

Rashmi Jain Jerry Jenkins Shengqiang Shu Mawsheng Chern Joel Martin

Additional file 10. Repeat annotation of KitaakeX genome.

Sequence (biology)

10.6084/m9.figshare.11293511

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Assembly and Validation of Two Gap-free Reference Genomes for Xian/indica Rice Reveals Insights into Plant Centromere Architecture

King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) (2020)

Jia‐Ming Song Wen‐Zhao Xie Shuo Wang Yi‐Xiong Guo Jesse Poland

ABSTRACT Rice ( Oryza sativa ), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome completed almost two decades ago. However, all sequenced genomes to date contain gaps and missing sequences. Here, we report, for the first time, the assembly and analyses of two gap-free reference genome sequences of the elite O. sativa xian/indica rice varieties ‘Zhenshan 97 (ZS97)’ and ‘Minghui 63 (MH63)’ that are being used as a model system to study heterosis. Gap-free reference genomes also provide global insights into the structure and function of centromeres. All rice centromeric regions share conserved centromere-specific satellite motifs but with different copy numbers and structures. Importantly, we demonstrate that >1,500 genes are located in centromere regions, of which ~15.6% are actively transcribed. The generation and release of both the ZS97 and MH63 gap-free genomes lays a solid foundation for the comprehensive study of genome structure and function in plants and breed climate resilient varieties for the 21 st century.

Oryza

Source

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Transcriptome response to phosphorus starvation in rice

Acta Physiologiae Plantarum (2011)

Hongmei Cai Weibo Xie Tong Zhu Xingming Lian

Starvation response

Plant Physiology

10.1007/s11738-011-0832-7

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Citations (29)

Genome‐wide association analyses reveal the genetic basis of combining ability in rice

Plant Biotechnology Journal (2019)

Junxiao Chen Hao Zhou Weibo Xie Duo Xia Guanjun Gao

Combining ability is a measure for selecting elite parents and predicting hybrid performance in plant breeding. However, the genetic basis of combining ability remains unclear and a global view of combining ability from diverse mating designs is lacking. We developed a North Carolina II (NCII) population of 96 Oryza sativa and four male sterile lines to identify parents of greatest value for hybrid rice production. Statistical analyses indicated that general combining ability (GCA) and specific combining ability (SCA) contributed variously to different agronomic traits. In a genome-wide association study (GWAS) of agronomic traits, GCA and SCA, we identified 34 significant associations (P < 2.39 × 10-7 ). The superior alleles of GCA loci (Ghd8, GS3 and qSSR4) accumulated in parental lines with high GCA and explained 30.03% of GCA variance in grain yield, indicating that molecular breeding of high GCA parental lines is feasible. The distinct distributions of these QTLs contributed to the differentiation of parental GCA in subpopulations. GWAS of SCA identified 12 more loci that showed dominance on corresponding agronomic traits. We conclude that the accumulation of superior GCA and SCA alleles is an important contributor to heterosis and QTLs that greatly contributed to combining ability in our study would accelerate the identification of elite inbred lines and breeding of super hybrids.

Genome-wide Association Study

Mating design

Genetic Association

Inbred strain

10.1111/pbi.13134

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Citations (35)

Additional file 5: Table S4. of Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice

Figshare (2015)

Jinhong Wu Fangjun Feng Xingming Lian Xiaoying Teng Haibin Wei

Annotation of candidate genes anchored by associated SNPs. (XLSX 34 kb)

Genome-wide Association Study

Table (database)

10.6084/m9.figshare.c.3642296_d3

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Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

Proceedings of the National Academy of Sciences (2010)

Weibo Xie Qi Feng Huihui Yu Xuehui Huang Qiang Zhao

Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge to genotype individual lines in a population for linkage map construction based on low-coverage sequences without the availability of high-quality genotype data of the parental lines. In this paper, we report a method for constructing ultrahigh-density linkage maps composed of high-quality single-nucleotide polymorphisms (SNPs) based on low-coverage sequences of recombinant inbred lines. First, all potential SNPs were identified to obtain drafts of parental genotypes using a maximum parsimonious inference of recombination, making maximum use of SNP information found in the entire population. Second, high-quality SNPs were identified by filtering out low-quality ones by permutations involving resampling of windows of SNPs followed by Bayesian inference. Third, lines in the mapping population were genotyped using the high-quality SNPs assisted by a hidden Markov model. With 0.05× genome sequence per line, an ultrahigh-density linkage map composed of bins of high-quality SNPs using 238 recombinant inbred lines derived from a cross between two rice varieties was constructed. Using this map, a quantitative trait locus for grain width ( GW5 ) was localized to its presumed genomic region in a bin of 200 kb, confirming the accuracy and quality of the map. This method is generally applicable in genetic map construction with low-coverage sequence data.

SNP genotyping

Tag SNP

Linkage (software)

10.1073/pnas.1005931107

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Citations (313)